The 1000 Genomes Project ran between 2008 and 2015, creating a deep catalogue of human genetic variation. The International Genome Sample Resource (IGSR) was set up to ensure the future usability and accessibility of this data.
Get a subset of data from a BAM or VCF file.
Convert a set of Ensembl IDs from a previous release into their current equivalents.
Identify variation patterns in a chromosomal region of interest for different individuals.
Convert a VCF file into a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview.
123FASTQ is a user-friendly software solution for preprocessing Illumina FASTQ reads, integrating quality control analysis, trimming, and format conversion. It aims to simplify NGS data preprocessing and improve workflow efficiency.
An intuitive and efficient tool for filtering VCF files.
Tool to evaluate 13C chemical shift assignments of RNA.
Webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM.
16S-ITGDB is an integrated database for improving taxonomic classification of 16S ribosomal RNA (rRNA) sequences.
Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. It has the unique ability to classify small Hypervariable Regions of 16S rRNA.
Code and supporting data for the article: "Exploring the role of normalization and feature selection in microbiome disease classification pipelines."
Comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing.
Cloud-based platform. Providing bioinformatic analysis of bacteria. Species identification (16S, WGS), typing (MLST, cgMLST, SNP), antibiotic resistance profiling, virulence. Possibility to add metadata for transmission analysis.
19 and Me: COVID-19 Risk Score Calculator is a tool that synthesizes reported COVID-19 geographic case data and rapidly evolving scientific research to help you ballpark how much risk this disease poses to you.
Demonstrates Professor Grigoryan's illustration of geometrical interpretation of the 1-D DFT.
Geometrical interpretation of the 1-D DFT
Mapping-free variant detection from DNA-seq data of matched samples.
2019nCoVAS is a web service for different analyses including transmission, genome, and psychological stress.
2020plus classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene from small somatic variants by using Random Forests.
A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members.
Webserver for the comparison of secondary structure algorithms and the secondary structure of protein structures.
2B-Alert Web, an open-access tool for predicting neurobehavioral performance, which accounts for the effects of sleep/wake schedules, time of day, and caffeine consumption, while incorporating the latest scientific findings in sleep restriction, sleep extension, and recovery sleep.
coex-simulation is a computational simulator developed to explore the relationship between events in single cells and bulk tissue expression profiles, aiming to clarify conditions under which intracellular regulatory signals propagate. The simulator and related data are available on Borealis and GitHub.
Two dimensional cepstral spectrum. The present function calculates the cepstral spectrum of image either gray scale or RGB colored. This spectrum is useful for analysis of an image and suitable for pre-processing of an image for machine learning purposes.
Web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.
Web server for protein secondary structure visualization.
This preprocessing tool is design for 2D digital mammograms in DICOM format. It standardizes and harmonizes images through a configurable pipeline that includes spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization, optional denoising, contrast enhancement, and mask processing (if available).
2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
Algorithms for 2D AR and 2D ARMA parameters estimation.
2DE-pattern is a database containing data on proteins/isoforms/proteoforms profiles.
An imputation method that recovers false zeros (known as dropouts) in single cell RNA sequencing (scRNA-seq) data. It features preventing excessive correction by predicting false zeros and imputing their values accurately by making use of the interrelationships between both genes and cells. 2DImpute takes as input a normalized scRNA-seq data matrix (genes in rows and cells in columns) with or without log-transformation. It outputs the imputed data in the same dimension and the same log-transformation.
A toolkit for content-based local image search.
The 2D semiconductor database (2DSdb) provides an ideal platform for computational modeling and design of new 2D semiconductors and heterostructures in photocatalysis, nanoscale devices, and other applications.
A software system designed as a user friendly, platform-independent software package for electron crystallography.
Algorithm that searches graphs produced from the de novo assembler cortex.
2lpiRNApred is a 2-layer integrated program for identifying piRNAs in the first layer and determining if piRNAs have the function of instructing target mRNA deadenylation in the second layer.
Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.
2SigFinder implements multiscale statistical algorithm to predict genomic islands from a single genome. It uses small-scale test with large-scale features to score small region deviating from the host and large-scale statistical test with small-scale features to identify multi-window segments for identification of genomic islands. 2SigFinder is a novel prediction method, the first combined use of small-scale and large-scale statistical testing for genomic island detection. 2SigFinder was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. Genomic island (GI) is a cluster of genes in prokaryotic genomes that have probable horizontal origins.
Manually curated 3C (Chromosome conformation capture) database.
A method for adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms.
3D Cardiomics is a web application that enables the viewing of the 3D transcriptome of the human heart.
A 3D convolutional neural network to estimate protein model accuarcy based on local structure quality assessment.
3DChrom is a web application for reconstructing three-dimensional structures of chromatins and TADs using Hi-C data and multidimensional scaling.
The 3D Genome Viewer is a deskop application to view and explore 3D genome models from Hi-C data using virtual reality technology. The goal of 3DGV is to build fully immersive VR genome browser where the user can seamlessly interact.
Script that analyzes microglia morphology from 3D data. Outputs include cell and territorial volume, branch length, and number of branch and end points.
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Related to bio.tools/fossilj.
Creates high-quality 3D/4D animations using a natural-language based syntax.
A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling. The main steps of the pipeline are: - Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample. - Alignment on refseq reference transcriptome is performed using bwa. - Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix. If secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2. - If DEG are found, annotation is performed using the database GO and KEGG. - A report is provided listing the main quality controls performed and the results found. Cite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1
An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues.
3CAC is a three-class classifier designed to classify contigs in mixed metagenome assemblies as phages, plasmids, chromosomes, or uncertain. 3CAC generates its initial classification by existing classifiers: viralVerify, PPR-Meta, PlasClass, and deepVirFinder. Thus, prior to running 3CAC, installation of these tools are required.
Pathogenicity prediction of human variants using multitask learning with evolutionary constraints.
3d-SPADE is a method to find reoccurring spike patterns in parallel spike train data, and to determine their statistical significance. It is a part of Elephant.
The 3D-Beacons Network provides unified programmatic access to experimentally determined and predicted structure models.
This workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). Workflow included in the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
3D-BioInfo + BioExcel: Protein Conformational Ensembles Generation
3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure.
An open-source active surface tool for single-cell segmentation in 3D microscopy images. It is a plugin for Medical Imaging Interaction Toolkit (https://www.mitk.org/).
An interactive tool for users to browse through sagittal, axial and coronal views of CT/MRI images.
3D CT MRI images interactive sliding viewer
A web server for generation of 3D-structural DNA models with a defined conformation by providing control over both ‘global’ and ‘local’ conformational features.
Generate in 3D the diffusion gradient vector field as in Xu and Prince 1998
3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC.
Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.
3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.
A toolbox for performing image registrations on 4D RTOG files or any other volumetric image.
3D Free Form Image Registration Toolbox (GUI)
Software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.
3D chromatin organization webserver is a 3D genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. 3D genome organization plays a critical role in its functioning. Alterations of this organization caused by structural variants (SVs) may lead to changes in gene transcription or even to disease. The recent advent of Chromosome Conformation Capture (3C) based techniques such as ChIA-PET and Hi-C allows us to investigate genome spatial organization. The rising volume of sequencing data in turn enables highly accurate identification of structural variation. Combination of those two sources of information can reveal mechanisms of genome regulation.
MATLAB script for converting a image stack into a 3D array.
3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
Computations of joint angles and displacements, moments and forces (lower / upper limb)
Tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.
3D photoacoustic visualization studio. Bio Optics and Acoustics Laboratory.
Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
3D-QSAR is a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets. The underlying idea of any field-based 3-D QSAR is that differences in a target propriety, e.g., biological activity, are often closely related to equivalent changes in shapes and intensities of noncovalent calculated interaction surrounding the molecules (also called molecular interaction fields, MIFs).
3D RNA-seq appA powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. 3D RNA-seq is currently under a dual-licensing model.
3D Shepp-Logan Phantom is a 3D extension of MATLAB's phantom function - generates a phantom consisting of an arbitrary number of ellipsoids in 3D.
3D-Speckler is a semi-automated software tool for calibrating fluorescence microscopy, enabling precise quantification of fluorescence puncta, including nanoscale 2D/3D particle size, precise locations, and intensity information. It utilizes multispectral fluorescence beads of known sizes alongside the software to calibrate imaging systems.
3D Fluorescence Speckle Analyzer (3D-Speckler)
3D-SURFER is a web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons.
3D-XGuide is a software framework providing a foundation for rapid prototyping of new approaches in the field of XR navigation guidance. Actual software release offers graphical user interface with basic functionality including data import and handling, calculation of projection geometry and transformations between related coordinate systems, rigid 3D-3D registration, and template-matching-based tracking and motion compensation algorithms in 2D and 3D.
An Web Server for RNA 3D structure prediction.
An interactive software for 3D segmentation and analysis of dendritic spines.
This software contains 2D and 3D Shepp-Logan phantoms in both the image and Fourier domains.
Three Dimensional Analytical Magnetic Resonance Imaging Phantom in the Fourier Domain
Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.
Spanish Ministry of Science and Innovation
A light and robust tool to do 3D cell instance segmentation for cell membrane images. It is useful when the cells clump together.
3DCOMB is a software which can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments.
3DeFDR is a statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions
3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies.
Robust computational infrastructure capable of supporting the automatic and standardised benchmarking of image processing applications for cryoEM.
The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
A web-server to benchmark computational models for 3D Genomics.
3DGene is a database and visualization tool that provides predicted 3D conformations of active genes in GM12878 human lymphoblastoid cells, generated using the e-HiP-HoP framework. The database offers interactive visualizations and downloadable simulation data, revealing insights into gene structure and regulatory networks.
3D graph and text based neural network for drug-drug interaction prediction.
3DIANA (3D Domain Interaction Analysis) is a web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling
Collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The web server visualizes these interfaces along with atomic details of individual interactions using Jmol.
3D-Genome Interaction Viewer & database is a comprehensive resource of 3D genome and 3D cancer genome. 3D genome organization is tightly coupled with gene regulation in various biological processes and diseases. 3D Interaction Viewer and Database (3DIV) is a database providing chromatin interaction visualization in a variety of options from one-to-all chromatin interaction with epigenetic annotation to unique dynamic browsing tools allowing examination of large-scale genomic rearrangement mediated impacts in cancer 3D genome.
3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.
3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
A command line tool for bio bank-scale mapping of variants to protein structures.
This is an in-house code of the FORTH/ICE-HT Laboratory of Simulation of Advanced Materials and Processes, Patras, Greece, providing a reliable 3D reconstruction and simulation of a membrane bioreactor for lactose hydrolysis with immobilized enzymes. The membrane model is coupled to a macroscopic model of a single membrane fiber unit to produce lactose concentration profiles, lactose consumption predictions, and performance index estimates.
Object-oriented, webGL based JavaScript library for online molecular visualization – No Java required! With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications.
Database for exploring the conformational features of DNA. It enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc.
A package of Python scripts that sensitively detects nested, hierarchical domains in HiC data.
Application for two- and three-dimensional fish morphological phenotype extraction from point cloud analysis.
An accessible simulation framework to model the interplay between chromatin and loop extrusion.
3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view.
3DRobot is a program devoted for automated generation of diverse and well-packed protein structure decoys.
3DRS, a web-based tool to share interactive representations of 3D biomolecular structures and Molecular Dynamics trajectories
3DSNP is a database linking noncoding Variants to 3D interacting genes. It is an integrated annotation database linking genome-wide noncoding SNPs and small INDELs to 3D interacting genes via chromatin loops.
A 3-dimensional quantification algorithm for LC–MS labeled profile data
Tool for superposing two or more protein structures that uses RASMOL for visualization, some browser configuration is necessary.
3D Transcription Factor (3DTF) is a web-server for the analysis of protein-DNA binding sites. It calculates the positional weight matrix (PWM), representing the DNA-binding specifity of the protein.
Tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D.
It can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, it utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods.
Optimized Levenshtein distance for clustering third-generation sequencing data.
Prediction of potentially immunopathogenic SARS-CoV-2 epitopes via a novel immunoinformatic approach. Choose FASTA files for Peptide Vaccine Candidate Inputs. Load Peptide Vaccine Candidates from OptiVax. Liu, G., Carter, B., Bricken, T., Jain, S., Viard, M., Carrington, M., & Gifford, D. K. (2020). Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions. Cell systems, 11(2), 131–144.e6.
3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
The metabolome-microbiome-metadata correlation analysis platform (3MCor) is a web server for integrative correlation analysis of metabolome and microbiome under the instruction of phenotype and with the consideration of confounders. 3MCor is independent to measurement platforms. Along with integrative correlation analysis of metabolome and microbiome under the instruction of metadata (phenotypes and confounders).
Feature grouping and scoring in multi-omics.
3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
A web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.
Software for detecting gene conversion events in whole genomes.
Web-server developed with the aim of retrieving 3’UTR genomic coordinates and nucleotide sequences of the transcripts assembled by standard RNA-seq analysis protocols.
The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.
Curated database of chromatin interaction data covering five organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Plasmodium falciparum, and Saccharomyces cerevisiae.
Weakly supervised prediction of N4-acetyldeoxycytosine DNA modification from sequences
Federated Brain Graph Evolution Prediction using Decentralized Connectivity Datasets with Temporally-varying Acquisitions.
4D Nucleome Data Portal is a resource for searching and visualizing curated nucleomics data. The 4D Nucleome program aims to understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension). The 4DN Data Visualization Workspace allows users to create 1D or 2D genome displays. Registered users can save and share the displays they create. The Visualization Workspace is powered by HiGlass. The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization.
The 4DNvestigator is a MATLAB toolbox that analyzes time-series genome-wide chromosome conformation capture (Hi-C) and gene expression (RNA-seq) data.
Digitally Predicting Protein Localization and Manipulating Protein Activity in Fluorescence Images Using Four-dimensional Reslicing GAN.
A spatial–temporal root architectural modeling method based on 4D data from X-ray Computed Tomography (CT) by cylindrical fitting
A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.
A web application for identification of DNA N4-methylcytosine sites in the mouse genome.
4mC-w2vec is a web tool for identifying DNA N4-methylcytosine sites in the rosaceae genome with a deep learning model relying on distributed feature representation.
Generic webserver for predicting N4-methylcytosine (4mC) sites.
4mCNLP-Deep is a tool the identification of N4-methylcytosine. It performs natural language processing by exploiting deep learning algorithm.
Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences.
A pipeline with emphasis on SNP detection. It will detect SNPs in NGS data where no reference sequence nor strain information is available.
4SALE allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.
4SpecID is a cross-platform program to audit and annotate reference DNA libraries. It is oriented to ensure the golden standards for forensic applications.
Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data.
'5'_ORF_Extender' is a tool that can perform a systematic identification of extended coding regions (CDS) at the 5´ end of known mRNAs, using an EST-based approach.
A web server for nosocomial bacterial antibiogram investigation and epidemiology survey.
A novel online tool for predicting DNA N6-methyladenine sites in genomes.
6mA-Pred is a web tool for identifying DNA N6-methyladenine sites based on deep learning.
A Bioinformatics Tool for the Prediction of DNA N6-Methyladenine Modifications Based on Feature Fusion and Optimization Protocol.
A community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed.
A web application for predicting 9aaTAD activation domains in a sequence.
A tool for analysis of differentially expressed omics entities across multiple pairwise comparisons.
AAI-profiler [1] is a fast homology search tool that takes a query proteome (protein sequences in FASTA format) as input and plots the AAI (Average Amino-acid Identity) values of species in the Uniprot database. AAI-profiler is powered by SANS [2] and the processing time for a bacterial proteome is a few minutes.
Tool for looking at aligned nucleotide and amino acid sequences to observe variations in hydropathy index, volume, and charge of residues of a protein.
A database for chemically defined antibodies.
Antibodies Chemically Defined Database (ABCD)
An R package to calculate equilibirum conditions with and without correction for ionic strength using Davies' equation.
Experimental Brain Computer Interface Software for the ModularEEG.
Adaptive boosting-based computational model for predicting potential miRNA-disease associations.
R Package for Calculating the Abnormal Blood Profile Score.
Mass screening of contigs for antimicrobial resistance or virulence genes.
The Accessory-based source attribution (AB_SA) method aims at attributing the origin of bacterial strains associated to human cases or isolated in environment.
Accessory-based source attribution (AB_SA)
Allele CAlling proCedure for Illumina Amplicon sequencing data.
ACCOST is a Python script that assigns statistical significance to differences in contact counts in Hi-C experiment.
Machine learning toolbox for clustering analysis and visualization.
A free tool for drug repurposing using consensus inverse docking strategy.
ACPP is a Support Vector Machine based tool to predict whether the given peptide is an Anti-cancer peptide or Not. The three different modes include (i) Protein scan with apoptotic domain prediction; (ii) Multiple peptide mode; and (iii) Peptide mutation mode for prediction and design of anti-cancer peptides. Refer: "ACPP: A Web Server for Prediction and Design of Anti-cancer Peptides." International Journal of Peptide Research and Therapeutics 21.1 (2015): 99-106" for more deatils.
Computational Tool for the Prediction and Analysis of Anticancer Peptides.
ACPred-Fuse is a web application that automatically can predict protein sequences with or without anticancer activity in peptide form.
A multi-scale resource of biological maps to study disease mechanisms.
Atlas of Cancer Signalling Network (ACSN)
Automated Identification of Cell Types in Single Cell RNA Sequencing | Automated Cell Type Identification using Neural Networks | ACTINN (Automated Cell Type Identification using Neural Networks) is a bioinformatic tool to quickly and accurately identify cell types in scRNA-Seq. For details, please read the paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz592/5540320 All datasets used in the paper are available here: https://figshare.com/articles/ACTINN/8967116
a latent Dirichlet model to compare expressed isoform proportions to a reference panel. actor is an R package which takes transcript expression as input and uses a latent Dirichlet model to compare to GTEx tissues. actor provides gene level similarities to the GTEx tissues and identifies collections of genes, or gene classes, which align similarly to GTEx tissues
Automated preprocessing and analysis of actigraphy data. OBJECTIVES:To introduce a novel software-library called Actigraphy Manager (ACTman) which automates labor-intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. DESIGN:Descriptive. METHODS:Use cases are described for performing a common actigraphy task in ACTman and alternative actigraphy software. Important inefficiencies in actigraphy workflow are identified and their consequences are described. We explain how these hinder the feasibility of conducting studies with large groups of athletes and or longer data collection periods. Thereafter, the information flow through the ACTman software is described and we explain how it alleviates aforementioned inefficiencies.
A comprehensive web platform of antimicrobial peptides tailored to the user's research. Antimicrobial peptides (AMPs) are part of the innate immune response to pathogens in all of the kingdoms of life. They have received significant attention because of their extraordinary variety of activities, in particular, as candidate drugs against the threat of super-bacteria.
leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra | Learning molecular vectors for metabolites from spectra-structure pairs] | We propose ADAPTIVE, which has two parts: learning two mappings 1) from structures to molecular vectors and 2) from spectra to molecular vectors
Automated Deconvolution Augmentation of Profiles for Tissue Specific cells.
a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci. We developed ADDO, a highly-efficient tool designed to detect, classify and visualize quantitative trait loci (QTLs) with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single nucleotide polymorphism (SNP) effects into additive, partial dominance, dominance and overdominance categories. A matrix multiplication approach is used to accelerate the computation: a genome scan on 20 million markers from 836 individuals takes about 8.5 hours with 10 CPUs. Additivity and dominance are the major genetic components underlying variations in complex traits
Discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.
Risk calculator to predict ADHD in young adulthood.
Bayesian Optimization with Unknown Constraints using ADMM. There exist many problems in science and engineering that involve optimization of an unknown or partially unknown objective function. Recently, Bayesian Optimization (BO) has emerged as a powerful tool for solving optimization problems whose objective functions are only available as a black box and are expensive to evaluate. Many practical problems, however, involve optimization of an unknown objective function subject to unknown constraints. This is an important yet challenging problem for which, unlike optimizing an unknown function, existing methods face several limitations. In this paper, we present a novel constrained Bayesian optimization framework to optimize an unknown objective function subject to unknown constraints.
Broad-Spectrum Profiling of Drug Safety via Learning Complex Network.
A novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
Scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark.
We construct a novel method named alternative splicing network(AEN) combining gene expression levels with AS patterns to analyze cellular heterogeneity, identify novel cell types, and infer the regulatory mechanisms of alternative splicing. By applying the AEN method to gastrula data, pan-cancer T-cell data, and lung cancer tumor cell data, we have successfully revealed the hidden alternative splicing heterogeneity in these cells and identified key alternative splicing events and related splicing factors during cell transformation. The application of AEN method provides new insights into the understanding of cellular heterogeneity and its related physiological and pathological processes.
A web tool which provides several novel survival analysis approaches. It computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting.
Advanced Expression Survival Analysis (AESA)
A shiny web tool for heatmap generation of genetic expression datasets using R packages. Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a *.CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for interactive expression data visualization that can be easily deployed without any restrictions to any operating system used by any online user
The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations.
The Allele Frequency Net Database (AFND)
Another Gff Analysis Toolkit (AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.
A Robot Annotator for Argonaute Proteins. Welcome to AgoNotes home page! AGONOTES is an online service tool to identify Argonaute protein in proteins of all domains of life and annotate the argonaute domains. Users can submit any protein with fasta formation into the input field, or save proteins as a file ended with .faa, .fasta, .fa or .txt and then upload this file
> CORRECT NAME OF TOOL COULD ALSO BE 'ags.sh acn.sh tools', 'AGS', 'ACN' | Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data | Here, we present the ags.sh and acn.sh tools dedicated to the computation of the Average Genome Size (AGS) and 16S rRNA gene Average Copy Number (ACN), respectively. The ags.sh and acn.sh tools compute these metagenomic traits based on the (ultra-fast) annotation of 35 universally distributed single-copy genes in unassembled metagenomic data | Pereira-Flores, E., Glöckner F. O., and Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinformatics. 2019;20(1):453. doi:10.1186/s12859-019-3031-y
Anti-Inflamamtory Compounds Database for drug discovery.
annotation-assisted isoform discovery with high precision. AIDE: annotation-assisted isoform discovery and quantification from RNA-seq data. AIDE is a statistical method which identifies full-length mRNA isoforms from a novel perspective: using the likelihood ratio test to find novel isoforms in a stepwise manner given annotated isoforms, by prioritizing and selectively borrowing information from the annotated isoforms. Please refer to our preprint at Biorxiv for detailed description of our method
mapping distal regulatory elements using convolutional learning on GPU. BACKGROUND:The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional annotation problem, within the bounds of the hardware constraints and the model's complexity. In our system AIKYATAN, we annotate distal epigenomic regulatory sites, e.g., enhancers. Specifically, we develop a binary classifier that classifies genome sequences as distal regulatory regions or not, given their histone modifications' combinatorial signatures. This problem is challenging because the regulatory regions are distal to the genes, with diverse signatures across classes (e.g., enhancers and insulators) and even within each class (e.g., different enhancer sub-classes)
Assessing concordance among human, in silico predictions and functional assays on genetic variant classification.
Interactive calculator for Artificial Intelligence (AI) Thyroid Imaging Reporting and Data System (TI-RADS).
Jointly integrating VCF-based variants and OWL-based biomedical ontologies in MongoDB.
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. ALACD is to get the drug-lncRNA assoications via bi-level optimization and decoded in R. It includes SVM standard algorithm for argumenting the genes' co-expressed lncRNAs (enhancering-lncRNA-mRNA-coexpression.R), and the optimization procedure for optimal identification of genes aassociated with both lncRNAs and drug to get the drug-lncRNA assoications (optimizating.R). crossvalSVM.R and getperf.R are for SVM cross-validtion and generating the evluation criteria, respectively. It also includes the DEGanalysis.R for differential expression analysis, and survival-analysis.R for surivival analysis of lncRNAs
Rapid detection of candidate horizontal gene transfers across the tree of life.
> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design | BACKGROUND:Dietary supplements (DSs) are widely used. However, consumers know little about the safety and efficacy of DSs. There is a growing interest in accessing health information online; however, health information, especially online information on DSs, is scattered with varying levels of quality. In our previous work, we prototyped a web application, ALOHA, with interactive graph-based visualization to facilitate consumers' browsing of the integrated DIetary Supplement Knowledge base (iDISK) curated from scientific resources, following an iterative user-centered design (UCD) process. METHODS:Following UCD principles, we carried out two design iterations to enrich the functionalities of ALOHA and enhance its usability
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype | Deep learning frame for genetic disease | Synthetic data https://drive.google.com/open?id=1Mya0YdT4Hf9wUfbcX6y5mubEFWky6Jg-
PURPOSE:The automated segmentation of each lung and trachea in CT scans is commonly taken as a solved problem. Indeed, existing approaches may easily fail in the presence of some abnormalities caused by a disease, trauma, or previous surgery. For robustness, we present ALTIS (implementation is available at http: lids.ic.unicamp.br downloads) - a fast automatic lung and trachea CT-image segmentation method that relies on image features and relative shape- and intensity-based characteristics less affected by most appearance variations of abnormal lungs and trachea. METHODS:ALTIS consists of a sequence of image foresting transforms (IFTs) organized in three main steps: (a) lung-and-trachea extraction, (b) seed estimation inside background, trachea, left lung, and right lung, and (c) their delineation such that each object is defined by an optimum-path forest rooted at its internal seeds
Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis.
A web application for automatic mendelian literature evaluation.
AMICI provides a multi-language (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML or PySB and automatically compiles such models into .mex simulation files (Matlab), C++ executables or Python modules. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood-based output functions. The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but it is also applicable to a wider range of differential equation constrained optimization problems.
annotation of metabolite origins via networks to integrate microbiome and metabolome data. Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data. It is recommended to install AMON in a conda environment. The environment can be created by first downloading the environment file. A command line tool for predicting the compounds produced by microbes and the host. AMON includes two scripts. extract_ko_genome_from_organism.py takes a KEGG organism flat file and makes a list of KOs present in that file. AMON.py predicts the metabolites that could be produced by the KOs used as input. This can be compared to the KOs present in the host or from some other gene set as well as to as set of KEGG metabolites
An R Package for Working with Antimicrobial Resistance Data.
A GUI-based, open-source system for imaging samples in multi-well plates | Described here are instructions for building and using an inexpensive automated microscope (AMi) that has been specifically designed for viewing and imaging the contents of multi-well plates. The X, Y, Z translation stage is controlled through dedicated software (AMiGUI) that is being made freely available. Movements are controlled by an Arduino-based board running grbl, and the graphical user interface and image acquisition are controlled via a Raspberry Pi microcomputer running Python. Images can be written to the Raspberry Pi or to a remote disk. Plates with multiple sample wells at each row column position are supported, and a script file for automated z-stack depth-of-field enhancement is written along with the images
Attentive neural cell instance segmentation.
Atomic angle- and distance-dependent statistical potential for protein structure quality assessment.
ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: i) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; ii) A multispecies genomic browser; iii) a Genomicus gene synteny browser.
Additional Neural Matrix Factorization model for computational drug repositioning | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” #Author Xin-Xing Yang Southeast University Email:220174323@seu.edu.cn | Open the "ANMF.py" file and run it directly. In the Data folder is the test example we provide | We use Keras with Theano as the backend
Flux prediction using artificial neural network (ANN) for the upper part of glycolysis.
ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching.
Analysis and Performance Assessment of Label-free Proteome Quantification.
AOE (All Of gene Expression) - an integrated index for public gene expression databases.
Opportunities and Challenges with in Vitro Testing and Adverse Outcome Pathway Approaches | Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki) | This wiki is hosted by the Society for the Advancement of Adverse Outcome Pathways (SAAOP) and serves as one component of a larger OECD-sponsored AOP Knowledgebase (AOP-KB) effort. The AOP-KB represents the central repository for all AOPs developed as part of the OECD AOP Development Effort by the Extended Advisory Group on Molecular Screening and Toxicogenomics. All AOPs from the AOP Knowledgebase are available via the e.AOP.Portal, which is the primary entry point for the AOP-KB. More information about the AOP-KB efforts, the organizations supporting these efforts, and the other modules of the AOP-KB are available on the About page
A proposed methodology and inventory of effective tools to link chemicals to adverse outcome pathways | Welcome to the Adverse Outcome Pathway Exploratory Research Assistant (AOPERA)! | AOPERA is designed to identify existing tools that can assist you in the process of linking your chemical to an adverse outcome pathway (AOP). This informational tool is specifically targeted to users with an uncharacterized chemical and limited toxicity information, but can also assist you if you already have information that links your uncharacterized chemical to a molecular initiating event (MIE), a key event (KE), or an adverse outcome (AO), or if you have a characterized chemical
A Sequence-Based Classifier of Antioxidant Proteins Using a Support Vector Machine. AOPs-SVM: Sequence-based Classifier of Antioxidant Proteins Using a Support Vector Machine. Input your sequence:(FASTA format)
A Python package for adaptive optics modelling and analysis.
Proteotypic peptide prediction tool by taking the peptide digestibility into consideration.
decoding alternative polyadenylation across human tissues. The APA atlas refers to " A lternative P oly A denylation atlas in human tissues". Widespread alternative polyadenylation (APA) occurs during cell proliferation and differentiation, exhibits strong tissue specificity. Recent studies have highlighted the important role of APA in transcription regulation. Here we systematically characterize APA profile in 9,475 samples across 53 human tissues from Genotype-Tissue Expression (GTEx) project with two algorisms, and analyzed the association between APA events with traits and mRNA expression. These APA events may uncover novel mechanisms for the transcription regulation, development of tissues and phenotypes
APEC (Accessibility Pattern based Epigenomic Clustering) - single cell epigenomic clustering based on accessibility pattern.
The APHIRM Toolkit is a set of OHS risk management procedures that target both physical and psychosocial hazards. A participative hazard identification and risk management toolkit for improving the risk management of musculoskeletal disorders.
An auto-adaptive parentage inference software that tolerates missing parents. Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents. Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions. The main function of this package is the function APIS(), which is the parentage assignment function
APproximate PArallel and stochastic GrAph querying TOol for biological networks.
Systematic Identification of Novel Cancer Genes through Analysis of Deep shRNA Perturbation Screens. APSiC: Analysis of Perturbation Screens for the Identification of Novel Cancer Genes. A web portal using the Shiny framework in R has been developed to visualize rank profiles of the DRIVE shRNA screen and corresponding gene expression data from TCGA at https://apsic.shinyapps.io/APSiC/
Sequencing-based quantitative mapping of the cellular small RNA landscape. Processing scripts for AQ RNA-seq. This repo contains python processing scripts for AQRNA-seq data analysis. The scripts were used in conjuction with open-source tools/algorithms such as fastxtoolkit and blast as described below
Tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein.
A database and toolkit for researchers working on environmental mercury geochemistry. AQUA-MER is useful for researchers who want to investigate mercury speciation in defined environments i.e., to which chemical elements and groups it will bind and in what proportions, given an input of concentrations of chemicals.
Active and Regulatory site Prediction (AR‐Pred) to identify protein regulatory and functional binding sites.
accurate, reliable and active histopathological image classification framework with Bayesian deep learning. This repository contains an implementation of ARA-CNN - a Bayesian deep learning model intended for histopathological image classification. ARA stands for Accurate, Reliable and Active. Any method that works on patient data needs to be accurate and reliable, meaning that in addition to very high classification accuracy it should also provide a measure of uncertainty for each prediction. ARA-CNN adheres to these requirements. Moreover, the uncertainty measurement can be used as an acquisition function in active learning, which significantly speeds up the learning process on new histopathological datasets. Uncertainty can also be used to identify mislabelled training images
comprehensive antibiotic resistance detection from Burkholderia pseudomallei genomes | Comprehensive resistance detection from WGS data | ARDaP - Antimicrobial Resistance Detection and Prediction | ARDaP was written by Derek Sarovich (@DerekSarovich) (University of the Sunshine Coast, Australia) with database construction, code testing and feature design by Danielle Madden (@dmadden9), Eike Steinig (@EikeSteinig) (Australian Institute of Tropical Health and Medicine, Australia) and Erin Price (@Dr_ErinPrice)
ARMOR (Automated Reproducible MOdular RNA-seq) Workflow for Preprocessing and Differential Analysis of RNA-seq Data.
Development and validation of a predictive model for American Society of Anesthesiologists Physical Status. BACKGROUND:The American Society of Anesthesiologists Physical Status (ASA-PS) classification system was developed to categorize the fitness of patients before surgery. Increasingly, the ASA-PS has been applied to other uses including justification of inpatient admission. Our objectives were to develop and cross-validate a statistical model for predicting ASA-PS; and 2) assess the concurrent and predictive validity of the model by assessing associations between model-derived ASA-PS, observed ASA-PS, and a diverse set of 30-day outcomes. METHODS:Using the 2014 American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) Participant Use Data File, we developed and internally cross-validated multinomial regression models to predict ASA-PS using preoperative NSQIP data. Accuracy was assessed with C-Statistics and calibration plots
The Automated Self-Administered 24-Hour (ASA24) Dietary Assessment Tool is a free web-based tool for collection of automatically coded dietary recalls and/or food records.
ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates.
A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data. This repository contains the implementation of ASD-DiagNet algorithm
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.
A Program for Assembling Splice Junctions Analysis | RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and characterizes all splice junctions from high-throughput RNA sequencing (RNA-seq) data. ASJA processes assembled transcripts and chimeric alignments from the STAR aligner and S tringTie assembler. ASJA provides the unique position and normalized expression level of each junction. Annotations and integrative analysis of the junctions enable additional filtering. It is also appropriate for the identification of novel junctions. Implementation and Dependencies
classifying functionally diverse protein families using alignment score matrices. the three scripts in this directory comprise ASM-clust, an approach to de novo classify complex protein superfamilies ASM-clust is intended to. ASM-Clust is implemented in bash with two helper scripts in perl, and will take a protein fasta file as the sole input. Fasta files are processed with ASM_clust.sh, which then:
Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals.
An online database for exploring over 2,000 Arabidopsis small RNA libraries.
An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. Welcome to ATB assistant discrimination!. Home Document Datasets Contact Us. Approximately one third of the world's population is infection with Mycobacterium tuberculosis. They are at a high risk progression to active tuberculosis (ATB) during their lifetime, so it is urgent and vital to develop diagnostic methods that can distinguish ATB from latent tuberculosis infection. Please input single sample data in the text form:. Please Cite: Jiangpeng Wu, Jun Bai, Wei Wang, Lili Xi, Pengyi Zhang, Jingfeng Lan, Liansheng Zhang*, Shuyan Li*. ATBdiscrimination: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. J. Chem. Inf. Model., 2019, doi: 10.1021/acs.jcim.9b00678
Prediction of the Classes of Anatomical Therapeutic Chemicals Using a Network-Based Label Space Partition Method | codes for the drug class prediction paper | Codes and dataset for "Network-based label space partition for predicting the classes of anatomical therapeutic chemicals"
And/Or Tree Ensemble for inferring accurate Boolean network topology and dynamics | # Download the development version of ATEN from GitHub: | Note: please note that set.seed() is not suitable for the Package parallel. In order to make the results reproducible, we introduced function clusterSetRNGStream(), more deatails please see the Pacakge parallel | B, the number of And/Or trees in ATEN. This parameter always depends on the size/noise of the data. We suggest you set a higher B for large/noisy networks. If you set a very large B, although it won't affect the results much, but it takes much time..
Design a prototype for automated patient diagnosis in wireless sensor networks | It is indeed necessary to design of an elderly support mobile healthcare and monitoring system on wireless sensor network (WSN) for dynamic monitoring. It comes from the need for maintenance of healthcare among patients and elderly people that leads to the demand on change in traditional monitoring approaches among chronic disease patients and alert on acute events. In this paper, we propose a new automated patient diagnosis called automated patient diagnosis (AUPA) using ATmega microcontrollers over environmental sensors. AUPA monitors and aggregates data from patients through network connected over web server and mobile network. The scheme supports variable data management and route establishment. Data transfer is established using adaptive route discovery and management approaches
Automatic adaptive LASSO for genome-wide prediction.
Toward automated pathogenic variant evidence retrieval directly from the full-text literature | PURPOSE:Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach. METHODS:Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates. RESULTS:AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor
Identifying Crohn's disease signal from variome analysis | prediction of individual predisposition to disease x through variation analysis | After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown
An web application that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains.
AcCNET (Accessory genome Constellation Network) - application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels.
AcRanker is a machine learning system developed in python that ranks proteins in a proteome as per their Anti-CRISPR tendencies predicted using sequence features.
AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis.
ActiveDriver is a computational method for identifying post-translational modification (PTM) sites (i.e., active sites) in proteins that are significantly mutated in cancer genomes. ActiveDriver provides signalling-related interpretation of single nucleotide variants (SNVs) identified in cancer genome sequencing.
Accurate, Detailed, and Automatic Modelling of Laser-Scanned Trees | AdTree implements the tree reconstruction method described in the following paper: | 3D Trees reconstructed from point clouds
An R package for data Adaptive Robust Estimation in Linear Regression with Application in GTEx Gene Expressions.
A comprehensive bioinformatics knowledge-base for food additive chemicals. A comprehensive food additive database. Supported search options:Text query, Structure, Fragment, Similarity, MCS. Food additives are considered to be the catalysts and headstones of the modern food industry, affecting every step of food production, processing, and storage. Fields searchable in this way are:CAS number,JECFA number,FEMA number,CoE number,Name,InChI,InChI key,INS
An R package for probability distributions and general purpose optimization | Several lifetime distributions have played an important role to fit survival data. However, for some of these models, the computation of maximum likelihood estimators is quite difficult due to presence of flat regions in the search space, among other factors. Several well-known derivative-based optimization tools are unsuitable for obtaining such estimates. To circumvent this problem, we introduce the AdequacyModel computational library version 2.0.0 for the R statistical environment with two major contributions: a general optimization technique based on the Particle Swarm Optimization (PSO) method (with a minor modification of the original algorithm) and a set of statistical measures for assessment of the adequacy of the fitted model
R-based tool to support topic discovery for systematic and literature reviews.
A Web resource enabling to inspect the neuroanatomy of the fruit fly, equipped with a graphical interface enabling users to color structures on brain sections.
bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression. Alignment-Free methods Adjusted by Neural Network. Afann (Alignment-Free methods Adjusted by Neural Network) is an alignment-free software that supports fast calculation of different dissimilarity measures including d2star, d2shepp, CVtree, Manhattan, Euclidean and d2. It also adjusts the bias of d2star and d2shepp calculated from sequencing samples
framework for the analysis of Aspergillus fumigatus isolates based on their microsatellite profile.
A mathematical model for the prediction of change in aggregation rate upon point mutation. Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases (including type II diabetes, corneal dystrophy and most of neurodegenerative disease like Alzheimer's disease, Parkinson's disease, huntington's disease etc.) as well as for biotechnology and bio-material science products (such as human recombinant proteins, monoclonal antibodies, industral enzymes and vaccines). AggreRATE-Pred is a linear regression based tool which can predict the change in aggregation rate upon point mutation for the given protein
Package for structure-based prediction of protein aggregation properties and rational design of protein solubility.
The RDF Knowledge-based Database for plant molecular networks.
Browser for ontologies for agricultural science based on NBCO BioPortal.
Tool introducing a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data.
AliTV-interactive visualization of whole genome comparisons. Visualize whole genome alignments as linear maps. For the perl part, see AliTV-perl-interface. You do not need to install anything to try the interactive visualization of AliTV. Just navigate to the demo page to try all the features on an example dataset (seven chloroplast genomes). You can also import your own json files on that page. When loading your own data into AliTV it is not transferred to a server but remains on your local machine. Read the documentation at readthedocs
Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data.
a tool for personalized and allele-specific sgRNA design | A software tool for personalized and allele-specific CRISPR editing | The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is open-source software that incorporates single nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing one or multiple haplotypes of a sequenced genome, currently supporting eleven Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer
Method for the identification and analysis of cancer driver targets.
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging
AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data.
A method for sequence discovery with deep reinforcement learning.
> CORRECT NAME OF TOOL COULD ALSO BE 'Conclusions:AluMine' | alignment-free method for the discovery of polymorphic Alu element insertions | Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes | git clone https://github.com/bioinfo-ut/AluMine | This GitHub repository stores various scripts required to discover and genotype polymorphic Alu element insertions. There are four different workflows: REF-plus discovery, REF-minus discovery, merging and filtering workflow and genotyping workflow. REF-plus and REF-minus workflows generate text file containing 32-mer pairs that can be subsequently used for genotyping using FastGT package. The scripts are written in PERL and bash | Please cite: Puurand T, Kukuškina V, Pajuste F-D, Remm M. (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA 10:31. [https://doi.org/10.1186/s13100-019-0174-3](doi: https://doi.org/10.1186/s13100-019-0174-3)
R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.
Text mining tool for extracting information about microbial biodiversity in food.
Data architecture and visualization for a large-scale neuroscience collaboration. Database for experimental neuroscience laboratories. Documentation: http://alyx.readthedocs.io. The setup.py script sets up postgres (it creates the database and postgres user), it sets up the alyx/alyx/settings_secret.py file with the postgres database connection information, it creates the Python virtual environment with the dependencies (including django), and it creates all the required SQL tables. Note that the postgres username and password are distinct from Alyx (Django) users and password. There is only one postgres user that is only used locally for maintenance task or by Django
Identification of single nucleotide variants using position-specific error estimation in deep sequencing data | Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling
Systematic processing of ribosomal RNA gene amplicon sequencing data. This is the AmpliconTagger home page. AmpliconTagger pipeline - for various types of amplicon sequencing data. By Julien Tremblay - julien.tremblay_at_nrc-cnrc.gc.ca
This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).
Collection of amyloidoses and other clinical disorders related to amyloid deposition.
A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules.
Software package for quantitative analysis of plant ER architecture and dynamics.
Package for trans-cell type prediction of transcription factor binding sites.
Estimating the number of people in hidden populations is needed for public health research, yet available methods produce highly variable and uncertain results. The Anchored Multiplier calculator uses a Bayesian framework to synthesize multiple population size estimates to generate a consensus estimate.
Web-based exploration of numerical chromosomal variation in single cells.
A comprehensive database with multiple animal reference panels for genotype imputation.
Anncolvar builds a feed-forward neural network for approximation of a collective variable of a molecular system. Molecular simulations are slow due to fact that a studied system tends to stay in local energy minima. Methods such as metadynamics address this problem by application of artificial forces acting on collective variables. Collective variables are some descriptors of the state of the molecular system. For example, when simulation binding of a ligand to protein it is possible to use their distance as a collective variable and by applying force onto this collective variable you can accelerate binding and unbinding. However, some sophisticated collective variables are difficult to calculate. For this purpose we developed Anncolvar to approximate such collective variables using artificial neural network.
Interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data.
a Django-based sample, reagent, and experiment metadata tracking system. Annot and information about what Annot is can be found here: https://gitlab.com/biotransistor/annot . This here is just tutorial material for the tutorial described here: http://annot.readthedocs.io/en/latest/man_tutorial.html . Welcome to Annotamentum’s Documentation. — Annot 5 documentation. Welcome to Annotamentum’s Documentation.¶. Django admin based sample, reagent and experiment metadata tracking. Summary: Annot is a web application, developed for biological wetlab experiment layout, sample and reagent logging, so that data is ready for sharing and analysis. On its core annot makes use of the acpipe_anjson library and acjson - assay coordinate json - file format. The use of controlled vocabulary from ontologies for sample and reagent annotation is enforced. Annot’s modular implementation can be adapted to a variety of experimental paradigms
Integrated tool for annotation and ranking of structural variations.
Generative Adversarial Networks for Anonymizing Private Medical Data. Scikit-learn library package (version 0.18). Keras library package (version 2.0.6)
Automating the design of oligonucleotides for capture/enrichment technologies. AnthOligo is a web-based application developed to automatically generate oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. It automates the complex process of checking multiple applications so that the oligos selected successfully pass certain specific parameter criteria and then get shortlisted as a possible use case for RSE (region specific extraction) processes
A Web Application for Predicting Antibacterial Activity of Chemical Compounds. Predict Targets for Drawn Structure. Discovery of novel antibacterial agents is the high-priority task because the existing therapy do not provide the necessary safety and sufficient long-term efficacy due to the emerging resistance [1]. The process may be optimized using (Q)SAR methods based on the accumulated experimental data in the field. Nowadays, data on antibacterial action of chemical compounds are well represented in public domain. ChEMBL database [2], for example, contains records on activity of chemical compounds against 1386 bacteria. We extracted bioactivity records on minimum inhibitory concentrations (MICs) of chemical compounds from ChEMBL_24 and prepared them as follows:. antiBac-Pred allows user to predict the fact that chemical compound can inhibit the growth of one or more of 353 bacteria in concentration below the 10000 nM
Web-resource for in silico prediction of anti-HIV/AIDS activity | MOTIVATION:Identification of new molecules promising for treatment of HIV-infection and HIV-associated disorders remains an important task in order to provide safer and more effective therapies. Utilization of prior knowledge by application of computer-aided drug discovery approaches reduces time & financial expenses and increases the chances of positive results in anti-HIV R&D. To provide the scientific community with a tool that allows estimating of potential agents for treatment of HIV-infection and its comorbidities, we have created a freely-available web-resource for prediction of relevant biological activities based on the structural formulae of drug-like molecules
The comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors | Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species
Web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models.
A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states and enriched epigenetic marks. For gene lists in search results, gene expression profiling analysis and functional enrichment analysis tools are provided to systematically extract biological themes from gene lists. Additionally, the basic structural and functional annotations of each gene can be obtained, such as gene families, KEGG annotations, GO terms, orthologues in thirteen species and Pfam domains. In addition, some functional support toolkits are also provided, such as GO analysis, blast, motif analysis, ID conversion, sequence extraction and the UCSC genome browser. We hope that AppleMDO will benefit apple research communities and serve as a reference for other fruit trees
Assembly based variant calling package for stLFR and hybrid assembly for linked-reads | Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads | Install through Bioconda (The updated version 1.2.11): | Aquila_stLFR_assembly_based_variants_call --help | (Please ensure channels are properly setup for bioconda before installing) | Aquila_stLFR utilizes Python3 (+ numpy, pysam, and scipy), SAMtools, and minimap2. To be able to execute the above programs by typing their name on the command line, the program executables must be in one of the directories listed in the PATH environment variable (".bashrc")
Proteome-wide structure-based prediction of protein-protein interactions in Arabidopsis.
Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.
ArrowSAM is an in-memory Sequence Alignment/Map (SAM) representation which uses Apache Arrow framework (A cross-language development platform for in-memory data) and Plasma (Shared-Memory) Object Store to store and process SAM columnar data in-memory.
An automation system for a sequencing core facility. StackStorm packs to automate sequencing center operations. Event-driven sequencing center automation. It forms the core of the Arteria automation system, which you can read about on our website or preprint. This pack integrates with a series of bioinformatic micro-services, which can be found at https://github.com/arteria-project. This pack provides re-usable units for automating tasks at a sequencing core facility using the StackStorm event-driven automation platform. Handling sequencing data from massive parallel sequencing can be a daunting task! And while the process of handling sequencing data will share many of its characteristics across centers, the current norm is one center one solution. This creates a situation where reuse is difficult to achieve and the wheel is invented over and over again. This is a situation that we hope can be remedied in the form of the Arteria project
Computational validation of fusion gene detection tools without relying on simulated reads | MOTIVATION:Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, real world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. RESULTS:Here we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore can be applied to any RNA-seq dataset without the need for any simulated reads
A complete network for ascorbic acid (including associated pathways) with a list of the identified genetic variants in tomato genome through a methodology that integrates gene annotations and transcriptome. It represents the only available collection, exhaustive and detailed, on ascorbic acid network in tomato.
a web server for allele-specific sgRNA design in precision medicine | Abstract Allele-specific targeting by CRISPR provides a point of entry for personalized gene therapy of dominantly inherited diseases, by selectively disrupting the mutant alleles or disease-causing single nucleotide polymorphisms (SNPs), ideally while leaving normal alleles intact. Despite unprecedented specificity and tremendous therapeutic utility of allele-specific targeting by CRISPR, few bioinformatic tools have been implemented for the allele-specific purpose. We thus developed AsCRISPR ( A llele- s pecific CRISPR ), a web tool to aid the design of guide sequences that can discriminate between alleles. It can process with query sequences harboring single-base or short insertion-deletion (indel) mutations, as well as heterozygous SNPs deposited in the dbSNP database. Multiple CRISPR nucleases and their engineered variants including newly-developed Cas12b and CasX are included for users’ choice
Whole-genome annotation and functional analyses based on RNA expression data.
Web analytics tool for the detection of variants from an assembly.
Combining evolutionary conservation and proteomics to assess prokaryotic gene predictions | MOTIVATION:A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy. RESULTS:Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer, and Prodigal on genomes spanning the prokaryotic tree of life
Assembling Exon Using Gene Capture Data | Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads
A new method for studying the spatial distribution of mRNA in astrocytes | Abstract Cells with a complex shape often use mRNA distribution and local translation to regulate distal functions. These mechanisms have recently been described in astrocytes, the processes of which contact and functionally modulate neighbouring synapses and blood vessels. In order to study the distribution of mRNA in astrocytes, we developed a three-dimensional histological method that combines mRNA detection via in situ hybridization with immunostaining of the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP). Three-dimensional confocal images were analyzed using AstroDot, a custom Image J plug-in developed in-house for the identification and quantification of mRNAs in GFAP-immunolabelled astrocyte somata, large processes and fine processes
An event-based tool for analyzing and quantifying calcium or glutamate imaging data.
Astrocyte Quantification and Analysis (AQuA)
Cross-Species Protein Function Prediction with Asynchronous-Random Walk | Description :This page includes the codes of AsyRW which are implemented and tested on Matlab2015b version by Ms. Zhao (YingWen Zhao, Email: ywzhao@email.swu.edu.cn) and free for academic usage. You can run it at your own risk. For other purposes, please contact the corresponding author Dr. Yu (Guoxian Yu, Email: gxyu@swu.edu.cn). If you have any problem on using these codes, just contact Dr. Yu or Ms. Zhao via Email
Database of fusion transcripts in Arabidopsis thaliana.
A deep convolutional neural network toolkit for epigenomics. SDK for deep learning based processing of Atac-seq data. AtacWorks is a deep learning toolkit for track denoising and peak calling from low-coverage or low-quality ATAC-Seq data. AtacWorks trains a deep neural network to learn a mapping between noisy (low coverage/low quality) ATAC-Seq data and matching clean (high coverage/high quality) ATAC-Seq data from the same cell type. Once this mapping is learned, the trained model can be applied to improve other noisy ATAC-Seq datasets
a platform of the microbiome of the Atacama Desert | The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information
A Robust Sequence-Based Prediction of Anti-Tubercular Peptides Using Extremely Randomized Trees | Welcome to the Home Page of AtbPpred | AtbPpred is a web based two-layer prediction server for anti-tubercular peptides. In the first layer, we applied a two-step feature selection procedure and identified the optimal feature set individually for nine different feature encodings, whose corresponding models were developed using extremely randomized tree (ERT). In the second-layer, the predicted probability of AtbPs from the above nine models were considered as input features to ERT and developed the final predictor. For a given peptide, AtbPpred predicts its class and probability values
specific, sensitive, and speedy trimming of sequencing reads. An NGS read trimming tool that is specific, sensitive, and speedy. (production). Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer (https://github.com/marcelm/cutadapt, DOI:10.14806/ej.17.1.200), with the primary improvements being:
Cell type prioritization in single-cell data. Augur is an R package to prioritize cell types involved in the response to an experimental perturbation within high-dimensional single-cell data. The intuition underlying Augur is that cells undergoing a profound response to a given experimental stimulus become more separable, in the space of molecular measurements, than cells that remain unaffected by the stimulus. Augur quantifies this separability by asking how readily the experimental sample labels associated with each cell (e.g., treatment vs. control) can be predicted from molecular measurements alone. This is achieved by training a machine-learning model specific to each cell type, to predict the experimental condition from which each individual cell originated. The accuracy of each cell type-specific classifier is evaluated in cross-validation, providing a quantitative basis for cell type prioritization
Hierarchical and Programmable One-Pot Oligosaccharide Synthesis | Auto-CHO is a free-to-use software for providing glycan synthetic solutions by one-pot approach | Auto-CHO is an open source (MIT License) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis | Auto-CHO is an open source (MIT Licence) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis
Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE).
Improvements on AutoDock Affinity Maps and Associated Software Tools | Precomputed affinity maps are used by AutoDock to efficiently describe rigid biomolecules called receptors in automated docking. These maps greatly speed up the docking process and allow users to experiment with the forcefield. Here, we present AutoGridFR (AGFR): a software tool facilitating the calculation of these maps. We describe a new version of the AutoSite algorithm that improves the description of binding pockets automatically detected on receptors, and an algorithm for adding affinity gradients which help search methods optimize solution using fewer evaluations of the scoring functions. AGFR supports the calculation of maps for various advanced docking techniques such as covalent docking, hydrated docking, and docking with flexible receptor sidechains
An automatic classification tool for PVS1 interpretation of null variants | Abstract Null variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGen’s SVI Working Group and achieved an interpretation concordance of 95% (53 56)
Autotuner is a used to identify proper parameters during metabolomics data processing.
A complete, open-source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Autopilot enables qualitatively greater experimental flexibility by allowing arbitrary numbers of hardware components to be combined in arbitrary experimental designs.
Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays and copy number analysis on select Axiom arrays.
An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors | Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is an unsupervised learning algorithm written in MATLAB that serves to discover behaviors that are not pre-defined by users | B-SOID: Behavioral segmentation of open field in DeepLabCut
High-throughput detection and tracking of cells and intracellular spots in mother machine experiments | BACteria in Mother Maching Analyzer (BACMMAN) is a software allowing fast and reliable automated image analysis of high-throughput 2D/3D time-series images from mother machine. Mother machine is a very popular microfluidic device allowing investigating biological processes in bacteria at the single-cell level | BACMMAN: BACteria in Mother Machine Analyzer | BACMMAN was designed to analyse data from Mother machine experiments
A Bayesian Hierarchical Model Approach for Gene Set Enrichment Analysis. Bayesian Analysis of Gene Set Enrichment. This repository contains the software package BAGSE designed for gene set enrichment analysis. BAGSE performs both enrichment (hypothesis) testing and quantification. It requires gene-level association evidence (in forms of either z-scores or estimated effect sizes with corresponding standard errors) and pre-defined gene set annotations as input
Tool that determines if two BAM files came from the same sample or patient by comparing common SNP positions.
Bayesian mixture model for single-cell sequencing (BAMM-SC) method for clustering droplet-based single cell transcriptomic data from population studies.
Automated checkup tool for matched sample pairs in NGS cohort.
Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty | BANDITS: Bayesian ANalysis of DIfferenTial Splicing | BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts
cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis | Software required for Bart-Seq technology – a cheap technology to analyze (single) cells using forward and reverse barcoding for target genes | Demultiplexing pipeline for BARTSeq | Software required for Bart-Seq – a cost-effective target enrichment technology using forward and reverse barcoding to analyze selected set of genes in single cells and/or bulk RNA/DNA samples | The pipeline can be run via snakemake [-j 4] [-s …/bartseq/Snakefile] [-d …/mydata], where -j specifies the number of threads, and the other parameters default to ./Snakefile and ., respectively
Tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins.
an expression atlas of blood-based biomarkers in the early diagnosis of cancers. The early detection of cancer holds the key to combat and control the increasing global burden of cancer morbidity and mortality. Blood-based screenings using circulating DNAs (ctDNAs), circulating RNA (ctRNAs), circulating tumor cells (CTCs) and extracellular vesicles (EVs) have shown promising prospects in the early detection of cancer. Recent high-throughput gene expression profiling of blood samples from cancer patients has provided a valuable resource for developing new biomarkers for the early detection of cancer. However, a well-organized online repository for these blood-based high-throughput gene expression data is still not available
BCIgePred (Linear B cell IgE Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell IgE epitopes.
A Customized Biosynthetic Chemical Space Explorer with Multifunctional Objective Function Analysis. Select all Deselect all Toggle select. ( Note:The less enzymes/biotransformations you select, the shorter the runtime is.)
An Interpretable Sequence-Based Protein Crystallization Predictor. The training set is readily available for ease of use at: https://drive.google.com/file/d/1FRWIcs4xvK2O5OCqhg7u5g_4qm2zJn2d/view and can be used in combination with Step 2 to generate the BCrystal model
Prediction of Homolytic Bond Dissociation Enthalpies for Organic Molecules at near Chemical Accuracy with Sub-Second Computational Cost.
BEACON is a computational framework designed to perform Bayesian analysis on expression and gene dependency data across different cell lineages. The model integrates expression as the dependent variable and gene dependency data as the independent variable. The framework uses JAGS (Just Another Gibbs Sampler) for Bayesian inference and MCMC (Markov Chain Monte Carlo) simulations to estimate parameters of interest, including the correlation between gene expression and dependency.
Pipeline for processing barcode sequencing data from multiplexed experiments. Applicable to any experiment in which pools of genetically barcoded cells are grown under different conditions, with the resulting barcode DNA isolated from those cells combined into one 2nd-gen sequencing run via the use of indexed PCR primers.
Tool for Biomedical Entity Expansion, Ranking, and Exploration.
Environment for exploration and analysis of networks encoded in Biological Expression Language.
a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes | BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data | BERMUDA: Batch Effect ReMoval Using Deep Autoencoders
BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.
Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line | Bayesian Gene Selection Criterion (BGSC) approach | The datasets analyzed during the current study are available in the BGSC repository. The raw data files are in the folder rawdata including the Einzelanalyse_nonorm_nobkgd_SF767-1.txt.gz and ControlProbeProfile_SF767-1.txt.gz. The lists of genes predicted for all of the four classes can be found in the folder PredectionResult
Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites | AIM AND OBJECTIVE:The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. MATERIALS AND METHODS:In this study, we aim to relieve the negative impact of class imbalance by boosting multiple granular support vector machines (BGSVM). In BGSVM, each base SVM is trained on a granular training subset consisting of all minority samples and some reasonably selected majority samples
An integrated Web-database for bovine sequencing variations and selective signatures.
BItsliced Genomic Signature Index (BIGSI) searches a collection of raw (fastq/bam), contigs or assembly for genes, variant alleles and arbitrary sequence.
Computationally inferring a gene regulatory network for Mycobacterium abscessus | BINDER (BayesIan gene regulatory Networks inferreD via gene coExpression and compaRative genomics) is a hybrid approach, integrating coexpression and comparative genomics to infer prokaryotic regulons | Code, data and results for 'BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus'
Bayesian Estimation of Genetic Regulatory Effects in High-throughput Reporter Assays | Bayesian Inference of Regulatory Differences | Photo by Bill Majoros. Used with permission | [6/16/2018] First version of BIRD released - The first version of BIRD has been released on GitHub at https://github.com/bmajoros/BIRD | [8/23/2018] Experiment design web tool released - A web tool is now available for power and sample size estimation: http://67.159.92.22:8080/ | BIRD (Bayesian Inference of Regulatory Differences) is a software suite for identifying regulatory variants in data from STARR-seq and other massively parallel reporter assays (MPRAs)
BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license.
BIII (BioImage Informatics Index, biii.eu)
Brain tISue segmentatiON pipeline using T1-weighted magnetic resonance images and a random forests classifier | Abstract Introduction Accurate differentiation of brain tissue types from T1-weighted magnetic resonance images (MRIs) is a critical requirement in many neuroscience and clinical applications. Accurate automated tissue segmentation is challenging due to the variabilities in the tissue intensity profiles caused by differences in scanner models and acquisition protocols, in addition to the varying age of the subjects and potential presence of pathology. In this paper, we present BISON (Brain tISue segmentatiON), a new pipeline for tissue segmentation. Methods BISON performs tissue segmentation using a random forests classifier and a set of intensity and location priors obtained based on T1-weighted images
An efficient and scalable RNAseq analysis workflow with interactive report generation. BISR-RNAseq pipeline submitted for ICIBM-2019. Submission files for the ICIBM2019 conference
A comprehensive tool for the identification and annotation of gene families in genome assemblies | BITACORA: A Bioinformatics tool for gene family annotation | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families in the genomes of non-model organisms | BITACORA: A pipeline for the identification and annotation of gene families in genome assemblies | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families
A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates | Liu, Y., Chen, X., & Li, G. (2019). A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates. Statistical methods in medical research, 0962280219864710 | This program implements the BJASS joint screening method for DLBCL data (stored in matlab.mat) described in Section 4 of the paper
Basic Local Alignment for Networks Tool.
Package for the next level of genome-wide association studies.
Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. A R package to perform genome-wide allele-specific expression. BLMRM: A Bayesian Logistic Regression Model for Genome-Wide Detection of Allele-Specific Gene Expression. This R package provide a powerful and flexiable method (BLMRM) to detect ASE genes and detect ASE variation within genes simultaneously while maintaining low computational requirements
Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo. Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling. BLUES: Binding modes of Ligands Using Enhanced Sampling. Gill, S; Lim, N. M.; Grinaway, P.; Rustenburg, A. S.; Fass, J.; Ross, G.; Chodera, J. D.; Mobley, D. L. “Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo” - Journal of Physical Chemistry B. February 27, 2018
Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays.
Exploring Integrative Analysis using the BioMedical Evidence Graph | A graph database for merging and analyzing connected data | Discover The BMEG is a graph database that collects data from over 20 different large scale resources and aggregates them into a single coherent resource. Sources include:
Software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.
Automated BioModel Selection System for gene circuit designs, supports bio-model automated fitting and selection processes, providing a means to efficiently derive the best model candidate that could capture the transient (time-series) dynamic profiles of a bio-part or device using characterization data.
R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction.
Drug repositioning based on bounded nuclear norm regularization | BNNR is a novel computational method, which utilizes Bounded Nuclear Norm Regularization algorithm to identify potential novel indications for known or new drugs. The code in this package implements Bounded Nuclear Norm Regularization (BNNR) for drug repositioning, which is implemented in Matlab2014a
Model to detect and classify relations in text, representing each entity of domain-specific ontologies as the sequence of its ancestors in the ontology. BO-LSTM is implemented as a recurrent neural network with long short-term memory units and using open biomedical ontologies.
Simulation that applies bioinformatics algorithm – block optical content scoring (BOCS) – which uses DNA k-mer content for rapid, broad-spectrum identification of genetic biomarkers.
Executable pathway analysis using ensemble discrete-state modeling for large-scale data | BONITA- Boolean Omics Network Invariant-Time Analysis is a package for the inference of Boolean rules and pathway analysis on omics data. It can be applied to help uncover underlying relationships in biological data. Please see our publication for more information: [insert eventual publication here]
BOOSTER is an alternative method for calculating the branch supports of phylogenetic trees, using the bootstrap. With large trees and moderate phylogenetic signal, BOOSTER tends to be more informative than the standard Felsenstein bootstrap method.
BORIS: R package for Bayesian Outbreak Reconstruction Inference and Simulation. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates.
The Brain Predictability toolbox (BPt) is a Python based Machine Learning library designed for working with Neuroimaging data. This library is particularly suited towards working with large neuroimaging datasets, where a large number of subjects with potentially multimodal data are avaliable.
Software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing.
Bayesian method for estimating splicing isoform proportions from single cell RNA-seq data.
Systems biology web tool for microRNA and omics data integration.
Block Regression Mapping (BRM) is a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing.
HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases.
Web-based quantitative trait locus linkage analysis and bulk segregant analysis of yeast sequencing data.
An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access. On this website we provide access to our annotation integration efforts for Bacillus subtilis 168. We integrated the gene annotations from BsubCyc, Rfam, RefSeq, SubtiWiki, and some additional resources (see manuscript for details). Each gene indicates from which reources its annotation stem from, and links to the respective resources are provided where applicable. The integration overall improved the annotation of non-coding RNAs (ncRNA) in B. subtilis. Based on public transcription start sites (TSS) and termination sites (TTS), we created a comprehensive annotation of operons, transcripts, and transcriptional units (TU) for 93% of the genes in the genome. We provide the BSGatlas in form of a UCSC browser hub, a downloadable GFF3 file, and as a light-weight interactive quick browser directly on this side
an R package to facilitate the conduct and reporting of Bayesian network Meta-analyses. Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis”]. BUGSnet: Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis. [Home] [Installation] [RStudio Server] [Vignettes]. BUGSnet is a new feature-rich R package to conduct high-quality Bayesian NMA analyses and facilitate compliance with best practice guidelines and reporting. Bayesian analyses are conducted with JAGS (BUGS code is automatically generated by the package based on the user’s inputs.) Outputs are highly customizable and include network plots, tables of network characteristics, data plots, league tables and league heat plots, SUCRA plots, rankograms, forest plots, leverage plots, traceplots and posterior mean deviance comparison plots
> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/pymzml (GITHUB.COM) | > CORRECT NAME OF TOOL COULD ALSO BE 'BUStools suite', 'BUStools suite tools', 'BUS' (bio.tools/bus), 'kallisto' (bio.tools/kallisto) | The Barcode, UMI, Set format and BUStools | Materials associated with the manuscript "The Barcode, UMI, Set format and BUStools" by Páll Melsted, Vasilis Ntranos and Lior Pachter | Tools for working with BUS files | R vignettes for processing BUS format single-cell RNA-seq files
A Benchmarking Variation Simulator Mimicking Human Variation Spectrum
A R package for genomic selection and its application to a wheat breeding programme | Abstract We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates of Breeding values (GEBV) for genomic selection. BWGS relies on existing R-libraries, all freely available from CRAN servers. The two main functions enable to run 1) replicated random cross validations within a training set of genotyped and phenotyped lines and 2) GEBV prediction, for a set of genotyped-only lines. Options are available for 1) missing data imputation, 2) markers and training set selection and 3) genomic prediction with 15 different methods, either parametric or semi-parametric. The usefulness and efficiency of BWGS are illustrated using a population of wheat lines from a real breeding programme. Adjusted yield data from historical trials (highly unbalanced design) were used for testing the options of BWGS
Bayesian weighted Mendelian randomization for causal inference based on summary statistics. BWMR (Bayesian Weighted Mendelian Randomization). Code for the experiments in BWMR. BWMR (Bayesian Weighted Mendelian Randomization), is an efficient statistical method to infer the causality between a risk exposure factor and a trait or disease outcome, based on GWAS summary statistics. 'BWMR' package provides the estimate of causal effect with its standard error and the P-value under the test of causality
Application designed to view the frequency content of recorded brainwave files. It uses wavelets rather than a conventional FFT to analyse the data for maximum flexibility and resolution.
A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Sus scrofa) Pathogen Any pathogen Acinetobacter baumannii ATCC 17978 Campylobacter jejuni subsp. jejuni 81-176 Escherichia coli CFT073 Escherichia coli M12 Escherichia coli O157:H7 str. EDL933 Haemophilus influenzae Rd KW20 Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 KPPR1 Mycobacterium avium subsp. paratuberculosis K10 Porphyromonas gingivalis ATCC 33277 Salmonella enterica Serovar Typhimurium SL1344 Salmonella enterica Serovar Typhimurium ST4 74 Serratia marcescens Strain UMH9 Streptococcus pyogenes M1 5448 Vibrio cholerae O1 biovar El Tor str. N16961 Vibrio parahaemolyticus RIMD 2210633
A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.
Pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing.
an R package for integrating, analyzing and visualizing bacterial microscopy data | Abstract High-throughput analyses of single-cell microscopy data is a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP ( Bac terial t oolbox for M icroscopy A nalysis & P lotting), a software package that allows researchers to transform cell segmentation and spot detection data generated by different programs automatically into various plots
Tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process.
> CORRECT NAME OF TOOL COULD ALSO BE 'genetic algorithm Bagging-SVM', 'druggable', '93.78' | Accurate prediction of potential druggable proteins based on genetic algorithm and Bagging-SVM ensemble classifier | Discovering and accurately locating drug targets is of great significance for the research and development of new drugs. As a different approach to traditional drug development, the machine learning algorithm is used to predict the drug target by mining the data. Because of its advantages of short time and low cost, it has received more and more attention in recent years. In this paper, we propose a novel method for predicting druggable proteins. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC), dipeptide composition (DPC) and reduced sequence (RS), getting the 591 dimension of drug target dataset
Robust and window-insensitive mixture model approaches for localizing balancing selection.
A Next-Generation Information System for Musa genomics
Software for analysis of nucleic acid structures and trajectories.
Large-scale discovery tool for potential causative mutations in human coding and noncoding genome.
Integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.
A hierarchical Bayesian deconvolution model with stochastic search variable selection | Bayesian deconvolution model for intracellular component exploration (BayICE)
Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.
Application of Bayesian predictive probability for interim futility analysis in single-arm phase II trial | The tool provides futility interim analysis plan using the Bayesian predictive design in single arm early phase II clinical trial. It also generates statistical plan so clinicians could easily incorporate it into the clinical trial protocol. (reference: Application of Bayesian predictive probability for interim analysis in single-arm early phase II trial. Chen et al; submitted) | devtools::install_github("dungtsa/BayesianPredictiveFutility",force = TRUE) | The shiny applictaion provides futility interim analysis plan for the Bayesian predictive design design in single arm early phase II clinical trial and generates a statistical plan to be easily incorporated into the clinical trial protocol | Simply run the following from an R console:
Method for read extraction and realignment of high-throughput sequencing data.
self-correction of short reads via mapping on de Bruijn graphs. de Bruijn graph cOrrectiOn from graph aLignment. Bcool clone and compile Bcalm2 Bgreat2 Btrim and Ntcard
simple alignment tool for optical systems. BeamDelta is called from the command line using the following format:. A simple GUI interface for python-microscope which allows a compatible camera (see python-microscope compatibility list) to be used for optical alignment purposes. The GUI will display live images, calculate and mark beam centroids and then store an alignment centroid position. Once a position is stored the live centroid then displays a pixel based delta position to allow precise alignment between the marked position and the new beam. We include a suggested parts list in BeamDelta-parts-list.csv which enables the construction of a two camera alignment setup. This hardware configuration will allow both lens alignment and co-aligning two beams and has a small footprint so can relatively easily be mounted within an existing setup
A mine with common bean data from the Legume Info tripal.chado database
The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. Bellerophon is a pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies. The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate
Benchmarking gene and variant prioritization algorithms for GWAS data.
Program for reconstruction of amyloid structures containing adjacent β-arches.
Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure.
A computational framework to explore large-scale biosynthetic diversity. BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity. It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency... BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.
BiGG Models is a website for browsing gold-standard genome-scale models, multi-strain genome-scale models and expansion across the phylogenetic tree. BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions.
Spark-based highly scalable aligner for bisulfite sequencing data.
Bipartite Tight Spectral Clustering (BiTSC) Algorithm for Identifying Conserved Gene Co-clusters in Two Species. Yidan Eden Sun, Heather J. Zhou and Jingyi Jessica Li. $ python3 BiTSC.py ./data/orthologs_data_uniq.csv ./data/dm_timecourse_FPKMs.csv ./data/ce_timecourse_FPKMs.csv 30 10 100 0.8 10 10 ./data/result 0.90 0.95 1.00
A novel algorithm based on bi-random walks to identify disease-related lncRNAs. EMAIL: jhu@nwpu.edu.cn, yiqun.gao@nwpu-bioinformatics.com. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. BiWalkLDA.m: BiwalkLDA framework to predict potential lncRNA-disease association. normFun.m: Laplacian normalization
A Comprehensive Database for Biased GPCR Ligands | A manually curated database of biased GPCR ligands | BiasDB[1] is a manually curated database containing all published biased GPCR ligands. BiasDB currently contains 615 bias cases of signaling bias representing 481 individual ligands for 61 receptors. We provide information about the chemical structure, target receptor, type of bias, assay categories used for bias determination, reference ligand and literature source. BiasDB is a resource for medicinal chemists, pharmacologists and researchers interested in biased GPCR signaling
Reconstructing high-resolution image datasets of cleared and expanded samples | ImgLib2/BDV implementation of Stitching for large datasets | The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy
phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. Phosphoglycerylation prediction using evolutionary information of amino acids. Run the file Bigram_PGK.m to obtain statistical measures of the Bigram_PGK predictor. The algorithm runs on the train and test data to obtain the values. Preprocessing_BigramPGK.m file was used to carry out preprocessing for Bigram_PGK predictor, which includes feature extraction for segment size of ±32, filtering, and construction of train and test sets for 10-fold cross-validation. Everytime the algorithm is executed, it will have a slightly different combination of samples for train and test sets. Nevertheless, the performance will be similar
Software for fast genome distance estimation on a typical personal laptop.
BindSpace decodes transcription factor binding signals by large-scale sequence embedding | The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data from hundreds of TFs and embedding over 1 M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance, in vitro and in vivo, and can distinguish between signals of closely related TFs
Binner is a Java application for deep annotation of untargeted LC-MS metabolomics data. It takes a numerical feature table obtained from any preprocessing software (e.g. XCMS, MZmine) as input and outputs a file with clusters of closely eluting, highly correlated metabolite features that are most related, along with their pairwise correlations, mass differences, and putative annotations.
A web-based tool for data and algorithms integration.
Integration of Structured Biological Data Sources using Biological Expression Language.
A pre-trained biomedical language representation model for biomedical text mining | BioBERT: a pre-trained biomedical language representation model | This repository provides pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details | This repository provides fine-tuning codes of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details. This project is done by DMIS-Lab
Tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji).
Efficient Ensemble Refinement by Reweighting. BioEn - Bayesian Inference Of ENsembles. BioEn integrates a broad range of experimental data to refine ensembles of structures. For a detailed description of the procedures and the algorithm, we refer to [Hummer2015]
Visual designer for biofeedback. Provides environment and tools to create various types of processing tasks.
Program for real-time biophysical data acquisition, processing, and display.
BioFabric is an open-source network visualization tool.
BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines.All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.
BioGRID Open Repository of CRISPR Screens (ORCS)
A triple store with RDF graphs obtained from various curated databases, queryable by SPARQL and through the Cytoscape plugin BioGateway App.
BioGears® is a open source, comprehensive human physiology engine that will drive medical education, research, and training technologies.
an R/CRAN package for integrated data analysis pipeline in biomedical study. generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions. The BioMedR package offers an R package for generating various molecular descriptors for chemicals, proteins, DNAs RNAs and their interactions. Calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA/RNA descriptors from nucleotide sequences, and six types of interaction descriptors using three different combining strategies
BioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL.
R package for Biological interpretation of DNA methylation data in the TCGA cancers context.
A database for metazoan biomineralization proteins. Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and proteins, which give them extra hardness and special attributes. Biomineralization proteins are also known to be associated with multiple bone disorders and are therefore of biomedical importance. Herein we describe BioMine-DB, a biomineralization centric protein database. Availability and implementation: BioMine-DB can be accessed at http: biomine.net, SQL dump, FASTA files and source code are available for download as well at https: github.com bishoyh biomineDB "
The biological network mining workflow identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language (SBML). The repository contains the scripts for a workflow that identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language.
Bioinformatics workflows in the functional Nix language
Python tool for integration of protein structure and sequence-based features.
A tool for the detection of bistability and multi-steady state behaviour in signaling and gene regulatory networks. https://sites.google.com/view/bioswitch. BioSwitch is a Matlab software tool for detection of multi-steady state behaviour in biochemical reaction networks (specially suited for signaling and gene regulatory networks)
A tool to search and map bioinformatics identifiers and special keywords | A bioinformatics tool to search and map identifiers and special keywords | Biobtree is a bioinformatics tool which process large datasets effectively and provide uniform search and mapping functionalities with web interface and web services for genomic research
Package that facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches.
A software tool for quantitative image analysis of microbial biofilm communities | Software tool for quantitative analysis of microbial biofilm images | Developed by Raimo Hartmann, Hannah Jeckel, Eric Jelli, Knut Drescher | Analysis supports any biofilm type
A collection of 40+ well-documented Docker images of commonly used bioinformatics applications and pipelines.
A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a period of 10 years. For every sequenced species, genome annotation will be followed by functional annotation for individual genes and pathways. Network biology can facilitate functional annotations of genomes in the context of collaborative interactions between genes. BiomeNet is a database of scored functional networks enabling network biology for every sequenced genome of Earth’s biome. With protein sequences of target species submitted by users, BiomeNet will transfer co-functional links between orthologous proteins from 95 source networks (comprising ~8 million links), which were previously constructed and validated for 18 species (5 animals, 6 plants, 5 bacteria, and 2 fungi)
A Shiny R app for microbiome visualization, built around the "microbiome" package.
Biomine Explorer is a web application that enables interactive exploration of selected publicly available biological knowledge. It is based on the results of the Biomine project that develops methods for the analysis of public biological data sources (annotated sequences, proteins, domains, and orthology groups, genes and gene expressions, gene and protein interactions, scientific articles, and ontologies). All information is handled as networks and Biomine provides probabilistic network search algorithms to automatically extract the most relevant subnetworks. The most prominent feature of Biomine Explorer is interactive exploration of its large probabilistic networks by using an interactive network visualisation interface. Network editing features and private network repositories are also available as well as a repository of publicly available graphs. All links to Biomine graphs are permanent so they can be used in scientific publications or published on the web.
Jožef Stefan Institute, Department of Knowledge Technologies
Demonstrating and facilitating best practices for bioinformatics command-line software | Demonstrating best practices for bioinformatics command line tools | Bionitio provides a template for command line bioinformatics tools in various programming languages | The purpose of the tool is to provide an easy-to-understand working example that is built on best-practice software engineering principles. It can be used as a basis for learning and as a solid foundation for starting new projects. We provide a script called bionitio-boot.sh for starting new projects from bionitio, which saves time and ensures good programming practices are adopted from the beginning (see below for details)
A Fast and Accurate Exhaustive Higher-Order Epistasis Search. BitEpi: An exhaustive search of higher-order epistatic interactions. BitEpi is software for an exhaustive search of higher-order epistatic interactions between genomic variants (SNPs) given a binary phenotype (Case/Control). BitEpi performs an exhaustive search that means it tests all possible combinations of SNPs. For example, the 4-SNP search of 50 SNPs (data.csv) requires to test all "4 out of 50" 4-SNP combinations (230300 4-SNP combinations)
Building machine learning models for predicting the bitter and sweet taste of small molecules.
A Bioconductor and Bioconda package for differential extreme value analysis. A tool for differential extreme-value analysis. Differential extreme outlier analysis using Blacksheep. https://blacksheep.readthedocs.io/en/master/. conda install -c bioconda blksheep. Requirements (automatically taken care of with pip and conda)
BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies.
A cloud-based peptide search engine for MS/MS sequencing.
An integrated data warehouse for the Bovine Genome Database
A random forest model for inferring higher-order trait interactions associated with complex biological phenotypes.
Bio and Neurofeedback Application, designed to work with various Electroencephalography (EEG) amplifiers. It supports Human-Computer-Interface functions and NeuroServer Software Framework to transmit live recordings via Internet or LAN.
a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets | BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets : available in both Python and Matlab : | Welcome to BrainSpace’s documentation! — BrainSpace 0.1.0 documentation | Free document hosting provided by Read the Docs
Systematic Identification of Cell-Cell Communication Networks in the Developing Brain. Since the generation of cell-type specific knockout models, the importance of inter-cellular communication between neural, vascular, and microglial cells during neural development has been increasingly appreciated. However, the extent of communication between these major cell populations remains to be systematically mapped. Here, we describe EMBRACE (embryonic brain cell extraction using FACS), a method to simultaneously isolate neural, mural, endothelial, and microglial cells to more than 94% purity in ∼4 h. Utilizing EMBRACE we isolate, transcriptionally analyze, and build a cell-cell communication map of the developing mouse brain. We identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural, and microglial cells in silico and experimentally confirm the APOE-LDLR, APOE-LRP1, VTN-KDR, and LAMA4-ITGB1 interactions in the E14.5 brain
Interactive, web-based tool for testing hypotheses and developing predictive models.
combining phylogenetic and network analyses for orthology assignment. orthology assignment using phylogenetic and network analyses. Broccoli, a user-friendly pipeline designed to infer with high precision orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm (label propagation). Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups
Deep-learning contact-map guided protein structure prediction in CASP13 | contact-guided protein structure prediction | C-I-TASSER (Contact-guided Iterative Threading ASSEmbly Refinement) is a composite approach that uses contact information to enhance the accuracy of protein structure and function predictions | [View example output] [Check previous jobs] [Server statistics] [Help] [Forum]
C-InterSecture (Computional tool for InterSpecies analysis of genome architecture) - pipeline to cross-species comparison of Hi-C map. C-InterSecture was designed to liftover contacts between species, compare 3-dimensional organization of defined genomic regions, such as TADs, and analyze statistically individual contact frequencies.
Powerful rare variant association testing in a copula-based joint analysis of multiple phenotypes. Copula-Based Joint Analysis of Multiple Phenotypes. We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2019, submitted)
Consensus Cancer Driver Gene Caller | Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C3), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results
Consensus Cancer driver gene Caller (C3)
Cross Cell-type Correlation in DNaseI hypersensitivity (C3D) - tool to predict 3D genomic interactions between cis-regulatory elements.
A web application for flexible protein-peptide docking.
An interactive machine-learning approach for sex estimation with the pelvis | The pelvis is consistently regarded as the most sexually dimorphic region of the human skeleton, and methods for sex estimation with the pelvic bones are usually very accurate. In this investigation, population-specific osteometric models for the assessment of sex with the pelvis were designed using a dataset provided by J. A. Serra (1938) that included 256 individuals (131 females and 125 males) from the Coimbra Identified Skeletal Collection and 38 metric variables. The models for sex estimation were operationalized through an online application and decision support system, CADOES. Different classification algorithms generated high accuracy models, ranging from 85% to 92%, with only three variables; and from 85.33% to 97.33%, with all 38 variables
The semi-automated open-source calcium imaging analyzer | CalciumImagingAnalyser is free software for the extraction and analysis of calcium imaging footage. Designed to be fast, user-friendly and portable, it includes such functions as spatiotemporal and network analysis | CALciumIMagingAnalyser (CALIMA) is a free application for the extraction and analysis of calcium imaging data. Read more below or go straight to the download section
Codon Aversion Motifs for Alignment-free Phylogenies.
Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation. Community Assembly Model Inference. For full Installation instructions and initial uses, refer to vignette ‘CAMI_Installation.Rmd’. Briefly, you can install the R package using devtools::install_github("ruffleymr/CAMI")
Community Assembly Model Inference (CAMI)
Software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets.
Comparative analysis of metabolic network decomposition based on previous and two new criteria. Metabolic networks can model the behavior of metabolism in the cell. Since analyzing the whole metabolic networks is not easy, network modulation is an important issue to be investigated. Decomposing metabolic networks is a strategy to obtain better insight into metabolic functions. Additionally, decomposing these networks facilitates using computational methods, which are very slow when applied to the original genome-scale network. Several methods have been proposed for decomposing of the metabolic network. Therefore, it is necessary to evaluate these methods by suitable criteria.
R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis.
CANDO is a open-source, unique computational drug discovery, design, and repurposing platform.
Computational Analysis of Novel Drug Opportunities (CANDO)
Cross-disease Attention Network for Joint Diabetic Retinopathy and Diabetic Macular Edema Grading. Diabetic retinopathy (DR) and diabetic macular edema (DME) are the leading causes of permanent blindness in the working-age population. Automatic grading of DR and DME helps ophthalmologists design tailored treatments to patients, thus is of vital importance in the clinical practice. However, prior works either grade DR or DME, and ignore the correlation between DR and its complication, i.e., DME. Moreover, the location information, e.g., macula and soft hard exhaust annotations, are widely used as a prior for grading. Such annotations are costly to obtain, hence it is desirable to develop automatic grading methods with only image-level supervision. In this paper, we present a novel cross-disease attention network (CANet) to jointly grade DR and DME by exploring the internal relationship between the diseases with only image-level supervision
A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.
Antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
The Comprehensive Antibiotic Resistance Database (CARD)
contextualizing large signaling networks with CARNIVAL. CAusal Reasoning for Network Identification with integer VALue programming in R. CARNIVAL is an R-package providing a framework to perform causal reasoning to infer a subset of signalling network from transcriptomics data. This work was originally based on Melas et al. with a number improved functionalities comparing to the original version. Transcription factors’ (TFs) activities and pathway scores from gene expressions can be inferred with our in-house tools DoRothEA & PROGENy, respectively. TFs’ activities and signed directed protein-protein interaction networks +/- drug targets and pathway scores are then used to derive a series of linear constraints to generate integer linear programming (ILP) problems. An ILP solver (CPLEX) is subsequently applied to identify the sub-network topology with minimised discrepancies on fitting error and model size
The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation | Colored Abstract Simplicial Complex Library | Colored Abstract Simplicial Complex (CASC) Library | CASC is a modern and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes with user-defined classes stored directly on the simplices at each dimension. This is achieved by taking advantage of the combinatorial nature of simplicial complexes and new C++ code features such as: variadic templates and automatic function return type deduction. Essentially CASC stores the full topology of the complex according to a Hasse diagram. The representation of the topology is decoupled from interactions of user data through the use of metatemplate programming
Colored Abstract Simplicial Complex (CASC)
Distance Measures for Tumor Evolutionary Trees. MOTIVATION:There has been recent increased interest in using algorithmic methods to infer the evolutionary tree underlying the developmental history of a tumor. Quantitative measures that compare such trees are vital to a number of different applications including benchmarking tree inference methods and evaluating common inheritance patterns across patients. However, few appropriate distance measures exist, and those that do have low resolution for differentiating trees or do not fully account for the complex relationship between tree topology and the inheritance of the mutations labeling that topology.
A robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome. Cosolvent Analysis Toolkit (CAT). Authors: Frances Sabanes Zariquiey, Joao V. de Souza, Agnieszka K. Bronowska.
Tool for generating comprehensive annotations of alternative transcript events.
A novel threading algorithm with predicted contacts. CATHER is a threading algorithm for template-based modeling. It uses an iterative algorithm to combine both sequential information and contact maps to improve the threading performance. For a submitted query protein sequence, the returned results include the predicted structure
An ultrasensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data | An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data | HomePage: http://bioinfo.life.hust.edu.cn/CATT | An ultra-sensitive and accurate tool for characterizing T cell receptor sequence in bulk and single cell TCR-Seq and RNA-Seq data. The tool can be found in: | CATT(CharActerzing TCR repertoires) is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq, scRNA-seq and any TCR contained sequencing data)
A database for disease/trait causal variants identified using summary statistics of genome-wide association studies. A GWAS fine-mapping pipeline used in CAUSALdb. CAUSALdb integrates large numbers of GWAS summary statistics and identifies credible sets of causality by uniformly processed fine-mapping
Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways.
Controllability based Biological Network Analysis (CBNA) is a tool to uncover coding and non-coding cancer drivers (i.e. miRNA cancer drivers).
Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding | A pipeline for completing circular bacterial genomes using a sampling strategy | Since CCBGpipe implements many analytical tools, we strongly recommend you to run it with Docker. Alternatively, you can install all dependencies as listed in the Installation section | This pipeline is designed to complete circular bacterial genomes using a sampling strategy from a sinlge MinION with barcoding
CCC-Tool (Charting Continuous Colormaps) is a tool for creating, editing, and analyzing such application-specific colormaps.
an accurate method and web server for cancer cell line authentication using gene expression profiles. Abstract Cancer cell lines (CCLs) as important model systems play critical roles in cancer researches. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphisms, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication, http: bioinfo.life.hust.edu.cn web CCLA ) to authenticate 1,291 human CCLs of 28 tissues using gene expression profiles. CCLA curated CCL-specific gene signatures and employed machine learning methods to measure overall similarities and distances between the query sample and each reference CCL
Software-as-a-service approach for fully-automated microbiome profiling | Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https: ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface
Pipeline to classify organisms in metagenomes or metatranscriptomes accurately.
Clusters of Colocalized Sequences. Abstract 0.1 Motivation Potential transcription factor (TF) complexes may be identified by testing whether the binding sequences of individual TF proteins form clusters with each other. These clusters may also indicate TF inhibition due to competitive occupancy of enhancer regions. Genome annotation data containing the coordinates of enhancer sequences is highly accessible via position-weight matrix tools. 0.2 Results An algorithm called CCSeq (Clusters of Colocalized Sequences) was developed for identifying clusters of sequences along a one-dimensional line, such as a chromosome, given genome annotation files and a cut-off distance as inputs.
An Online Package for Evaluation of Complex Detection Methods | Complex Detection Analyzer Package (CADP) helps you to execute protein complex detection methods and compare their results in a quick and compact ways. It computes a wide range of evaluation criteria and visualize the comparison of methods in tables and multiplots. It assists you in filtering detected clusters by providing a protein name (STRING ID) as a query and by setting constraint on maximum and minimum number of proteins in detected clusters. The list of methods for detecting protein complexes is as follows: | You may look for the values of evaluation criteria for a specific threshold. This can also be done by CDAP. The PPI datasets are: | You can also upload the result of any other method for evaluating its results. The valid format for uploaded file is described here | The list of evaluation criteria is as follows:
Common Data Elements for Unruptured Intracranial Aneurysm and Subarachnoid Hemorrhage Clinical Research.
Clinical Drug Experience Knowledgebase | Washington University in St. Louis | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | YOU AGREE THAT THE INFORMATION PROVIDED ON THIS WEBSITE IS PROVIDED “AS IS”, WITHOUT ANY WARRANTY OF ANY KIND, EXPRESSED OR IMPLIED, INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR NON-INFRINGEMENT OF ANY THIRD-PARTY PATENT, COPYRIGHT, OR ANY OTHER THIRD-PARTY RIGHT | Build your own query by selecting various table columns and a filtration predicate; then press the to launch the query
Clinical Drug Experience Knowledgebase (CDEK)
Modeling multilocus selection in an individual-based, spatially-explicit landscape genetics framework. An individual-based, eco-evolutionary model for spatially-explicit simulation of population viability in landscape demogenetics. Welcome to the CDMetaPOP v1.0 release! This release includes installation instructions, version notes, some examples, and technical documentation. Baseline Requirements. CDMetaPOP requires the Python2.7.x interpreter, NumPy package, and SciPy package. Remember that Python modules usually require particular Python interpreters, so be sure the version ID for any external Python module or package (e.g. NumPy or others) matches the version of your Python interpreter (normally v2.7.x). aTo avoid Python installation errors, we highly recommend installing Python from any number of the freely available bundlers, e.g., Canopy, ActiveState, Anaconda.
Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.
A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data. CDSeq MATLAB code. CDSeq is a novel computational complete deconvolution method for dissecting tissue heterogeneity. CDSeq: A complete deconvolution method for dissecting tissue heterogeneity. Added data-dilution option to speed up the algorithm. We provided explaination in the manuscript which you can find on bioRxiv. Check out the demo.m in CDSeq_012 for details
A portal for geographic reference data for the Amazon.
Collection of continuous and complete records of patients with rare diseases, and their follow-up through a web-based Information System.
A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. There are two comparison strategies for the NMI and ARI depending on the availability of true labels of patients. If you upload an empirical pre-determination of subtypes for samples by experts or clinicians based on clinical phenotypes, images or experience, CEPICS will take it as gold standard to compare. If you don’t have any subtype information, CEPICS will calculate NMI and ARI between the results of every two methods for each k, and then calculated the average NMI and ARI for each method at each k
Software pipeline and associated machine-learning framework for identifying regulatory single nucleotide polymorphisms (rSNPs) in the noncoding genome for post-analysis of genetic regions identified in genome-wide association studies (GWAS).
Library of model implementations for sharing deep-learning image segmentation and outcomes models | Deep learning-based auto-segmentation of swallowing and chewing structures in CT | Matlab based platform for Radiological Research | CERR (pronounced 'sir'), stands for Computational Environment for Radiological Research. CERR is MATLAB based software platform for developing and sharing research results using radiation therapy treatment planning and imaging informatics. CERR has a wide variety of dose, imaging, and structure analysis and comparison tools. CERR is open-source and GNU GPL copyrighted
Computational Environment for Radiological Research (CERR)
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction | Transcriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature-viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time
Detecting distant-homology protein structures by aligning deep neural-network based contact maps. fold recorgnition by eigen-decomposition of contact map. CEthreader (Contact Eigenvector-based threader) is a new threading algorithm that combines contact-map with profile-based alignments for protein fold recognition.
A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals | Chassis selection from 70 candidate orgainisms for more than 6,000 target molecules production | CF-Targrter: We present CF-Targeter to solve several biological problems, including host organism selection, biosynthetic pathway design and quantitative evaluations of pathways. It is very useful for those who plan to biosynthesize a target molecule but do not know which host organism should be selected, what the heterologous pathway is or what maximum theoretical yields could be achieved | Tips: please choose a search type
A statistical method for identifying consistently important features across samples. (software for the manuscript "A statistical method for identifying consistently important features across conditions"). CFD itself is implemented in Go (source code is in the go/src/ directory), and figures for the manuscript were generated in Python, using the produce_manuscript_figures.py code
A cell-free epigenome atlas in human diseases | Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species | Welcome to CFEA (Cell-Free Epigenome Atlas) | The cell-free DNA (cfDNA) was shown to be a powerful tool for the noninvasive diagnosis of various diseases and accumulating evidence suggests large-scale epigenetic alterations such as cfDNA methylation (5mC), cfDNA hydroxymethylation (5hmC) and cfDNA nucleosome positioning (NP) can sensitively detect and classify cancers. The CFEA (Cell-Free Epigenome Atlas) data portal is the first database dedicated to human cell-free epigenomes
Rotation equivariant and invariant neural networks for microscopy image analysis | Conic Convolution and DFT Network (CFNet) combines a novel rotation equivariant convolution scheme, called conic convolution, and the DFT to aid networks in learning rotation-invariant tasks. This network has been especially designed to improve performance of CNNs on automated computational tasks related to microscopy image analysis
Analyzes images of cell colonies that emit a luminescent/fluorescent signal in the form of a luminescent halo around the colony. Automatically identifies both the colonies and their emitted luminescent halos and returns quantitative data on features
An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Clinical Genome & Ancestry Report (CGAR) enables users to identify and prioritize phenotype-associated variants from genome sequencing with a user-friendly and interactive online platform.
Clinical Genome and Ancestry Report (CGAR)
Developing the Web Server for CpG Island related Density and LAUPs (Lineage-associated Underrepresented Permutations) Study | WA web server for CpG Island study:CpG Island related density and LAUPs (Lineage-associated Underrepresented Permutations) analysis
Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells | Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors in the development and progression of cancer | However, detection of genetic interactions in the cancer genome is a major obstacle in the research of identifying biomarkers for cancer cell drug resistance and sensitivity
A contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm.
Splice sites detection using chaos game representation and neural network. Email: hoangthanhtungvn@gmail.com. Project description: We propose to use chaos game representation and neural network for splice sites detection. DNA sequences are mapped to numerical sequences using chaos game representation. Numerical sequences are used as feature inputs to neural networks for splice sites classification
Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing | CGRs, molecules and reactions manipulation.
Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC) - tools to pick causative mutation from bulks segregant sequencing.
An integrated database for Cricetulus griseus and CHO cells
Web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.
The Role of Circular RNA CDR1as/ciRS-7 in Regulating Tumor Microenvironment | CIBERSORT is an analytical tool developed by Newman et al. to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data | Absolute mode (beta) is now available
a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Causal Inference and Directional Enrichment Methods on Biological Networks. Launching Causal Inference Engine... CIE is a platform for inference of active transcriptional regulators of differential gene expression. CIE provides a user-friendly web-app and an R-package to run inference queries on casual regulatory netowrks. Several regulatory networks are provided in the platform, including a TF-gene intraction network constructed from ChIP-seq and tissue specific gene expression data, a netowrk based on STRING-DB, and curated TF-gene interaction networks such as TRRUST and TRED. The R-package provides functionality for custom networks as well. Causal Inference Engine: Directional Enrichment Analysis on Biological Networks.
Central Informative Nodes in Network Analysis (CINNA) package gathers all required functions for centrality analysis in weighted/unweighted and directed/undirected networks.
Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.
CircRNA Identifier. A de novo circular RNA identification tool.
Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences.
Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.
CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.
A Python software development and analysis toolkit for the CIViC knowledgebase | Clinical Interpretations of Variants in Cancer | CIViCpy — civicpy 1.0.0-rc1 documentation | A python interface for the CIViC db application | Sorry, something went wrong. Reload? | Sorry, we cannot display this file | CIViCpy is an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase | You have reached the code repository for CIViCpy, a python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC) | Sorry, this file is invalid so it cannot be displayed | CIViCpy lets you pull data from CIViC using the civic module and interact with records as dynamic objects. With the aid of caching, it is easy to explore relationships between CIViC records (e.g. assertions, genes, variants) without worrying about querying CIViC more than once for the same data
CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases.
GPU-accelerated image processing for everyone. CLIJ is an OpenCL - ImageJ bridge and a Fiji plugin allowing users with entry-level skills in programming to build GPU-accelerated workflows to speed up their image processing. Increased efforts were put on documentation, code examples, interoperability, and extensibility. CLIJ is based on ClearCL, JOCL, Imglib2, ImageJ and SciJava
CLINE (Comparison of bioLogIcal deNdrogram structurEs), is a web-tool specifically designed for the visual comparison of dendrograms, with an emphasis on the display of matching clusters that, even when not isomorphic, can be perceived as having the same biological meaning.
Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to the iCLIP workflows also FLASH, and uvCLAP.
An interactive retrieval system for clinical trial studies with context-dependent protocol elements. Clinical trial protocol includes all the steps that should be conducted in clinical trial and all clinical trial start with development of the protocol. The purpose of our study is to provide context-dependent protocol element selection system for the development of objective and successful clinical trial protocols. We have developed a database and search application for protocol structure retrieval
Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses | PURPOSE:We have created a cloud-based machine learning system (CLOBNET) that is an open-source, lean infrastructure for electronic health record (EHR) data integration and is capable of extract, transform, and load (ETL) processing. CLOBNET enables comprehensive analysis and visualization of structured EHR data. We demonstrate the utility of CLOBNET by predicting primary therapy outcomes of patients with high-grade serous ovarian cancer (HGSOC) on the basis of EHR data. MATERIALS AND METHODS:CLOBNET is built using open-source software to make data preprocessing, analysis, and model training user friendly. The source code of CLOBNET is available in GitHub
Chlamydomonas Library Project (CLiP) provides access to a collection of mutant strains in the green alga Chlamydomonas reinhardtii, a powerful model system for studying a broad range of fundamental processes including the biology of chloroplasts, photosynthesis, cilia/flagella, eyespots, and algal lipid accumulation.
A simple classification scheme for data elements of clinical data based on semantics
A Public Omics Database for Systematic and Comparable Information of CMV. Cytomegalovirus is a double-stranded DNA virus in the same family as herpesvirus found every where,infect people of all ages. Cytomegalovirus Treatment & Management Kauser Akhter, MD Assistant Professor, Department of Internal Medicine, Florida State University College of Medicine; Associate Program Director, Infectious Diseases Fellowship Program, Orlando Health; Updated: Jan 05, 2017
A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. [Source] CNAPE: A Software for Copy Number Alteration Prediction from Gene Expression in Human Cancers. Copy number alterations (CNAs) are important features of human cancer. While the standard methods for CNA detection (CGH arrays, SNP arrrays, DNA sequencing) rely on DNA, occasionally DNA data are not available, especially in cancer studies (e.g. biopsies, legacy data). CNAPE comes into play by predicting CNAs based on gene expression data from RNA-seq
Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes.
Convolutional neural network for efficient estimation of regional brain strains. Three pretrained CNN neural network models are provided based on all of the brain response samples available in the published study (N=3069). They correspond to the peak maximum principal strain (MPS) of the whole brain (WB), MPS of the corpus callosum (CC), and fiber strain (FS) of the CC, all assessed at the 95th percentile levels
Problems with homepage (January 6th, 2021) | CNN-SuccSite is a web server for characterization and identification succinylation sites based on deep learning method.
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. CNN-based Annotation of Bacterial Type IV Secretion System Effectors. The CNN-T4SE is a tool that can be run in windows and linux operating systems. It is used to identify effector proteins through the amino acid sequence, evolutionary information in the form of a position-specific scoring matrix, secondary structure and solvent accessibility information of the proteins.
Copy Number Variation Detection in Bacterial Circular Genome. Abstract Motivation Whole genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. Results We show that the replication bias is widespread using ~200 bacterial WGS data. We develop CNV-BAC that can properly normalize the replication bias as well as other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementation CNV-BAC is available at https: github.com LinjieWu CNV-BAC. Contact ruibinxi@math.pku.edu.cn
association analysis of CNVs with gene expression and quantitative phenotypes | Summarization and expression/phenotype association of CNV ranges | The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes
Visually Exploring Copy Number Aberrations in Cancer Genomes. CNVScope interchromosomal heatmaps. A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization. Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps. CNVScope is a visualization toolkit for seeing copy number data in a relationship fashion, both utilizing tools that find regions of interest (much like domains in Hi-C terminology), visualize the relationships in vibrant color (blue for negative association, red for positive), and integrates several different relevant types of data (RNASeq, sample information, Cancer Gene Census data, and structural variants)
Multi-omics Approach to Detecting Clinically Associated, Combinatory Genomic Signatures.
Component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states.
Ronan Fleming on behalf of the COBRA Toolbox Development Community
Context-specific biological knowledge representation for systemic physiology analysis.
Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra | COLMARm 13C-1H HSQC, HSQC-TOCSY and TOCSY Query and Verification | Visit a step by step how-to with figures here | Bingol, K.; Li, DW.; Zhang, B.; Brüschweiler, R.; Comprehensive metabolite identification strategy using multiple two-dimensional NMR spectra of a complex mixture implemented in the COLMARm web server; Anal. Chem; 2016, 88, 12411-12418;
Data-Analysis Package for Combinatorial Materials Science.
Web-based application used to download, collect and manage gene expression data from public databases.
A tool to explore and visualize intercellular communication. Abstract Intercellular communication plays an essential role in multicellular organisms and several algorithms to analyse it from single-cell transcriptional data have been recently published, but the results are often hard to visualize and interpret. We developed COMUNET (Cell cOMmunication exploration with MUltiplex NETworks), a tool that streamlines the interpretation of the results from cell-cell communication analyses. COMUNET uses multiplex networks to represent and cluster all potential communication pathways between cell types. The algorithm also enables the search for specific patterns of communication and can perform comparative analysis between two biological conditions. To exemplify its use, here we apply COMUNET to investigate cell communication patterns in single-cell transcriptomic datasets from mouse embryos and from an acute myeloid leukemia patient at diagnosis and after treatment
CCA (canonical correlation analysis) ON Features for INter-dataset Effect Detection.
COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results.
The CORDERLY software analyses colloidal ordering via the 2D fast Fourier transform, the radial distribution function, the spatial distribution function, and the angular distribution. The spatial distribution function plots the resulting analysis in Cartesian and polar coordinates (angular distribution).
Cores of Recurrent Events (CORE) is software tool for delineating regions of recurrent DNA copy number alteration in cancer.
CORGi (COmplex Rearrangement detection with Graph-search), a method for the detection and visualization of complex local genomic rearrangements.
COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats.
Computational Omics and Systems Biology Group
A Normalized Measure of Codon Usage Preferences. COUSIN is a bioinformatic tool which aims to calculate the Codon Usage Preferences (CUPrefs) of sequences using a novel index named COUSIN. In addition, numerous functions are proposed to enhance your CUPrefs analysis experience !
Genome-wide association analysis of age-at-onset traits using Cox mixed-effects models | Abstract Age-at-onset is one of the critical phenotypes in cohort studies of age-related diseases. Large-scale genome-wide association studies (GWAS) of age-at-onset can provide more insights into genetic effects on disease progression, and transitions between different stages. Moreover, proportional hazards or Cox regression generally achieves higher statistical power in a cohort study than a binary trait using logistic regression. Although mixed-effects models are widely used in GWAS to correct for population stratification and family structure, application of Cox mixed-effects models (CMEMs) to large-scale GWAS are so far hindered by intractable computational intensity. In this work, we propose COXMEG, an efficient R package for conducting GWAS of age-at-onset using CMEMs
Integrated plastome sequence annotator and analyzer.
R package for p-value adjustment when looking for an optimal transformation of a single explanatory variable in generalized linear models.
An Open-Source C++ and Python Library for Polarizable Embedding. C++ and Python library for Polarizable Embedding. CPPE is an open-source, light-weight C-Plus-Plus library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field calculations and post-SCF methods. A convenient Python interface is also available
The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets and classifies germline DNA variants identified from next-generation sequencing in the context of cancer predisposition and inherited cancer syndromes. The workflow can also report incidental findings (ACMG v3.0) as well as the genotypes of common germline variants associated with cancer risk, as reported in the NHGRI-EBI GWAS catalog.
Cancer Predisposition Sequencing Reporter (CPSR)
whole plant modelling framework for the simulation of water and carbon related processes. Output of CPlantBox-PiafMunch coupling. Simulation output of CPlantBox-PiafMunch coupling. Example 2-4
K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment | CQF-deNoise enables fast k-mer counting with memory usage nearly unaffected by sequencing errors
The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.
Software package for conditional robustness analysis of cancer systems biology models in MATLAB.
CRB-Anim is the online catalog of biological resources of the french national infrastructure supporting research on domestic animals.
Conditional Robust Calibration (CRC) - Bayesian method for nonlinear model calibration and robustness analysis using omics data.
Colo-Rectal Cancer Risk Prediction (CRCRpred) webserver can be used to distinguish high risk CRC patients from low risk CRC patients given the protein concentration of one or more apoptotic proteins (Bak, Bax, Bcl2, BclXL or Mcl1) involved in the process of Mitochondrial Outer Membrane Permeabilization (MOMP), which is defunct in the case of cancer. The risk estimation is based on statistical and survival analysis on recent CRC datasets.
Consensus Reverse Docking System for Target Fishing | Identification of putative drug targets is a critical step for explaining the mechanism of drug action against multiple targets, finding new therapeutic indications for existing drugs, and unveiling the adverse drug reactions. One important approach is to use the molecular docking. However, its widespread utilization has been hindered by the lack of easy-to-use public servers. Therefore, it is vital to develop a streamlined computational tool for target prediction by molecular docking on a large scale. RESULTS:We present a fully automated web tool named CRDS (Consensus Reverse Docking System) which predicts potential interaction sites for a given drug. To improve hit rates, we developed a strategy of consensus scoring
Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks | Clustering of Genomic Regions Analysis Method | Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach
cath-resolve-hits (CRH)- tool that resolves domain matches suspiciously quickly.
Design tool for CRISPR-mediated gene editing, repression and activation.
Improved CRISPR/Cas9 tool for genome editing in plants
Suite of web applications for analysing Clustered Regularly Interspaced Short Palindromic Repeats.
Easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
A fast and intuitive tool for designing guide RNA for genome editing | The RNA-guided CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeat-CRISPR-associated 9) system has become a revolutionary technology for targeted genome engineering. The critical step of this technology requires the design of a highly specific and efficient guide RNA (gRNA) that will guide the Cas9 nuclease to the complementary DNA target sequence. CRISPR-Explorer is a new and user-friendly web server for selecting optimal CRISPR sites. It implements the latest scoring schemes of gRNA specificity and efficiency based on published empirical studies. The gRNA design results are generated instantly, thus removing wait times. The user can visualize the high-quality gRNAs with detailed design information through an interactive genome browser. Furthermore, the user can define and specify the parameters for gRNA selection in the Batch Design mode, which recognizes various input formats
Software for designing CRISPR/Cas guide RNA with reduced off-target sites.
A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.
Gateway to publicly accessible CRISPRs database.
A novel constrained reconstruction model towards high-resolution sub-tomogram averaging.
Web server for predicting the in vivo structure of RNA molecules.
A tool for the prediction of ancestry in cattle | Added an avenue for data that plink does not have a "species ID" for. In this case users, will specify "NA" as the plink_species_ID in their input file. It is now required to specify chromosome number for the data in the input | CRUMBLER has now been successfully ran in Pigs, following these updates
A comprehensive framework to predict condition-specific regulatory units. We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.
Visualization environment for plotting properties of crystalline solids as computed by means of the CRYSTAL code.
Pairwise visual comparison of small RNA secondary structures with base pair probabilities.
C2Structure: Extracting Structural Information Directly From NMR Chemical Shifts. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts.
R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR.
Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR) | Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins in cerebrospinal fluid between two or more disease groups. As the number of such studies is growing, it is no longer straightforward to obtain an overview of which specific proteins are increased or decreased between the numerous relevant diseases and their many subcategories, or to see the larger picture or trends between related diseases
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.
An Online Platform for Automated NGS Data Analysis and Sharing. CSI NGS Portal is an online platform for fully automated NGS data analysis and sharing . CSI NGS Portal uses a single, randomly generated, persistent, secure and http-only browser cookie for the sole purpose of user recognition for data authorisation.
A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples. A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing. Computation Subtraction-based Microbiome Discovery (CSMD). CSMD will work with a series of libraries listed in Table 2, including human-related genomes or sequences (21G) and all RefSeq bacteria genomes (150G, as of November 2018). The build process will then require approximately 500GB of additional disk space and 200GB of RAM. These genomes or sequences can be found in DBPATH/hg38/SEQ, DBPATH/AHG/SEQ, DBPATH/EHG/SEQ and DBPATH/RefSeq/bacteria/SEQ, respectively. And the indexed files will be saved in DBPATH/hg38, DBPATH/AHG, DBPATH/EHG and DBPATH/RefSeq/bacteria, respectively
Computation Subtraction-based Microbiome Discovery (CSMD)
A label-free method for dynamic measurement of single-cell volume. Kai Yao, Nash D Rochman, Sean X Sun (*ssun@jhu.edu) @ Johns Hopkins University
Cell Topography Regression Learner (CTRL)
Cross-validated Rank-based Marker Selection for Genome-wide Prediction of Low Heritability | Marker selection for genome-wide prediction | Cross-Validated Rank-based Marker Selection (CVRMS) | CVRMS is an R package designed to extract marker subset from ranked marker dataset induced by genome-wide association study (GWAS) or marker effect analysis for genome-wide prediction
CWL VM environment is a repository which can be deployed on cloud to execute Biobb Mutations Workflow.
Model-based cell clustering and population tracking for time-series flow cytometry data. CYBERTRACK is an R package for CYtometry-Based Estimation and Reasoning for cell populatiomn TRACKing
An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Cystic Fibrosis Missense Analysis. Website dedicated to the in silico analysis of missense variants in the CFTR gene. Welcome to the Cystic Fibrosis Missense Analysis Website. Data provided and calculated by CYSMA must be considered as predictions. If you are dealing with the genetics of cystic fibrosis or CFTR-related disorders, you may find this website useful. CYSMA has been developed as a tool to help you to predict the impact of novel uncharacterized missense variants when the information provided by CFTR patient databases such as CFTR-France, CFTR1 and CFTR2 remain insufficient
CaFE (Calculation of Free Energy) - a VMD plugin for binding affinity prediction using end-point free energy methods.
NIMG-70. QUANTITATIVE IMAGE ANALYSIS AND MACHINE LEARNING TECHNIQUES FOR DISTINGUISHING TRUE PROGRESSION FROM PSEUDOPROGRESSION IN PATIENTS WITH GLIOBLASTOMA. Perelman School of Medicine at the University of Pennsylvania. The Center for Biomedical Image Computing and Analytics (CBICA) was established in 2013, and focuses on the development and application of advanced computational and analytical techniques that quantify morphology and function from biomedical images, as well as on relating imaging phenotypes to genetic and molecular characterizations, and finally on integrating this information into diagnostic and predictive tools in an era of personalized medicine. Center for Biomedical Image Computing & Analytics. Cancer Imaging Phenomics Toolkit (CaPTk). CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer
Calcium Signaling Analyzer (CaSiAn), an open source software tool that allows for quantifying these signal characteristics including individual spike properties and time course statistics in a semi-automated manner.
General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.
Early Cancer Detection from Multianalyte Blood Test Results using Artificial Intelligence
CancerGeneNet is a resource that aims at linking genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancers in the cell network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGenNet bridges two interaction layers by connecting proteins whose activities are affected by cancer gene products to proteins that impact on cancer phenotypes. This is achieved by implementing graph algorithms that allow searching for graph path that link any gene of interest to the “hallmarks of cancer".
Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles | Liver Heptacellular Carcinoma Stage Prediction | CancerLSP is a web-bench Liver cancer stage prediction Server | Reference: Kaur H et. al., (2019) Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. https://doi.org/10.1371/journal.pone.0221476
Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.
Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. A Webserver to Predict the Progression of Skin Cancer. This database maintains comprehensive information of short self-assembling peptides forming nanostructures and their structures. Reference: Bhalla, S., Kaur, H., Dhall, A., Raghava, GPS. Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. Sci Rep 9, 15790 (2019) doi:10.1038/s41598-019-52134-4. https://doi.org/10.1038/s41598-019-52134-4. CancerSPP: A Webserver for predicting the progression of skin cancer. CancerSPP is a web-bench for skin cutaneous melanoma (SKCM) progression prediction
a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity data: 1) Intra-tumor or Intra-metastatic heterogeneity: the presence of multiple subclones within a primary tumor or a single metastatic lesion; 2) Inter-metastatic heterogeneity: the presence of different subclones in different metastatic lesions of the same patient. Somatic mutations and copy number alterations are available in CancerTracer, since both of them are principal factors drive heterogeneity in cancer. The structured heterogeneity data enables researchers to identify trunk mutations in different cancer types and investigate the molecular mechanisms underlying intratumor heterogeneity
Using existing tools in the Galaxy environment we generated the workflow CandiMeth (CANDIdate feature METHylation). This takes as input a differential methylation table from an R-based package and maps it to a reference genome build. A simple interface then allows the user to query the dataset with inputs as straightforward as lists of gene names, or as detailed as bed files containing specific chromosomal coordinates, for more sophisticated analyses.
A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space.
A java tool for designing probes for capture Hi-C applications. Here, we developed CaptureProbe, a user-friendly and graphical Java tool for designing capture probes for Capture Hi-C applications. CaptureProbe is easy-to-use, only need simple input files and provides abundant parameters for designing probes. CaptureProbe can design probes specifically for both genomic sites and genomic regions of interest. Comparisons with existing softwares (HiCapTools and GOPHER) indicated that CaptureProbe has a good design success ratio and better probe specificity. Citation: MA Y F, ADEOLA A C, SUN Y B, et al. 2020. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zool Res [J], 41: 94-96
A tool for the prediction and visualization of time-concentration profiles of drugs in heart tissue. Cardiac mechanistic physiologically based pharmacokinetic simulation application. User Interface (ui) application which implements PBPK models. Prediction of drug effect is valuable in terms of both safety and efficacy. physiologically based pharmacokinetic-quantitative system. 1) Download the tar.gz archive from the https: sourceforge.net projects cardiacpbpk files or clone github repository (if you have git packages installed in konsole terminal type ‘git clone https: github.com jszlek CardiacPBPK.git’)
R package for extraction and visualisation of heart rate profiles from wearable fitness trackers.
Platform for noninvasive assessment of pulse transit time and pulsatile flow in hyperelastic vascular networks.
Online tool for assessing genome editing results using NGS data.
A flexible, scalable and easy-to-use amplicon sequence data analysis pipeline. CASCABEL is a pipeline designed to run amplicon sequence analysis across single or multiple read libraries. The objective of this pipeline is to create different output files which allow the user to explore data in a simple and meaningful way, as well as facilitate downstream analysis, based on the generated output files.
Inference of Single-Cell Phylogenies from Lineage Tracing Data. A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction. This is a software suite for proecessing data from single cell lineage tracing experiments. This suite comes equipped with three main modules:. Phylogeny Reconstruction: a collection of tools for constructing phylogenies. We support 5 algorithms currently: a greedy algorithm based on multi-state compatibility, an exact Steiner-Tree solver, Cassiopeia (the combination of these two), Neighbor-Joining, and Camin-Sokal Maximum Parsimony. Target Site Sequencing Pipeline: a pipeline for extracing lineage information from raw fastqs produced from a lineage tracing experiment
Web-platform for sharing data and software for computational catalysis research.
Fast inference of causality from complex time series. Causal inference in non-linear dynamics systems. Welcome to CauseMap — CauseMap 0.1.0 documentation. CauseMap is an implementation of Convergent Cross Mapping (CCM), written in Julia. CauseMap is an implementation of Convergent Cross Mapping (CCM) [1], written in Julia
A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease | ABSTRACT Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge ( http: genomics.senescence.info cells ), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling | Automated, probabilistic assignment of cell types in scRNA-seq data | cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows
R/Bioconductor software for comparing single-cell RNA-seq analysis methods. Construct Benchmarks for Single Cell Analysis Methods. This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods
a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. Welcome to CellBender’s documentation! — CellBender documentation. Free document hosting provided by Read the Docs. Stephen J Fleming, John C Marioni, and Mehrtash Babadi. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. bioRxiv 791699; doi: https://doi.org/10.1101/791699.
We present CellBin, an image-facilitated one-stop pipeline for high-resolution and large field-of-view spatial transcriptomic data of Stereo-seq. CellBin provides a comprehensive and systematic platform for generating high-confidence single-cell spatial gene expression profiles, which specifically includes image stitching, image registration, tissue segmentation, nuclei segmentation and molecule labeling. CellBin is user-friendly and does not require a specific level of omics and image analysis expertise.
CellCountCV – a web-application for accurate cell counting and automated batch processing of microscopy images using fully-convolutional neural networks. This repository contains the code and examples accompaining our preprint https://doi.org/10.1101/867218. Working_with_CellCounter.ipynb — this notebook contains the examples of pretrained FCNN model usage in Python and through JSON-RPC calls to CellCountCV
Web application for exploration and analysis of cancer cell line pharmacogenomic data across different sources.
Tool for quantifying data from biological images, particularly in high-throughput experiments.
A software aims to calculate the similarity among different cells and predict their co-regulation networks.
Support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort.
Genetic barcode-based sample multiplexing for single-cell genomics.
Platform for interactive, 3D graphical simulation of immunological processes.
Probabilistic census-travel model to predict introduction sites of exotic plant, animal and human pathogens.
Software for interactive visualization of scRNA-seq data.
A toolbox for creating Cartesian Geometric Representations with Isometric Dimensions (Cgrids). The Cgrid-toolbox can be used to generate rectangular representations of brain areas.
ChAsE (Chromatin Analysis and Exploration) is a cross platform desktop application that provides an interactive graphical interface for analysis of epigenomic data. Features include: - Exploration and visualization of the data using an interactive heat map and plot interface - Clustering the data automatically or manually by sorting and brushing the heat map - Exporting results for downstream analysis or as high quality images for publications
Transcription factor enrichment analysis by orthogonal omics integration.
Computational package to process the next-generation sequence data generated from ChIA-PET experiments.
ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.
A comprehensive user-friendly tool for mining multi-sample ChIP-seq data | a tool for analysing and mining multi-sample ChIP-seq data | ChIPdig is a tool designed for the bulk analysis of ChIP-seq data comprising multiple samples. Its capabilities are organized into four analysis modules: | In the example above, the first command establishes communication with the Bioconductor repository and the second command installs package “edgeR”. Repeat the second command for the remaining Bioconductor packages used by ChIPdig:
> CORRECT NAME OF TOOL COULD ALSO BE 'RESULTS:ChIPseqSpikeInFree' | A ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in | A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications | We develop ChIPseqSpikeInFree, a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. This method is capable of revealing the similar magnitude of global changes as the spike-in method | Traditional reads per million (RPM) normalization method is inappropriate for the evaluation of ChIP-seq data when the treatment or mutation has the global effect
A Python3 framework to simulate read counts in a ChIP-seq experiment.
An R toolbox for modeling choices and response times in decision-making tasks. BACKGROUND:Decision-making is the process of choosing and performing actions in response to sensory cues to achieve behavioral goals. Many mathematical models have been developed to describe the choice behavior and response time (RT) distributions of observers performing decision-making tasks. However, relatively few researchers use these models because it demands expertise in various numerical, statistical, and software techniques. NEW METHOD:We present a toolbox - Choices and Response Times in R, or ChaRTr - that provides the user the ability to implement and test a wide variety of decision-making models ranging from classic through to modern versions of the diffusion decision model, to models with urgency signals, or collapsing boundaries.
improved chaperone binding prediction using position-independent scoring matrices | ChaperISM is an algorithm to identify Hsp70 binding sequences in proteins. It uses a position-independent scoring matrix which was trained on either qualitative or quantitative chemiluminescence data previously published, obtained from interaction between DnaK and different ligands. Both versions of ChaperISM, qualitative or quantitative, resulted in an improved performance in comparison to other state-of-the-art chaperone binding predictors
Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery | Aggregator Prediction-Webserver-ADMElab | Aggregation is one of the main reasons of false positives in HTS. To build a reliable prediction model, we collected a large dataset of aggregators and drugs to build several models based on the combination of different descriptors and algorithm, ChemAGG is a free webserver that could be used to easily filter out aggregators from potential lead molecules!
Comparative dataset of experimental and computational attributes of UV/vis absorption spectra. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. This work adapts the underlying table extraction mechanics of ChemDataExtractor version 1.3 , for higher precision extraction of maximum absorption peak wavelength data and associated extinction coefficients.
A Fast and Robust Coordination Environment Identification Tool. Coordination or local environments have been used to describe, analyze, and understand crystal structures for more than a century. Here, we present a new tool called ChemEnv< i>, which can identify coordination environments in a fast and robust manner. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen< i> package and the software can as well be used through a web app available on http: crystaltoolkit.org through the Materials Project.
ChemPager is a freely available data analysis tool for analyzing, comparing and improving synthetic routes. Functions include prediction of the cumulative process mass intensity of chemical routes, irrespective of their development status, by comparison with a set of reactions executed on large scale. Along with the prediction of this core green chemistry metric aims to improve existing routes and help the decision-making process among route alternatives without the need for experimental data.
Package for chemoinformatics calculations and machine learning.
Pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data.
An open-source automated experimental platform for biological science research. By combining heating, stirring, liquid handling, spectrometry, and optogenetics into a single easy-to-use platform, Chi.Bio can simplify laboratory protocols and drastically reduce equipment costs. No more will tired graduate students need to stay late in the lab to induce experiments, or run samples between incubators and plate readers.
A mine with chickpea data (both desi and kabuli varieties) from the Legume Information Systems (LIS) tripal.chado database
Open-source software for semi-automated segmentation and analysis of birdsong and other natural sounds. Abstract Audio recording devices have changed significantly over the last 50 years, making large datasets of recordings of natural sounds, such as birdsong, easier to obtain. This increase in digital recordings necessitates an increase in high-throughput methods of analysis for researchers. Specifically, there is a need in the community for open-source methods that are tailored to recordings of varying qualities and from multiple species collected in nature. We developed Chipper, a Python-based software to semi-automate both the segmentation of acoustic signals and the subsequent analysis of their frequencies and durations.
A comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. ChlamDB documentation — ChlamDB 2.0 (June 2019) documentation. A comparative genomics database of the phylum Chlamydiae and other PVC (Planctomycetes, Verrucomicrobia, Lentisphaerae). Problems and errors encountered on the ChlamDB website can be announced on the github page of the website
A visualisation tool for linking function to phylogeny in microbiomes | Interactive visualisation and data annotation for meta-omics data | Chordomics is a tool to visualize and interpret linked data, such as from metagenomics or metaproteomics where both taxonomic and functional data is obtained | The demonstration version of Chordomics is available at https://kmcd.shinyapps.io/chordomics/. Here, a toy dataset is provided to allow you to see the explorative capabilities Chordomics provides before you need to install it!
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts | Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts" | ChromDragoNN: cis-trans Deep RegulAtory Genomic Neural Network for predicting Chromatin Accessibility
A combined visualisation of phylogenetic and sequence data. Combined visualisation of phylogenetic and sequence data. Please see 'release' tab for executables and documentation below. ChromaClade is a desktop bioinformatics application that produces visualisations combining sequence and phylogenetic data. It annotates taxon names in a phylogenetic tree with amino acids found at individual sites in a corresponding sequence alignment. Residue-specific colour codes enable easy inspection by eye and the resulting trees can be viewed in any of several popular tree-viewing programs
A scalable whole-genome visualization of structural differences in prokaryotes. Colinear block visualisation tool. To create a fresh environment for chromatiblock to run in do:. Scalable, whole-genome visualisation of structural changes in prokaryotes. Will run chromatiblock on all fasta or genbank files in /path/to/fasta_directory/ and create an interactive webpage of the output. Intermediate files will be created in cb_working_dir
Cancer in silico Drug Discovery (CIDD) is a platform to integrate data from the TCGA, Connectivity Map (CMap) and Cancer Cell Line Encyclopedia to facilitate and automate discovery of candidate drug compounds with the ultimate goal for treatment or chemo-prevention of cancer.
A tool for predicting and analysing transcription factor binding sites | CIIIDER is a user-friendly tool for predicting and analysing transcription factor binding sites, designed with biologists in mind | Transcription factor binding site prediction and visualisation software
An integrated and validated compendium of ciliary genes.
The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental table.
Ciona robusta Anatomy and Development Ontology
Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space.
A Powerful Tool for Identifying circRNA Coding Ability. A Python3-base pipeline for translated circular RNA(circRNA) identification. CircCode is a Python3-base pipeline for translated circular RNA identification. It automatically tandem links sequence in series and processes a given ribosome profile data (including quality control, filtering and alignment). Finally, based on random forest and J48 classification, the final translated circular RNA was predicted. The user only needs to fill in the given configuration file and run the python scripts to get the predicted translated circular RNA
Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.
Integrated tool for the identification of circRNAs with protein-coding potential.
Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines | The CircRic refers to “circular RNA in cancers”. Circular RNAs (circRNAs) is class of non-coding RNA generated in a “back-splicing”. Recent studies have highlighted the important role of circRNAs in cancer. Here, we systematically characterize circRNAs expression profile in 935 cancer cell lines across 22 cancer lineages from Cancer Cell line Encyclopedia (CCLE), and analyzed the circRNAs biogenesis regulators, effect of circRNAs on drug response and association between circRNAs with mRNA, protein and mutation, and predicted RNA regulatory element in circRNAs
A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms. circacompare is an R package that allows for the statistical analyses and comparison of two circadian rhythms. This work is published here and can be cited as:. Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh, CircaCompare: A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz730
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. A method for circular DNA detection based on probabilistic mapping of ultrashort reads. Welcome to Circle-Map official repository!. Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome.
Web server for functional enrichment analysis of transcription factor ChIP-seq peaks.
CiteFuse enables multi-modal analysis of CITE-seq data. multi-modal analysis of CITE-seq data. CiteFuse is a streamlined package consisting of a suite of tools for pre-processing, modality integration, clustering, differential RNA and ADT expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualization of CITE-seq data
Clade Phylogenetic Profiling (CladePP) detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g. mammals, vertebrates, animals, plants) at which coevolution occurred.
Exploring the limit of using a deep neural network on pileup data for germline variant calling. Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling. Clair - Yet another deep neural network based variant caller. Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly, and epigenetic mark detection
Field-scouting software for the identification of wildlife in camera trap images.
A webapplication for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy.
An open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration | Click: Do GWAS analysis by yourself by Clicking | More than 30 cancer types, more than 10,000 samples | Including gene expression, copy number variation, methylation and mutation data categories | You are accessing a non-profit web site which is based on GDC data portal hosted by National Cancer Institute, USA. All data was downloaded from GDC public database. Please make sure you are aware of and obey the policy of GDC data portal. Please go to User`s Guide for more information | Beeswarm plot, Manhattan plot, Volcano plot, Mountain plot, Deflection plot, Linear regression analysis, significance test and
A novel method for allele-specific somatic copy-number alterations detection. Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data. A tool for large-scale CNV and CNA detection.
An open-access clinical epidemiology database resource encouraging online exploration of complex studies. The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical and epidemiologic studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework. Here we present an intuitive point-and-click website that allows users to visualize and subset data directly in the ClinEpiDB browser and immediately explore potential associations
Visual analytics tool for breast cancer treatment stratification.
Efficient tool for identifying disease-relevant nonsynonymous single nucleotide variants.
Quick evaluation of the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs).
Clinical Variant Annotation Pipeline (ClinVAP) creates a genetic report of somatic mutations from a variant call format (VCF) file. Please refer this document for implementation of the pipeline. Documentation of the pipeline is available at Wiki page.
Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.
Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Clirc: a user-friendly bioinformatics software to identify RBP-bound circRNAs through analysis of CLIP-Seq data. The Clirc software is designed to identify RBP-bound circRNAs in CLIP-Seq data. The Clirc software internally calls the gsnap aligner for alignment of CLIP-Seq reads. The CLIP-Seq technology comprises of three variants: HITS-CLIP, PAR-CLIP, and iCLIP. The Clirc software works on all three versions of them. It can also work on any type of RNA-Seq data in general, although non-polyA selected RNA-Seq is preferred. The Clirc software is designed to search for known circRNAs in high-throughput sequencing data whose coordinates are provided by users. The users can collect these coordinates from previous publication or their own search using RNA-Seq data. This avoids the common problem of short sequncing reads in CLIP-Seq data. But this approach cannot identify novel circRNAs in CLIP-Seq data
Clonal reconstruction from time course genomic sequencing data. ClonalTREE (Clonal reconstruction in Time couRse long-term Evolution Experiment). Usage: python3 ClonalTREE.py <VAF file> <algorithm> <fail threshold> <out prefix> <clones (optional)>
R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics.
Create Neighbor-joining or UPGMA phylogentic trees from a multiple sequence alignment using ClustalW.
R package for the analysis of hierarchical data using generalized linear models with the cluster bootstrap.
Enhanced prediction of gene and missense rare-variant pathogenicity by joint analysis of gene burden and amino-acid residue position. Rare variant association using position and burden signals. This method is designed for case-control studies where the condition under investigation is caused by rare variants in protein-coding regions. This is the case for most Mendelian diseases and therefore this method is relevant for these
ClusterScan is a tool to search for genomic clusters starting from genomic feature locations and their annotations. It allows the user to scan an annotation file (BED format with locations of specific features such as gene, transcripts, regulatory regions or anything that can be mapped on a genome) and get clusters coordinates in output. In order to build annotated clusters, ClusterScan needs an additional two-columns file, storing the feature ids and the corresponding categorical information (such as Gene Ontology classes, KEGG, Pfam accessions, etc).
The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.
CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models.
Count Corrector for nested genes and multi-mapped reads.
A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria | Computational Drug Repositioning Score
CoExpresso is a tool to investigate the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. Thorough assessment of different randomization methods and statistical scoring algorithms allows determining the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types as well as the identification of intrinsic structures in complex behavior to determine which proteins orchestrate complex function.
Collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information.
Comparative Metatranscriptomics Workflow is a standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads.
CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods) - exploration tool for conserved organizational motifs at both the metabolic and genomic level.
Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks
Method for Co-phosphorylation-based Kinase-substrate interaction prediction (CophosK).
A pipeline to decrypt the inter protein interfaces from amino acid sequence information | Abstract Computational methods have been devised in the past to predict the interface residues using amino acid sequence information but have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence are different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here we report a new hybrid pipeline for the prediction of protein-protein interaction interfaces from the amino acid sequence information alone based on the framework of Co -evolution, machine learning ( R andom forest) and Ne twork A nalysis named CoRNeA trained specifically on eukaryotic protein complexes
Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.
The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.
predictive models for the characterization of mRNA transcripts in Eukaryotes. CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species
Computes genomic breeding values using external information on the markers. The package fits a linear mixed model with heteroscedastic random effects, where the random effect variance is fitted using a linear predictor and a log link.
Coding Sequence optimization for Chlamydomonas reinhardtii
CODONOME collects the expression value of each codon (just called "codonome") and of each aminoacyl-tRNA synthetase (aaRS). To do this, the software is able to count the total mRNA codon number of any organism and to import and integrate any mRNA expression data source in tabulated text format.
The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.
Detecting Significant Associations and Dissociations in Pangenomes. A tool for the identification of coincident (associating and dissociating) genes in pangenomes. input/output files associated with the analysis performed in the manuscript describing coinfinder. Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Coinfinder is written primarily in C++ and is a command line tool which generates text, gexf, and pdf outputs for the user. Written in collaboration with Martin Rusilowicz
Python package for the analysis of bacterial fluorescence microscopy data.
Collaboration of deep neural networks for biomedical named entity recognition.
Tool that allows extracting from the Open PHACTS Discovery platform series of compounds annotated with experimental data that can be used directly for building QSAR predictive models.
artificial intelligence approach to quantify co-localization between mass spectrometry images | Methods for measuring co-localization of ion images | Measuring co-localization of ion images | This repository is devoted to a project on measuring co-localization of mass spectrometry images. The project is carried out by the Alexandrov team at EMBL Heidelberg. We created a webapp for ranking pairs of ion images, engaged external experts to rank images from their public data from METASPACE, consolidated the results into a gold standard set of ranked pairs of ion images, and, finally, developed and evaluated various measures of co-localization | Katja Ovchinnikova: pixel-based co-localization method development, gold standard preparation
Software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo.
Community predictions of hubs in gene regulatory networks. Abstract Summary Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs. We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub to the DREAM5 challenge data and an independent data set of human gene expression, proved a robust performance of ComHub over all data sets. Lastly, we implemented ComHub to work with both predefined networks and to do standard network inference, which we believe will make it generally applicable
A comparative platform on grapevine and tomato reporting paralog and related ortholog genes identified with an analytical, dedicated, procedure. It provides an update on functional annotations from the two species and it represents an internationally unique platform. It is in expansion in order to include other species, useful to study fruit development.
Tool for interactive analysis of disease comorbidities over large patient datasets.
A GUI based tool for comparison of multiple biological interaction networks. Interaction networks are a convenient way of representing the complex nature of multi-component systems. Examples of such complex systems include biological pathways, social interactions, financial markets, management systems, multiple modules in a programming language, etc. Recognizing the similarities and differences between multiple interaction networks becomes easier when aided by proper visualization tools. we present a GUI based network comparison tool CompNet, which allows to visually compare multiple networks based on node and edge similarities. Additionally, the tool can compare individual networks on the basis of general network properties, node neighborhoods and community similarities. CompNet is expected to be a valuable addition in the field of visual data mining especially for users aiming to visually compare more than two interaction networks at the same time
Problems with homepage (January 6th, 2021) | CompScore is a web application for boosting structure-based virtual screening performance by incorporating docking scoring function components into consensus scoring.
Simple and fast web tool for everyday list comparison, e.g. of genes. Shows the intersection, union, and Jaccard index. Allows easy copying & pasting of comparison results.
Differential analysis of combinatorial protein complexes.
ComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.
CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
Comprehensive database of transposable elements in conifers.
Software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.
machine-learning optimized long-range genome analysis workflow for next-generation sequencing | a machine-learning optimized long-range genome analysis workflow for next-generation sequencing | Current human genome sequencing assays in both clinical and research settings primarily utilize short-read sequencing and apply resequencing pipelines to detect genetic variants
A database portal containing esources that can be used to infer baseline species conditions.
Conterminator is an efficient method to detect incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison. It is free open-source GPLv3-licensed software for Linux and macOS.
Analysis of spatially organized protein expression in high-throughput screens.
Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Plugin to use continuousflex protocols within the Scipion framework. This plugin provides HEMNMA and StructMap protocols and is frequently updated.
Automatic Partial Charge Prediction by Machine Learning. In recent years, machine learning techniques have been widely used in biomedical research to predict unseen data based on models trained on experimentally derived data. In the current study, we used machine learning algorithms to emulate computationally complex predictions in a reverse engineering-like manner and developed ContraDRG, a software that can be used to predict partial charges for small molecules based on PRODRG and Automated Topology Builder (ATB) predictions. Both tools generate molecular topology files, including the partial atomic charge, by using different procedures.
A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network. BACKGROUND:The spatial distributions of different types of cells could reveal a cancer cell's growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key "hallmarks of cancer". However, the process by which pathologists manually recognize and localize all the cells in pathology slides is extremely labor intensive and error prone. METHODS:In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor cell, stromal cell, and lymphocyte classification, and extraction of tumor microenvironment-related features for lung cancer pathology images.
Set-based differential covariance testing for genomics. We describe four different summary statistics, to ensure power and flexibility under various settings, including a new connectivity statistic that is sensitive to changes in overall covariance magnitude
Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal. Welcome to the CorEx portal for gene expression analysis!. This website began as an extension of work applying the CorEx machine learning algorithm to gene expression data from ovarian cancer tumors as presented in this paper.
Transcriptomic database for 14 species of scleractinian corals.
Enables extraction of morphomic markers from CT images by non-technically skilled clinicians.
A genomics, genetics and breeding web portal for cotton research.
Applications for plant phenotyping | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods 'Coverage.exe' - instructions for use | "o To exclude everything but the interior of a quadrilateral, position cursor over its 4 vertices and click F1, F2, F3 & F4 in clockwise order:" "at top left click F1, at top right click F2, at bottom right click F3, at bottom left click F4." "o Click on radio button 1-10 to select colors to take into account (""Include"") and those to dis-count (""Ignore"")." o Not all 10 + 10 selctions need be filled
A mine containing both cowpea genetic and genomic data, courtesy UC-Riverside
Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data. Pathway-based sparse deep neural network for survival analysis. Cox-PASNet is a pathway-based sparse deep neural network for survival analysis
A Python Package for DNA Methylation Analysis. Python package to analyze DNA methylation data. $ pip3 install git+https://github.com/liguowang/cpgtools.git
The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas | Welcome to the CpnClassiPhyR Github Page! | a cpn60 universal target-based classification tool for phytoplasma | Phytoplasmas (‘Candidatus Phytoplasma’), first known as mycoplasma-like organisms, are wall-less, insect vectored bacteria that cause disease in more than a thousand different plant hosts, affecting weedy, ornamental and crop plants worldwide | Following the strategy previously used in the phytoplasma classification scheme based on the 16S rRNA gene, we developed a complementary, coherent system to classify phytoplasmas based on RFLP analysis of cpn60 UT sequences with seven endonucleases
Reference-Based Decompression in Node and the Browser.
Software to generate CRISPR guide RNAs against genomes annotated with individual variation.
Comprehensive circular RNA resource for crops in response to abiotic stress.
GUI application for viewing and handling Manhattan Plots. The user can zoom, select and crop Manhattan Plots and generate output both in the graphical and numerical format.
estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies | General descripiton of Crossmapper | Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific expression studies, and can be extended for the use in large sequencing facilities for resource optimization
A wisdom of the crowd-based Gene Ontology annotation tool | Abstract Motivation Protein function prediction tools vary widely in their methodologies, resulting in different sets of GO terms being correctly predicted. Ideally, multiple tools are combined to achieve a higher recall of GO terms while increasing precision. Results CrowdGO combines input predictions from any number of tools and combines them based on the Gene Ontology Directed Acyclic Graph. Using each GO terms information content, the semantic similarity between GO predictions of different tools, and a Support Vector Machine model, it achieves improved precision and recall compared to each of the tools separately (Figure 1). Availability CrowdGO can be found at https: gitlab.com mreijnders CrowdGO
Tracking Health Trends Using Public Social Media Data and Crowdsourcing.
Secure encryption tool for genomic data, namely in Fasta, Fastq, VCF, SAM and BAM formats, which is also capable of reducing the storage size of Fasta and Fastq files.
Live analysis and reconstruction of single-particle cryo-electron microscopy data with CryoFLARE. CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data. The FMI Live Analysis and Reconstruction Engine. Live analysis of Cryo EM data made easy. Import data from EPU or SerialEM
Software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source.
Automated computation of lattice energies of organic crystals exploiting the many-body expansion to achieve dual-level parallelism. Set of scripts to automate the calculation of crystal lattice energies. Automated calculation of crystal lattice energies with the many-body expansion. CrystaLattE has an interface with the quantum chemistry package PSI4. To run, the code requires a crystallographic information file containing structural information of the crystal and an input file specifying execution details. Work continues in the creation of a CrystaLattE pip package. So, for the moment, the instructions to download and install CrystaLattE and to create a conda environment that includes PSI4 are presented below. CyrstaLattE is a software that automates the computation of crystal lattice energies using the many-body cluster expansion
A cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq. Cumulus WDL workflows and Dockerfiles. Interactive single cell visualization in the cloud or on your desktop. Cumulus WDL workflows and Dockerfiles — Cumulus documentation. Clone the cirrocumulus repository:. Google Cloud Platform (GCP) Deployment Instructions. Free document hosting provided by Read the Docs
A Database of Predicted T-cell Epitopes from Overly Expressed Proteins in Metastatic Cutaneous Melanoma | Browse and download predicted melanoma epitopes with high expected clinical efficacy in anti-cancer immunotherapy | This page acts as a gateway to the Curatopes Melanoma database
Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model.
CyGenexpi is a Cytoscape plugin for validating/inferring genetic networks from time series expression data. It is based on a ordinary differential equation (ODE) model of gene regulation.
Ministry of Education, Youth and Sports of the Czech Republic
Differential discovery in high-throughput high-dimensional cytometry datasets.
A flexible solution for network extension in Cytoscape | The CyTargetLinker app extends biological networks with regulatory interactions, for example miRNA-target, TF-target or drug-target interactions | CyTargetLinker website and tutorials | CyTargetLinker - Extend your biological networks in Cytoscape
De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. CycloNovo: Algorithm for de novo cyclopeptide analysis of high-resolution tandem mass spectra. CycloNovo is a new algorithm that identifies spectra generated from cyclopeptides in large mass spectrometry datasets. CycloNovo can also de novo sequence the cyclopeptides represented by identified cyclospectra
Package to tackle cell cycle. It provides methods to recover cell cycle information and remove cell cycle factor from the scRNA-seq data.
A web-based tool to convert karyotypes to genomic coordinates | Sequence-Cytogenetic Bulk Conversion | Bulk Sequence - Cytogenetic Conversion Service | Use this page to get cytogenetic locations for features or sequence locations, or get sequence locations for cytogenetic locations | Organism: Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus
CytoGenetic Pattern Sleuth (CytoGPS) - web-enabled karyotype analysis tool for cytogenetics.
Institute for Informatics, Washington University School of Medicine
A Normalization Algorithm for Cytometry Data. A R library to normalize cytometry data.
Web-interface for simulating multi-dimensional cell imaging.
Single-cell transcriptional diversity is a hallmark of developmental potential
A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging | Microscopy Image Cytometry Toolkit | Cytokit is a collection of tools for quantifying and analyzing properties of individual cells in large fluorescent microscopy datasets with a focus on those generated from multiplexed staining protocols. This includes a GPU-accelerated image processing pipeline (via TensorFlow), CLI tools for batch processing of experimental replicates (often requiring conditional configuration, as things tend go wrong when capturing hundreds of thousands of microscope images over a period of hours or days), and visualization UIs (either Cytokit Explorer or CellProfiler Analyst) | Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google | Fortsæt til Google Cloud Platform | Skriv den tekst, du hører eller ser
Tool for collaborative multimodal imaging and our latest software developments to support next-generation digital pathology bridged to molecular investigations.
Cytoscape Automation combines Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio.
A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression
Identification of differentially-expressed genes in single-cell RNA sequencing data.
a data driven dynamic network construction method to infer gene regulatory networks. Gene regulatory network;Dynamic networks construction;Regression;DREAM challenge. D3GRN is a Data Driven Dynamic network construction method to infer Gene Regulatory Networks
DAMEfinder (Differential Allele-specific MEthylation finder) is an R-package that detects allele-specific methylation (ASM) in a cohort of samples, and detects regions of differential ASM within groups of interest, based on Bisulfite-sequencing files.
An open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Identification of pathogenic microorganisms in diagnostic samples. DAMIAN provides capabilities to detect known and novel pathogens in RNA and DNA samples of various sources. It integrates all required processing steps, ranging from the quality control of sequencing reads to the generation of comprehensive reports. The method works for any host organism
The Differential ATAC-seq Toolkit (DAStk) is a set of command-line tools to aid analyzing differential ATAC-seq data. By leveraging changes in accessible chromatin, we can detect significant changes in transcription factor (TF) activity. This is a simple but powerful tool for cellular perturbation analysis. In fact, the applications of DAStk are not necessarily limited to ATAC-seq, but can extend to comparing any pair of bedGraphs containing regions of interest, e.g. transcription regulatory elements (TRE) from nascent transcription assays like PRO-seq, or others like ChIP-seq peaks. To aid downstream analysis, DAStk also includes a graph that combines all human proteins in Uniprot, with their respective annotations, and all human Reactome data on biological pathways, biochemical reactions, and complex formation. This allows the user to query for existing knowledge about what aspects of the significantly changing TFs are shared among two or more of them.
> HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'hyperspectral', 'vegetation', 'planation', 'Cunninghamia' | UAV-Based High-Throughput Approach for Fast Growing Cunninghamia lanceolata (Lamb.) Cultivar Screening by Machine Learning | Accurate measurements of tree height and diameter at breast height (DBH) in forests to evaluate the growth rate of cultivars is still a significant challenge, even when using LiDAR and 3-D modeling. We propose an integrated pipeline methodology to measure the biomass of different tree cultivars in plantation forests with high crown density which that combines unmanned aerial vehicles (UAVs), hyperspectral image sensors, and data processing algorithms using machine learning. Using a planation of Cunninghamia lanceolate, commonly known as Chinese fir, in Fujian, China, images were collected using a hyperspectral camera and orthorectified in HiSpectral Stitcher
The Design Build Test Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and bio-based products.
Deep count autoencoder for denoising scRNA-seq data.
Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture.
Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.
Drug-drug interaction prediction using PASS | DDI-Pred: web-service for drug-drug interaction prediction
Data dependent-independent acquisition proteomics (DDIA) is a pipeline for combining and analysing Data dependent acquisition (DDA) and data independent acquisition (DIA) proteomics data.
Data dependent-independent acquisition proteomics (DDIA)
Bayesian non-parametric survival regression for optimizing precision dosing of intravenous busulfan in allogeneic stem cell transplantation | Allogeneic stem cell transplantation (allo-SCT) is now part of standard of care for acute leukemia (AL). To reduce toxicity of the pre-transplant conditioning regimen, intravenous busulfan is usually used as a preparative regimen for AL patients undergoing allo-SCT. Systemic busulfan exposure, characterized by the area under the plasma concentration versus time curve (AUC), is strongly associated with clinical outcome. An AUC that is too high is associated with severe toxicities, while an AUC that is too low carries increased risks of disease recurrence and failure to engraft. Consequently, an optimal AUC interval needs to be determined for therapeutic use
Multiplatform biomarker identification using a data-driven approach enables single-sample classification.
DDT (Drug Discovery Tool) - graphics user interface for Docking and Molecular Dynamics analysis
Distributed dual vigilance fuzzy adaptive resonance theory learns online, retrieves arbitrarily-shaped clusters, and mitigates order dependence. Dual Vigilance Fuzzy ART - Companion MATLAB Code. Distributed Dual Vigilance Fuzzy ART - Companion MATLAB Code.
Web-based platform for secure deposition, analysis, and sharing of plausibly pathogenic genomic variants from well-phenotyped patients suffering from genetic disorders.
Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout
A convolutional neural network based method for super-enhancer prediction. data and material In this folder, we include all the material and data used in the DEEPSEN
Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.
Dengue Virus identification from shotgun and targeted metagenomics.
Bioinformatics, Molecular Microbiology and Infection Unit
Software for Computational de Novo Design of Organic and Inorganic Molecules | DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind | DENOPTIM (De Novo OPTimization of In/organic Molecules) is a software meant for de novo design and virtual screening of functional compounds. In practice, DENOPTIM is meant for building chemical entities by assembling building blocks (i.e., fragments), processing each chemical entity as to produce its figure of merit (i.e., fitness), and designing new entities based on the properties of entities generated before.
Densitometry software written for Mathlab.
Sequence-based predictor of deleteriousness of amino acid variants in human proteins
Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.
Intrinsic disorder and disorder function prediction server. Predictors of disordered regions and their molecular functions - web server from Biomine lab. DEPICTER : DisorderEd PredictIon CenTER
DEPOD - the human DEPhOsphorylation Database, is a manually curated database collecting human phosphatases, their experimentally verified substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates.
Human Dephosphorylation Database (DEPOD)
Multi-domain tuberculosis data analysis resource.
DESSO is a deep learning-based framework that can be used to accurately identify both sequence and shape regulatory motifs from the human genome.
R package for accurate small RNA profiling based on differential expression of unique sequences.
DEWE is a software tool to perform genetic differential expression analysis of RNA-Seq data. DEWE offers built-in, easy-to-configure workflows that facilitate the execution of DE analyses. Currently, DEWE provides two differential expression analysis workflows: HISAT2, StringTie and R libraries (Ballgown and edgeR) and Bowtie2, StringTie and R libraries (Ballgown and edgeR).
DEWE: Differential Expression Workflow Executor
R package for aggregation and visualization of differential expression data.
DIA-DB is a web server for the prediction of diabetes drugs that uses two different approaches; a) comparison by similarity with a curated database of anti-diabetic drugs and experimental compounds, and b) inverse virtual screening of the input molecules chosen by the users against a set of protein targets identified as key elements in diabetes.
Neural networks and interference correction enable deep proteome coverage in high throughput. DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data. None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)
DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.
Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Remove debris-contaminated droplets from single-cell based data
Debris Identification using Expectation Maximization (DIEM)
predicting isoform functions from sequences and expression profiles via deep learning | Deep learning based prediction of IsoForm FUnctions from Sequences and Expression | DIFFUSE is a deep learning based method for predicting isoform functions by integrating the data of isoform sequences, domains and expression profiles.
Integration of immunome with disease gene network reveals pleiotropy and novel drug repurposing targets. Abstract Immune system is crucial for the development and progression of immune-mediated and non-immune mediated complex diseases. Studies have shown that multiple complex diseases are associated with several immunologically relevant genes. Despite such growing evidence, the effect of disease associated genes on immune functions has not been well explored. Here, we curated the largest immunome (transcriptome profiles of 40 different immune cells) and integrated it with disease gene networks and drug-gene database, to generate a Disease-gene IMmune cell Expression network (DIME). Is a Shiny app.
Disease-gene Immune cell Expression (DIME)
Exploring and visualizing possible GPCR dimer.
DIPY is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments
RNA contact predictions by integrating structural patterns. It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function.
Direct Information Reweighted by Contact Templates (DIRECT)
DISCo-microbe is an easy-to-use command-line program, for creation of diverse communities of organisms that can be distinguished through next-generation sequencing technology
Design of an Identifiable Synthetic Community of Microbes (DISCo-microbe)
A disease-focused resource that uses the causal interaction information annotated in SIGNOR and the protein interaction data in mentha to generate and explore protein interaction networks linking disease genes.
Molecular Genetic Group, University of Rome "Tor Vergata", Rome, Italy
Disorder predictor selection at the protein level. DISOselect accepts either single or multiple protein sequences. The input is limited to 1000 protein sequences. The user should submit the protein sequence(s) in FASTA format
The complete analysis of deep sequencing data from the DISSEQT paper is available at the collaborative science platform Synapse here. In order to view and download files you must create a Synapse account. (The scripts are also available in the examples folder for reference, but note that you will need a Synapse account to access the data files.)
Distribution-based modeling of Sequence space time dynamics (DISSEQT)
A tool for detecting bipartite motifs by considering base interdependencies | A DNA sequence motif finding program | DIpartite is a tool for detecting bipartite motif based on dinucleotide weight matrix | DIpartite predicts transcription factor binding sites (TFBSs) based on PWM or DWM. Bipartite motif is defined as two conserved blocks separated by variable gaps
Modelling the niches of wild and domesticated Ungulate species using deep learning | Abstract Knowledge of global biodiversity remains limited by geographic and taxonomic sampling biases. The scarcity of species data restricts our understanding of the underlying environmental factors shaping distributions, and the ability to draw comparisons among species. Species distribution models (SDMs) were developed in the early 2000s to address this issue. Although SDMs based on single layered Neural Networks have been experimented with in the past, these performed poorly. However, the past two decades have seen a strong increase in the use of Deep Learning (DL) approaches, such as Deep Neural Networks (DNNs). Despite the large improvement in predictive capacity DNNs provide over shallow networks, to our knowledge these have not yet been applied to SDM
An improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state | DLIGAND2 is a knowledge-based method to predict protein-ligand binding affinity based on a distance-scaled, finite, ideal-gas reference (DFIRE) state
DLITE Uses Cell-Cell Interface Movement to Better Infer Cell-Cell Tensions. Cell shapes and connectivities evolve over time as the colony changes shape or embryos develop. Shapes of intercellular interfaces are closely coupled with the forces resulting from actomyosin interactions, membrane tension, or cell-cell adhesions. Although it is possible to computationally infer cell-cell forces from a mechanical model of collective cell behavior, doing so for temporally evolving forces in a manner robust to digitization difficulties is challenging. Here, we introduce a method for dynamic local intercellular tension estimation (DLITE) that infers such evolution in temporal force with less sensitivity to digitization ambiguities or errors. This method builds upon previous work on single time points (cellular force-inference toolkit). We validate our method using synthetic geometries.
DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis | Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture. Results Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering
Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints | Extending genome-scale de novo protein modelling coverage using iterative deep learning-based prediction of structural constraints | See our paper in Nature Communications for more. Please cite the paper if you use DMPfold | You can also run DMPfold via the PSIPRED web server. This is a good way to get models for a few sequences, but if you want to run DMPfold on many sequences we strongly recommend you run it locally. The server version of DMPfold has restrictions on run time and uses parameters that give faster runs, so should not be used to benchmark DMPfold
A low-cost, automated DNA assembly platform for synthetic biology. Material for DNA assembly using BASIC on OpenTrons (DNA-BOT). Users looking to implement the DNA-BOT workflow are encouraged to consult the instructions. If you are looking to contribute to this project, please raise an issue or pull request. Otherwise, feel free to reach out to hainesm6
R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments.
DNA Chisel - A versatile sequence optimizer. DNA Chisel is a Python library for optimizing DNA sequences with respect to a set of constraints and optimization objectives. It comes with over 15 classes of sequence specifications which can be composed to, for instance, codon-optimize genes, meet the constraints of a commercial DNA provider, avoid homologies between sequences, tune GC content, or all of this at once!
An R based visualizer for network analysis of chromatin interaction data | A Shiny App for visualizing genomic data | Welcome to the github repository for DNA Rchitect, a Shiny App for visualizing genomic data | DNA Rchitect is a Shiny App for visualizing genomic data (HiC, mRNA, ChIP, ATAC etc) in bed, bedgraph, and bedpe formats. HiC (bedpe format) data is visualized with both bezier curves coupled with network statistics and graphs (using an R port of igraph). Shiny Apps are interactive web applications built with R using the shiny R package. Shiny apps are built with R wrappers for HTML, CSS, and JS to run R code in a web browser through a dynamic and reactive user interface that is powered by an underlying NodeJS engine. These apps can be locally hosted from an R session or hosted in the cloud through a ShinyServer
A chronological age predictor based on DNA methylation. Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing.
An expanded database and web-based tool for structural analysis of DNA-protein complexes. A Database and Web Tool for Structural Analysis of DNA-Protein Complexes. DNAproDB automatically lays out nucleotide and residue interactions maps elegantly. Use the form below to search DNAproDB. DNAproDB is processing pipeline, web server and database which aims to assist researchers in performing structural analysis of DNA-protein complexes. DNAproDB is a database, structure processing pipeline and web-based visualization tool which makes structural analysis of DNA-protein complexes easy
Personal computer compatible NGS analysis, annotation and visualisation.
KCL IoPPN: NIHR BRC-MH Bioinformatics Group
Analysis of several key factors influencing deep learning-based inter-residue contact prediction | Deep convolutional neural networks for protein contact map prediction | Web-server and datasets at http://sysbio.rnet.missouri.edu/dncon2/ | We tested in Ubuntu becasue the tool 'FreeContact' is easier to install in a Debian system. If you would like to install DNCON2 in some other operating systems, first test if 'FreeContact' can be installed in it. If, for some reason, you do not have a Ubuntu machine, and cannot install FreeContact, you can still use DNCON2. With just a few code updates you can skip using the FreeContact tool. You will get slightly less precise results
differential network local consistency analysis. Using Local Moran's I for detection of differential network local consistency
DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan-meQTL and HACER databases. Overall, DNMIVD mainly contains the following important resources:. DNA methylation is strongly related to cancer, currently, no resource integratively provides the DNA methylation based diagnostic and prognostic models, e-mQTL (expression–methylation quantitative trait loci), pathway-meQTL (pathway activity-methylation quantitative trait loci), differentially variable and differentially methylated CpGs, survival analysis, as well as functional epigenetic modules for different cancers, which are valuable information for researchers to explore DNA methylation profile from different aspects in cancer
DNA Methylation Interactive Visualization Database (DNMIVD)
Improved ab initio protein secondary structure prediction using advanced deep learning architectures.
Data-Driven Optimization of Mass Spectrometry Methods.
Domain-based transcriptome and proteome quality assessment.
Database Of Reconstructed MetAbolic Networks. We apologize for the inconvenience, but it appears that an internal error has occurred in the Dorman system. If this is the first time you have encountered this message, please use the Back button on your browser and try your last action again. If you are receiving this message repeatedly, please send an e-mail to (aec51 [at] case [dot] edu) with a detailed description of what you were doing when this message occurred so that we may try and resolve this issue. Thank you!
DMD Open-access Variant Explorer (DOVE) - web-based aid for DMD variant interpretation which additionally reports variant-specific predicted molecular eligibility for therapy.
DPre: Computational identification of differentiation bias and genes underlaying cell type conversions. DPre is a bioinformatic tool that enables the user to explore cell type conversion/ differentiation experiments. DPre may take the expression or the differentially regulated genes of the samples to rate transcriptional similarity with a reference dataset, the targets.
DQueST is a web applciation for reducing information overload for trial seekers using dynamic questionnaires.
Thermodynamically Consistent Estimation of Gibbs Free Energy from Data. The DR-thermo algorithm can be used to curate experimental thermodynamic data from different sources to generate reliable data-banks such that all measurements are modified to be thermodynamically consistent and any missing reaction or formation Gibbs energies can be predicted either directly or using group contributions.
updated data repository of antimicrobial peptides | Browse, Create and Mining Antimicrobial Peptides | 157 new entries are added to in DRAMP. 33 entries are natural AMPs including 31 animal AMPs and 2 plant AMPs. 124 entries are synthetic AMPs | A brief introduction to DRAMP database | DRAMP database is an information portal to biological active peptides. Peptides in this database come from three sources : Public databases (Swiss-Prot, PDB, PubMed), Clinical antimicrobial peptides (preclinical and clinical) and Patents | DRAMP(Data repository of antimicrobial peptides) is an open-access and manually curated database harboring diverse annotations of AMPs including sequences, structures, activities, physicochemical, patent, clinical and reference information | We are responsible for maintaining the website daily and updating the database regularly
A tool to Detect and Re-Align Mixed-up Samples based on multi-omics data. Need at least three types of -omics data to run this tool.
A user-friendly program for the analyses of radiation-induced biological responses utilizing established deterministic models at cell population and organ scales | PURPOSE:To develop a user-friendly program for biological modeling to analyze radiation-induced responses at the scales of the cell population and organ. METHODS:The program offers five established cell population surviving fraction (SF) models to estimate the SF and the relative biological effectiveness (RBE) from clonogenic assay data, and two established models to calculate the normal tissue complication probability (NTCP) and tumor control probability (TCP) from radiation treatment plans. Users can also verify the results with multiple types of quantitative analyses and graphical representation tools
DRIP-seq optimized peak annotator | DROPA is a fully customizable peak-annotation tool optimized for DRIP-seq peaks, which allows a finest gene annotation based on gene expression information. Its output can easily be integrated into pipelines to perform downstream analyses, while useful and informative summary plots and statistical enrichment tests can be produced. Although it is developed for R-loop mapping, DROPA can also be used to annotate other genomic sequencing data as in the case of Histone marks IP-seq, DNAse-seq, FAIRE-seq
DRUDIT, Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets.
DNA Readout Viewer is a free on-line service providing novel and intuitive visualisation modes for displaying sequence specific DNA-protein interactions.
Tool for the analysis of discrete data from multi-well plate assays.
Drug-Set Enrichment Analysis (DSEA) - computational method based on drug-induced gene expression profiles, which is able to identify the molecular pathways that are targeted by most of the drugs in the set.
A collection of databases, tools and web servers for structural biology.
de novo transcriptome assembly by using simplified suffix trees. DTA-SiST: a novel radical framework for de novo transcriptome assembly based on suffix trees. The RNA-seq has revolutionized our ability to transcripts reconstruction
How Precise Are Our Quantitative Structure-Activity Relationship Derived Predictions for New Query Chemicals? | QSPR Modeling of the Refractive Index for Diverse Polymers Using 2D Descriptors | QSAR Model Development Using DTC Lab. Software Tools | DTC lab - Software Tools - DTC lab is working in the field of molecular modelling mainly using different QSAR methodologies in various diverse area such as drug designing, toxicity, anti-oxidant studies etc | Drug Theoretics and Cheminformatics Laboratory | *Genetic Algorithm(MAE-based Fitness Function) | *Intelligent Consensus Predictor
A cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Drug-target interactions (DTIs) play a crucial role in target-based drug discovery and development
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data | MOTIVATION:RNA molecules can undergo complex structural dynamics, especially during transcription, which influence their biological functions. Recently developed high-throughput chemical probing experiments that study RNA cotranscriptional folding generate nucleotide-resolution 'reactivities' for each length of a growing nascent RNA that reflect structural dynamics. However, the manual annotation and qualitative interpretation of reactivity across these large datasets can be nuanced, laborious, and difficult for new practitioners. We developed a quantitative and systematic approach to automatically detect RNA folding events from these datasets to reduce human bias error, standardize event discovery, and generate hypotheses about RNA folding trajectories for further analysis and experimental validation
Algorithm based on the distance variation allowed by secondary structure (DVASS), which ranks restraints according to their importance to RNA tertiary structure prediction.
Web server for the (re-)modeling of loops in homology models. It follows a data-based approach, identifying loop candidates by mining the complete set of experimental structures available in the Protein Data Bank.
Fast and accurate genomic distances using HyperLogLog. dashing sketches and computes distances between fasta and fastq data.
A graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography. DatView displays plots of tabular data and syncs selections across plots. It was initially developed for serial crystallography data analysis with CrystFEL output files and includes a frame viewer for displaying 1D and 2D data from HDF5/CXI files.
DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters. This tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.
DAISY is an open-source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement.
The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science.
Automated Gene Data Integration with Databio | Automated data transformation for bioinformatics | Automated data integration tools | A simple Gene ID mapping service for Bioinformatics. Upload a gene-oriented data set, we'll automatically detect the identifiers in use, and offer to convert them to match other providers in just a few clicks | A web portal that does automated identifier translation for bioinformatics
Workflow and package for delivering successive versions of 'evolving data' directly into R.
Generative cooperative networks for joint surgical smoke detection and removal in order to remove surgical smoke and improve the quality of intra-operative imaging and reduce hazards in image-guided surgery. This is a highly desirable post-process for many clinical applications.
Deep Generative Models for 3D Compound Design. This repository contains our implementation of Deep Generative Models for 3D Compound Design (DeLinker). We provide two settings of DeLinker. The first setting generates linkers with the same number of atoms as the reference molecule. The second setting generates linkers with a specified number of atoms
Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network.
Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics | DecoMetDIA was developed to process SWATH-MS based data for metabolomics.
Tool for detecting contaminating organisms in human unmapped sequences.
On-demand decoy glycopeptide generator that can produce a high volume of decoys with low mass differences.
Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome. Tissue and Cancer Type Identification using Deep Neural Networks. Authors: Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi
Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning. DeepZ Plugin Release_v1.3 – Google Drev. Three-dimensional propagation and time-reversal of fluorescence images. Neural network learns fluorescence wave propagation and time-reversal to propagate a 2D fluorescence image onto user-defined 3D surfaces, enabling 3D imaging of fluorescent samples using a single 2D image, without mechanical scanning, additional hardware, or a trade-off of resolution or speed. For details, refer to our publication "Three-dimensional propagation and time-reversal of fluorescence images" [1]. (Video below: 3D reconstruction of a C. elegans using Deep-Z inference)
Attention mechanism-based deep learning pan-specific model for interpretable MHC-I peptide binding prediction. Deep learning prediction of MHC-I peptide binding with attention mechanism. Please download the full folder of "DeepAttentionPan_Code" to run the programs, or you may need to configure some directory paths. Usage: the codes can be used to train our models, output results on the testing set, output positional attention weights for chosen group of peptides. And they also can be used to test on single hla-peptide pair input from the command line.
A deep learning genome-mining strategy for biosynthetic gene cluster prediction | BGC Detection and Classification Using Deep Learning | DeepBGC: Biosynthetic Gene Cluster detection and classification | DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. DeepBGC employs a Bidirectional Long Short-Term Memory Recurrent Neural Network and a word2vec-like vector embedding of Pfam protein domains. Product class and activity of detected BGCs is predicted using a Random Forest classifier
A deep learning based method for estimating effective protein-ligand affinity.
A novel deep learning-based framework for cancer molecular subtype classification | a deep learning-based framework for cancer classification | After training, now you can use your DeepCC model to classify new sample(s). DeepCC can classify samples in a data set, as well as individual samples. The input data should be in the same format as above gene expression profile(s)
A deep-learning-based Python toolbox for inferring calcium imaging neuronal activity based on movie visualization. Abstract Two-photon calcium imaging is now widely used to indirectly infer multi neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the analysis of highly active neurons in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development. Indeed, the reliable inference of single cell activity is not achieved by the latest analytical tools that often lack proper benchmark measurements. To meet this challenge, we first developed a graphical user interface allowing for a precise manual detection of all calcium transients from detected neurons based on the visualization of the calcium imaging movie. Then, we analyzed our movies using a convolutional neural network with an attention process and a bidirectional long-short term memory network
Predicting the effect of mutations on protein-RNA binding with Deep Learning | This repository contains all DeepCLIP Python code | A context-aware neural network for modeling and predicting protein binding to nucleic acids using only sequence input | DeepCLIP is a neural network with shallow convolutional layers connected to a bidirectional LSTM layer
Deep Learning-Based Approach to Predict Gene Regulating Effects of Small Molecules | MOTIVATION:Recent advances in the areas of bioinformatics and chemogenomics are poised to accelerate the discovery of small-molecule regulators of cell development. Combining large genomics and molecular data sources with powerful deep learning techniques has the potential to revolutionize predictive biology. In this study, we present Deep Compound Profiler (DeepCOP), a deep learning based model that can predict gene regulating effects of low-molecular weight compounds. This model can be used for direct identification of a drug candidate causing a desired gene expression response, without utilizing any information on its interactions with protein target(s)
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer | SWISS-MODEL is a fully automated protein structure homology-modelling server. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide | DeepCalpain is a web server developed for understanding the enzyme-specific cleavage for calpains including m-calpain and μ-calpain
R package for deep learning of the back-splicing code for circular RNA formation.
A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites | Proteases are enzymes that cleave target substrate proteins by catalyzing the hydrolysis of peptide bonds between specific amino acids. While the functional proteolysis regulated by proteases plays a central role in the 'life and death' process of proteins, many of the corresponding substrates and their cleavage sites were not found yet. Availability of accurate predictors of the substrates and cleavage sites would facilitate understanding of proteases' functions and physiological roles. Deep learning is a promising approach for the development of accurate predictors of substrate cleavage events. RESULTS:We propose DeepCleave, the first deep learning-based predictor of protease-specific substrates and cleavage sites. DeepCleave uses protein substrate sequence data as input and employs convolutional neural networks with transfer learning to train accurate predictive models
Deep Neural Networks for Identification of DNA-binding Proteins.
A hybrid convolutional and recurrent neural network for compressing compression human mitochondrial genomes. DeepDNA, a novel unified model called deepDNA that combines the convolutional neural network (CNN) with the long short-term memory network (LSTM) for compressing human mitochondrial genome sequences. The experiment has shown that out method deepDNA is able to learn sequence local features through a convolutional layer, and to learn higher level representations of long-term sequences dependencies through a long short-term memory network (LSTM) layer. We evaluated the learned genome sequences representations model on human mitochondrial genome sequences compressing tasks and achieved a satisfactory result.
A new genome annotation predictor for identifying DNA binding proteins and RNA binding proteins using Convolutional Neural Network and Long Short-Term Memory. In this study, we proposed a new computational predictor called DeepDRBP-2L for identifying DBPs, RBPs and DRBPs. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two kinds of crucial proteins, which are involved in various cellule activities and associated with many diseases
A deep learning framework for identifying essential proteins. DeepEP is a deep learning framework to automatically predict essential proteins using PPI network and gene expression data.
Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning | Core code for the DeepHF prediction tool | SpCas9 & Base Editor Efficiency Prediction | This tool provides guide designs for Wild-type SpCas9, two highly specific Cas9 mutants(eSpCas9 (1.1) and SpCas9-HF1) and base editors (AncBE4max, ABEmax)
A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. DeepHLApan Server – A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. The stand-alone software is available in github
A user-friendly plugin to run deep learning models in ImageJ. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained deep learning models in ImageJ and Fiji. The plugin bridges the gap between deep learning and standard life-science applications. DeepImageJ runs image-to-image operations on a standard CPU-based computer and does not require any deep learning expertise.
An accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data. An accurate and efficient deep learning method for single-cell RNA-seq data imputation.
A general framework for interpreting wide-band neural activity. DeepInsight is a toolbox for the analysis and interpretation of wide-band neural activity and can be applied on unsorted neural data. This means the traditional step of spike-sorting can be omitted and the raw data can be used directly as input, providing a more objective way of measuring decoding performance.
An accurate prediction of MHC class I ligands using peptide embedding | The 5-fold cross-validation split used in the paper can be downloaded from here. The DeepLigand model provided in this repository is trained on all the five folds combined
Evaluating the quality of metagenomic assemblies
Deep learning for Metagenome Assembly Error Detection (DeepMAsED)
Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method | Deciphering the Hidden Patterns on Transcriptome Profiles with a Deep Learning Fashion
Constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. deep multiple sequence alignment generation. DeepMSA is a composite approach to generate high quality multiple sequence alignment with large alignment depth and diverse sequence sources by merging sequences from whole-genome sequence databases (Uniclust30 and UniRef90) and from metagenome database (Metaclust). Large-scale benchmark data show that DeepMSA profiles consistently improves contact prediction, secondary structure prediction, and threading over default HHblits or PSI-BLAST profiles
The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry (MS), also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences
Deep representation learning for disease prediction based on microbiome data. DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.
Fast and accurate microRNA search using CNN.
Predictor of protein sub-mitochondrial localization based on deep learning
Deep neural network based polyadenylation site analysis.
Protein-protein interaction site prediction through combining local and global features with deep neural networks. PPI sites prediction through combining local and global features with deep neural networks. DeepPPISP: Protein-protein interaction sites prediction through combining local and global features with deep neural networks. You can run the train.py file to train DeepPPISP and use the predcit.py file to see the predictive resluts. If you want to tune some hyper-parameters, you can change some values of hyper-parameters in config.py in utils folder. The PSSMs, raw sequences, secondary structures and labels are given in data_cache folder.
Phenotype-based variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data.
DeepPheno is a method for predicting gene-phenotype (HPO classes) associations from gene functional annotations (GO classes). Predicting single gene knockout phenotypes.
A software toolkit for fast and robust animal pose estimation using deep learning. DeepPoseKit is a software toolkit with a high-level API for 2D pose estimation of user-defined keypoints using deep learning—written in Python and built using Tensorflow and Keras.
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, more than 160 RNA modifications have been discovered; therefore, accurate identification of RNA-modification sites is fundamental for a better understanding of RNA-mediated biological functions and mechanisms. However, due to limitations in experimental methods, systematic identification of different types of RNA-modification sites remains a major challenge. Recently, more than 20 computational methods have been developed to identify RNA-modification sites in tandem with high-throughput experimental methods, with most of these capable of predicting only single types of RNA-modification sites
DeepRank is a general, configurable deep learning framework for data mining protein-protein interactions (PPIs) using 3D convolutional neural networks (CNNs). DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models.
DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Deepginsen is a lantipeptide that is genomically encoded distantly from its modification enzymes and discovered directly as a result of DeepRiPP within the genome and metabolome of Flavobacterium ginsengiterrae JCM 17337.
A accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network. Calling deletions using deep convolutional neural. DeepSV, an approach based on deep learning for calling long deletions from sequence reads.DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project. Our work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs
A deep learning-based screening web server for accelerating drug discovery. DeepScreening is a useful platform to help drug researchers do virtual screening conveniently and fast through deep learning. DeepScreening is a user-friendly web server for constructing deep learning models using public dataset or user provided dataset, which would help biologist and chemist virtual screening the chemical probes or drugs for a specific target of interest.
An interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction. A sequence-based pan model for peptide-MHC II binding affinity prediction.
Estimating isoform-level ribosome abundance and distribution with Ribo-seq data. For the estimation of Isoform-Level Ribosome Abundance and Distribution Accurately which needs Ribo-seq data only.
A Deep Learning Framework for Drug Side Effect Prediction. Drug failures due to unforeseen adverse effects at clinical trials pose health risks for the participants and lead to substantial financial losses
A deep learning-based model with unparalleled generalization performance | We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available at http: deepcrispr.info DeepCas9
Deep learning based splice junction sequence classifier.
Quantifying Neurodegenerative Progression With DeepSymNet. A data-driven method based that identifies longitudinal changes in 3D structural MRI data without relying on prior brain regions of interest, an atlas, or non-linear registration pipelines.
A machine learning approach to gene functional enrichment. Deep functional synthesis: a machine learning approach to gene function enrichment. Deep Functional Synthesis (DeepSyn) is function annotation tool that moves beyond gene function databases to dynamically infer the functions of a gene set from its associated network of literature and data, conditioned on the disease and drug context of the current experiment.
Deep Learning Approach to Identifying Breast Cancer Subtypes Using High-Dimensional Genomic Data.
Deep Learning Framework for Prediction of Ubiquitination Sites in Proteins.
A Deep Learning Approach for Virtual Screening of Big Chemical Datasets. Drug discovery is an extensive and rigorous process that requires up to 2 billion dollars of investments and more than ten years of research and development to bring a molecule “from bench to a bedside”. While virtual screening can significantly enhance drug discovery workflow, it ultimately lags the current rate of expansion of chemical databases that already incorporate billions of purchasable compounds. This surge of available small molecules presents great opportunities for drug discovery but also demands for faster virtual screening methods and protocols. In order to address this challenge, we herein introduce Deep Docking ( D 2 ) - a novel deep learning-based approach which is suited for docking billions of molecular structures.
Classifying Alternative Splicing Events Using Deep Learning | Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as "Splicing Codes". The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5'ss, alternative 3'ss, and constitutively spliced exons based only on the sequence of the exon junctions
Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. DeltaNeTS+ is a major improvement to our previous method DeltaNet. DeltaNeTS+ is a method for inferring direct gene targets of drug compounds and diseases from steady-state and/or time-series transcriptional profiles. DeltaNeTS+ incorporates gene regulatory information (if avaialbe) during the inference. DeltaNeTS+ generates a perturbation score for each gene in every sample. The score magnitude reflects the confidence that the transcription process of this gene was directly affected by the external stimuli. The score sign indicates the nature of the perturbation: positive for gene induction, negative for gene repression
Automated longevity and risk factor analysis in dental patient care | BACKGROUND AND OBJECTIVE:During routine patient care practitioners have to document several aspects. However, currently it is difficult to methodically analyze the longevity of therapeutic concepts in dental private practice. Thus, the aim of the present paper was to introduce a software (Dentareport) to compare the success of different treatment options and to identify risk factors for failures in dental patient care. METHODS:Dentareport has a digital interface to automatically collect data of electronic patient files of practice management programs. By using computer-aided routines descriptive analyses of the treatments can be visualized. Dentareport also visually displays a bivariate risk factor analysis of treatment options
Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | The Cancer Dependency Map Project at Broad Institute | A resource of data and computational tools to expose the vulnerabilities of cancer, and for identifying targets for therapeutic development and designing strategies to optimize patient responses | Explore the Cancer Dependency Map | The goal of the Dependency Map (DepMap) portal is to enable the research community to make discoveries related to cancer vulnerabilities by providing free and timely access to the datasets, visualizations, and analysis tools that are being used by the Cancer Dependency Map Project at the Broad Institute
Tool to determine the optimal read depth for reduced-representation sequencing.
Tool for designing primers that yields amplicons with distinct signatures.
A web server for engineering detectable pathways for bio-based chemical production.
Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry.
Assembly-free analysis and visualization of mobile genetic element composition.
Standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis. DiNGO is a standalone application based on open source code from BiNGO a Java based tool aimed to determine which Gene Ontology (GO) categories are overrepresented in a set of genes. DiNGO is a command line application which is able to do GO and HPO term enrichment on a set of genes or proteins. DiNGO is multithreaded application which offers fast processing of large datasets. In addition, the application offers gene/protein identifiers conversion tool as well as automatic download of HPO and GO annotation resources.
Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists.
Tool for discovery of new molecules by mass spectrometry.
Software package able to obtain quantitative self-diffusion data in a very straightforward manner allowing the calculation of radii including different molecular models which is not only restricted to spheres.
Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis.
Identification of disease-gene-chemical relationships from Medline abstracts.
Web-based database system for flow cell management.
Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data. A pipeline to generate a Deep Nerual Network cell type deconvolution model for bulk RNASeq samples from single cell experiment data. A pipeline to generate a Deep Neural Network cell type deconvolution model for bulk RNASeq samples from single cell rna-seq data. The pipeline runs in R 3.51 and python 3.6.8. conda create env -n digitalDLSorter
Rapid viral diagnosis from high-throughput sequencing data | High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method
Software Package for Assessing Reproducibility of Brain Networks and their Discriminability across Disorders.
Software for HPV detection in RNA sequencing data.
An easy-to-use web application and R package for discovering rhythmicity. An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface. Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity.
R package for multi-omic data driven prediction of synthetic lethality in cancers.
A classifier for identifying Y chromosome sequences in male assemblies | BACKGROUND:Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references. RESULTS:We develop a k-mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal
Scripts for disentangling small RNA-sequencing (sRNA-Seq) data for libraries containing information from two interacting organisms to study RNA communication between species.
Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interactions refers to geometric distances of amino acid pairs in polypeptide chains. For a detailed analysis of the amino acid distances, the database with three types of amino acid distances in a set of chains was created. Web application Distances of Amino Acids has also been developed to enable scientists to explore interactions of amino acids with different properties based on distances stored in the database. Web application calculates and displays descriptive statistics and graphs of amino acid pair distances with selected properties, such as geometric distance threshold, corresponding SCOP class of proteins and secondary structure types.
An R Package for Divergence Analysis of Omics Data | Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms
DiversityAgents (DWB-DA) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DA is focused on the management of agents, that means persons and organisations. In this context it is designed to manage names (variant names, different names, academic degrees, standardized abbreviations etc.), bibliographic data, postal addresses, agent relation to projects, resources like images and documents and additional agent-related data including agent IDs and the hierarchy of person-related data.
DiversityCollection (DWB-DC) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DC is designed for data describing collection events, collections, collection vouchers and specimens, parts of specimens, as well as observation and occurrence data with assigned multimedia objects and documents. It is processing any action concerning the gathering, storage, transaction and treatment of specimens in a collection and is also appropriate to store observation data with analyses added. DC is unique among collection management systems by its focus on biological relations between organisms linked together as one or more specimens or observations (e. g., host, parasite, hyperparasite, symbionts, etc.) and by its interoperability through internal and external services.
Universität Bayreuth, Department of Mycology
DiversityDescriptions (DWB-DD) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. DD has a generic database model. It is organising descriptions of organisms, taxa, syntaxa and any item, which is object of diversity research. The descriptions are characterized by a triple structure, namely ’item-descriptor-state’. The states can be generalized to one of the presently supported data types (categorical states, quantitative values and measures, molecular sequence data and free-form text). The descriptors (=properties) are not limited to morphological characters and functional traits, but could be physiological, ecological, behavioral , survey parameters, molecular descriptors, descriptors of a lab workflow, descriptors of data content schemes. Sample data and measurement data as gained by ecological field sampling are addressed with own functions.
DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DE is currently used in a core installation at the SNSB, Botanische Staatssammlung München to manage bibliographic information and standardized abbreviations of botanical and mycological exsiccatae in a global index. Exsiccatae are series of specimen collections which are distributed as a publication together with assigned printed matters. They are usually available in multiple copies worldwide. This standard list for Exsiccatal series with unique and stable series identifers is increasing the efficiency of the digitization of botanical and mycological collections.
DiversityGazetteers (DWB-DG) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DG is used to manage and visualize geographical dictionary entries with information about places (particular regions and locations). In conjunction with an automatically created background map, equipped with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines and areas) are displayed in their geographical context. Users with administrator rights may import places from other sources (e. g., ArcView shape files) or create places manually using the integrated Diversity GIS Editor. They may also organise the classification and naming of places.
The DiversityImageInspector (DWB-DII) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent tool. The DII is designed to scan a bulk of images for included barcodes and relevant EXIF metadata (e.g., GPS coordinates, date, time) and returns the results in a table. The table can be saved as text file (CSV) along with the corresponding image file names. DII is able to rename the multimedia input files by adding a prefix to the file name to fit, e. g., the naming convention of an image data repository. This feature might be used to organize the multimedia file storage, e. g. on a web server. DII combines the functions of two freeware tools: (a) ExifTool, to extract the search tags from the metadata of an image and (b) ZBar bar code reader, to find barcodes within a picture. The latter software supports barcodes of the following types: EAN-13/UPC-A, UPC-E, EAN-8, Code 128, Code 39, Interleaved 2 of 5 and QR Code.
University of Bayreuth, Chair of Databases and Information Systems
DiversityMobile (DWB-DM) is an smartphone app for biologists, ecologists and registered citizen scientists being experienced in recording observation data in the field. Data are entered into the app database which follows the Diversity Workbench (DWB) information model. Mechanisms of automated recording and storage of GPS data and manual recording of multimedia data are included. Data entry might be done offline. The DM virtual environment covers webservices for bidirectional data transfer with an institutional data repository. Features include the recording of research data and metadata with automatic inclusion of GPS data, recording of multimedia data (images, audio, video), data transfer from and to an institutional data repository via Wi-Fi. DM webservices are ready to download standardised pick lists with names of organisms, geographic maps and already available metadata of individual research projects. DM webservices are also used to upload research data to the data repository.
DiversityProjects (DWB-DP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DP is focused on the management of (research) projects, data collections, processed by the other DWB modules. It is managing metadata , labels, descriptors, and descriptions of projects, including data package-specific settings for a metadata standard-compliant publication. DP is organising the storage of (legal) documents, permits, information on publications and multimedia resources. DP is handling roles of persons and organisations involved in collection and research projects. The tool is organising project classification and hierarchy in relation to sister and umbrella projects as well as the storage of each type of stable identifier related to data packages. DP is managing issues on web presentation of data collections.
DiversityReferences (DWB-DR) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DR is focussed on the management of bibliographic data about each kind of scientific publications. The tool is handling literature annotations, abstracts, keywords and any kind of descriptors and publication object identifiers. DR is able to import and export literature citations and is used to organise documents and multimedia resources.
DiversitySamplingPlots (DWB-DSP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DSP is focussed on the management of sampling plots. It is a tool designed for biodiversity, geodiversity, ecological and geosciences research projects. In this context it is appropriate to design plots, organise the geographical position of geoobjects and the geometry of the plots as well as of georeferenced objects found on the plots. DSP is able to import sampling plots from other sources and formats (e. g., ArcView shape files) classifying them hierarchically and annotating them. The Diversity GIS Editor is integrated.
DiversityScientificTerms (DWB-DST) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DST is focussed on the management of collections of scientific terms and term concepts, i. e., particular domain-specific terminologies, glossaries and vocabularies (e.g. biostratigraphy, anatomical terminology). DST is able to organise terms together with synonyms, common names and equivalent terms ín different languages. The single terms are defined, (hierarchically) classified and referenced, for example, by linking online resources and external identifiers.
DiversityTaxonNames (DWB-DTN) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DTN is focused on the management of taxon names. Next to nomenclatural information on zoological, botanical, mycological, palaeontological, bacteriological taxon names like typification with type specimens, homotypic synonyms, basionyms, protologues and references according to the rules of the respective International Codes, it is designed to document taxonomic information. This includes accepted names (current names), heterotypic synonyms, name concepts and classifications as well as the history of changing taxonomic relations. DTN is also used to organise common names in various languages and regional taxon checklists with information on red list status and other taxon-based (ecological and nature conservation) parameters.
The Diversity GIS Editor (DWB-DGE) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent module of a DWB environment. Beside this, the DGE is an integrated part of DiversityCollection, DiversityGazetteers and DiversitySamplingPlots. The DGE allows for creating, visualizing, editing and storing samples within a geographical environment. In combination with a background map with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines, areas) may be displayed and edited. The screen and world coordinates of the objects are calculated. Color, thickness and transparency of the elements can be designed. The working area may be shifted or zoomed. The background map could either be loaded from a storage device or created with an online map server tool. Maps without world coordinates may be adjusted to a background map with coordinates by setting reference points. This function allows the georeferencing of historical maps.
The modularized Diversity Workbench (=DWB) represents a tool suite for the management of life and environmental sciences data. The DWB is handling different kinds of bio- and geodiversity data, taxonomies, terminologies, and facilitates the processing of ecological, molecular biological, observational, collection and taxonomic data. It is capable and flexible enough to be applied as data storage system for institutional data repositories. The DWB is set up on a system of 11 xml-enabled SQL relational databases. The rich clients are installed as desktop applications. The DWB might be run as an intranet solution and provide direct interoperability with clients of interlinked DWB databases including cloud services. DWB installations are flexible in the management of highly structured data, enable sophisticated user administration and allow for user-adapted data entry and data exchange. Further, the DWB design facilitates the dynamic integration of web services and external data resources.
Bayesian evidence analysis tool for systems biology.
Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy. An open source toolbox for reproducible diffusion MRI-based microstructure estimation. Dmipy: Diffusion Microstructure Imaging in Python. The Dmipy software package facilitates the reproducible estimation of diffusion MRI-based microstructure features. It does this by taking a completely modular approach to Microstructure Imaging. Using Dmipy you can design, fit, and recover the parameters of any multi-compartment microstructure model in usually less than 10 lines of code. Created models can be used to simulate and fit data for any PGSE-based dMRI acquisition, including single shell, multi-shell, multi-diffusion time and multi-TE acquisition schemes. Dmipy's main features include:
Deep architecture for synapse detection in multiplexed fluorescence images.
Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.
Assessing and improving the performance of consensus docking strategies using the DockBox package. Platform package to simplify the use of docking programs and consensus methods. DockBox is a python wrapper library designed to facilitate the use of standard docking programs either alone or in combination. In addition, DockBox enables to rescore the generated docking poses with different popular scoring algorithms as well as to analyze the results using different consensus docking/scoring strategies
Web Services for Molecular Docking Simulations | A Free Web Server for Protein-ligand Docking | Add missing hydrogen atoms, complete side chains, change protonation states. Simple and easy!
It is a new work-flow designed for a comprehensive analysis of circRNAs composed of: the circRNAs prediction, their classification and annotation using public databases, the back-splicing sequence reconstruction, the internal alternative structure definition, the alignment-free circRNAs quantification from RNA-Seq reads, and their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNA analysis thanks to its containerization and an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into an docker image following guideline provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/).
domain-oriented orthology inference. BACKGROUND:Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains. RESULTS:This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories
Dominance, Sharing, and Assessment in an Iterated Hawk-Dove Game. Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting is followed by the submission of subordinates. Although models have been developed to analyze specific strategies for resolving conflicts over resources, little work has focused on trying to understand why particular strategies are more likely to arise in certain situations. In this paper, we use a model based on an iterated Hawk-Dove game to analyze how resource holding potentials (RHPs) and other factors affect whether sharing, dominance relationships, or other behaviours are evolutionarily stable
Detection of doublets (technical errors) in single-cell RNA-seq count matrices.
Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models | Stochastic drift-diffusion (DrDiff) framework can evaluate free energy, drift and diffusion coefficients, transition path and first passage times using trajectory time traces | Drift-diffusion (DrDiff) framework
A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic species. Phase separation, or liquid-liquid phase separation (LLPS), is a ubiquitous and important mechanism for the formation of membraneless condensates in cells
Rendering glycans and annotating glycopeptide mass spectra. Render glycans and glycopeptides with fragmentation info. using the Symbolic Nomenclature for Glycans [SNFG]. Virtual Glycome Release notes FAQ. IUPAC-condensed Input (glycan or glycopeptide):. If you use this software, please cite: Cheng, K. et al., 'DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information', Glycobiology 27(3): 200-205, 2017 ( Abstract & Full Text )
DriverDBv4 is a cancer omics database which incorporates somatic mutation, RNA expression, miRNA expression, methylation, copy number variation and clinical data in addition to annotation bases.
Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication. Developer: Jianing Xi xjn@nwpu.edu.cn. Instructions to DriverSub (version 1.0.0). After the raw data are loaded, the script ./GenerateInputData.m with function ./bin/P02_GenerateMutData.m can generate the mutation matrix of BRCA and BLCA as ./InputData/D01_brca.mat and ./InputData/D02_blca.mat. The two generated .mat files are the input data of DriverSub
The data portal for drug combination and monotherapy sensitivity screenings. [v1.5] DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. https://doi.org/10.1093/nar/gkab438 [v1.4] DrugComb: an integrative cancer drug combination data portal. https://doi.org/10.1093/nar/gkz337
DrugCombDB is a comprehensive database dedicated to integrating drug combinations from various data sources, include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature.
Database for drug repurposing, combination therapy, and replacement therapy.
Web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning.
A database protal for drug target predictions based knowledge graph embeddings.
> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'nondecision', 'DM', 'two-choice' | an R package for analyzing two-choice reaction time data with the D∗M method | The decision process in choice reaction time data is traditionally described in detail with diffusion models. However, the total reaction time is assumed to consist of the sum of a decision time (as modeled by the diffusion process) and the time devoted to nondecision processes (e.g., perceptual and motor processes). It has become standard practice to assume that the nondecision time is uniformly distributed. However, a misspecification of the nondecision time distribution introduces bias in the parameter estimates for the decision model. Recently, a new method has been proposed (called the D∗M method) that allows the estimation of the decision model parameters, while leaving the nondecision time distribution unspecified
Fast calculation of the ABBA-BABA statistics across many populations/species.
Tool for identification of different modes of duplicated gene pairs.
Dwarna ('about us' in Maltese) is a blockchain-based dynamic consent application for biobanking. The application, which is served through a WordPress plugin, uses a Hyperledger Fabric blockchain, through Hyperledger Composer, to store research participants' consent changes. In this way, the blockchain stores an immutable consent trail. The application contains functionality to manage research studies, research participants and researchers in WordPress.
Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis | Geniesse, C., Sporns, O., Petri, G., Saggar, M. (in-press) Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience
A web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks | BACKGROUND:The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because of the dynamic nature of these processes, the analysis of the results is challenging. Therefore, there is a great need for bioinformatics tools that address this problem. RESULTS:Here we present DynOVis, a network visualization tool that can capture dynamic dose-over-time effects in biological networks. DynOVis is an integrated work frame of R packages and JavaScript libraries and offers a force-directed graph network style, involving multiple network analysis methods such as degree threshold, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure
Dynamic Retention Time Database for Steroidomics.
Interactive sequence logo with dynamic thresholding of matched quantitative proteomic data. Dynalogo can be run with the following code from within RStudio or deployed on a shiny server. To ensure compatibility, the user can download the current list of packages and Version numbers from the Dynalogo webite by clicking on the "Version Info" text at the top of the application located at https://dynalogo.cam.uchc.edu. Dynalogo: Dynamic Sequence Logos. Dynalogo is a web application which can be used to visualize and explore binding array (ie. peptide array) datasets. It was created to allow the dynamic visualizations of sequence logos for better insight into the relationship between affinity and specificity of binding domains. Please import your dataset or dowlnoad the sample dataset
Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances/dissimilarities of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances dissimilarities of shotgun metagenomes at the species level.
Scripts used during the genome assembly of Dysdera silvatica.
Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. vngFCM is a package designed to analyse fluocytometry data of small bacterial cells. Fluocytometer analysis of bacterial cells. install.packages("/path/to/E-Flow", repos=NULL, type="source"). This package has been designed to process FCM data by removing non viable cells, subtracting autofluorescence and reduce the effect of electronic noise coming from the cytometer. It has been designed for the analysis of bacterial cells, where the small dimensions and the low expression pose challanges in the correct interpretation of the data.
E-SNPs&GO is a machine-learning method the pathogenicity of human variations. E-SNPs&GO classify input variations into pathogenic or benign.
EAGS is a smoothing approach for spatial transcriptome data with ultrahigh resolution. Through the principal component information of the profiling of gene expression and the personally identifiable information between cells, it uses a two-factor adaptive smoothing weight mechanism to determine the neighborhood relationship of cells. Then it uses the self-developed smoothing weight formula to calculate the smoothing contribution and recalculate the gene expression of each cell.
Efficient and Adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics
Predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches.
Evolutionary-based BIClustering (EBIC), a next-generation biclustering algorithm for mining genetic data.
A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data.
Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. Abstract Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. The increasing amount of genomics data gathered from patients allows for better understanding of gene regulatory mechanisms that occur during disease development at a system level. However, integrating such a large amount of population data is still a challenging task. To address this, we developed an interpretable machine learning model, ECMarker, to predict gene expression biomarkers and regulatory networks specific for disease stages such as early cancer. In particular, ECMarker was built on the semi-restricted Boltzmann machine, a machine learning model with multiple hierarchical layers.
A new toolbox for time series analysis and forecasting. Some Features found in a few packages or none at all.
EDCluster is a method for obtaining stationary distributions that can be used to construct empirical stationary distribution mixture models.
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.
The Extensive de novo TE Annotator (EDTA)
Platform to enable EEG measurements and general purposes Brain Computer Interface experimentations.
A framework for realistic simulation of EEG scalp data using MRI-based forward models and biologically plausible signals and noise | BACKGROUND:Electroencephalography (EEG) is widely used to investigate human brain function. Simulation studies are essential for assessing the validity of EEG analysis methods and the interpretability of results. NEW METHOD:Here we present a simulation environment for generating EEG data by embedding biologically plausible signal and noise into MRI-based forward models that incorporate individual-subject variability in structure and function. RESULTS:The package includes pipelines for the evaluation and validation of EEG analysis tools for source estimation, functional connectivity, and spatial filtering. EEG dynamics can be simulated using realistic noise and signal models with user specifiable signal-to-noise ratio (SNR). License either MIT or GLP-2.0
Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways | Enzyme Function Initiative Tools | This website contains a collection of webtools for creating and interacting with sequence similarity networks (SSNs) and genome neighborhood networks (GNNs). These tools originated in the Enzyme Function Initiative, a NIH-funded research project to develop a sequence / structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic / physiological functions of unknown enzymes discovered in genome projects | The Enzyme Function Initiative tools are hosted at the Carl R | If you use the EFI web tools, please cite us: | A "From The Bench" article was recently published in Biochemistry and is available on the training resources page
A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge | Drug Repositioning Drug repositioning, or the identification of new indications for approved therapeutic drugs, has gained substantial traction with both academics and pharmaceutical companies because it reduces the cost and duration of the drug development pipeline and the likelihood of unforeseen adverse events. To date there has not been a systematic effort to identify such opportunities, in part because of the lack of a comprehensive resource for an enormous amount of unsystematic drug repositioning information to support scientists who could benefit from this endeavor | Experimental Knowledge-Based Drug Repositioning Database (EK-DRD) provides a versatile resource for the display, search and analysis of structure, function, pathway, disease, network and related experimentally-validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs
Ensemble Learning Approach for Stability Prediction of Interface and Core mutations.
The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data. A webapplication for managing, documenting and result analyzing of aPCR Data.
A cross-sectional analysis of the emergency events database from a pediatric perspective. The international disasters database. Disaster group: Two main groups of disasters are distinguished in EM-DAT: natural disasters and technological disasters. This field is automatically linked to the disaster sub-group and the disaster type. There is a third group ‘Complex disasters’ which include some major famine situation for which the drought were not the main causal factor. See Table 1 for the Disasters Classification. In 1988, the Centre for Research on the Epidemiology of Disasters (CRED) launched the Emergency Events Database (EM-DAT).
Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. Converts EMBL- or GenBank-formatted flat files to submission-ready checklists for submission to ENA via the interactive Webin submission system.
Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology | EMULSION Manual — EMULSION (Epidemiological Multi-Level Simulation framework) | Framework EMULSION is intended for modellers in epidemiology, to help them design, simulate, and revise complex mechanistic stochastic models, without having to write or rewrite huge amounts of code
A manually curated database of experimentally supported enhancers for human and mouse. Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons
Complete reimplementation of the evolutionary placement algorithm (EPA) that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER.
Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data.
Tool for designing peptide ligand libraries based on epitope–paratope interactions.
Analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies.
EPIFANY is a protein inference engine based on a Bayesian network.
Efficient Bayesian protein inference (EPIFANY)
genome wide transcription unit annotation using a multivariate probabilistic model of histone modifications. EPIGENE models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active transcription units. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network — Epigenomics. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network. The network is funded by the Canadian Institutes of Health Research (CIHR) and Genome Canada and is run by epigenetics researchers from across Canada. CEEHRC is Canada's contribution to the International Human Epigenome Consortium (IHEC)
A novel approach for condition-specific enhancer-promoter interaction prediction.
Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. EPIVAN(Promoter-Enhancer Interaction predictor with pre-trained Vector and Attention based neural Networks). EPIVAN is a new deep learning method that enables predicting long-range EPIs using only genomic sequences
Novel Sequence Insertion Detection by Constructing an Extended Reference. Next generation sequencing technology has led to the development of methods for the detection of novel sequence insertions (nsINS). Multiple signatures from short reads are usually extracted to improve nsINS detection performance. However, characterization of nsINSs larger than the mean insert size is still challenging. This paper presents a new method, ERINS, to detect nsINS contents and genotypes of full spectrum range size. It integrates the features of structural variations and mapping states of split reads to find nsINS breakpoints, and then adopts a left-most mapping strategy to infer nsINS content by iteratively extending the standard reference at each breakpoint. Finally, it realigns all reads to the extended reference and infers nsINS genotypes through statistical testing on read counts. We test and validate the performance of ERINS on simulation and real sequencing datasets.
Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search.
A unique tool to help understand HIV prevention among high-risk young women in Ukraine | Estimate time since infection from NGS diversity
Iintegrated Ethiopian traditional herbal medicine and phytochemicals database | ETM-DB is a free, online relational database containing Ethiopian herbal medicine, related compounds and target gene/proteins. Ethiopia is endowed with an affluence of botanical remedies that have proven useful over a long time, especially in the rural areas where modern health care is much less accessible. It is estimated that about 80% of the Ethiopian population, predominantly in the rural areas, use traditional medicine. There are about 6,500-7,500 plant species in Ethiopia, of which an estimated 12% are endemic to Ethiopia
A Low-Cost, Open Source, Self-Contained Bacterial EVolutionary biorEactor (EVE)
EVR is a chromosome 3D structure reconstruction tool using an Error-Vector Resultant algorithm based on DNA interaction data. With normalized or unnormalized IF matrix as input, the program generate a chromosome 3D structure output in a .pdb file. Using Cython and OpenCL, the program can run on CPUs/GPUS/APUs and thus usually faster than similar tools.
Proteome-scale discovery of protein interactions with residue-level resolution using sequence coevolution. Evolutionary couplings from protein and RNA sequence alignments. If you are simply interested in using EVcouplings as a library, installing the Python package is all you need to do (unless you use functions that depend on external tools). If you want to run the evcouplings application (alignment generation, model parameter inference, structure prediction, etc.) you will also need to follow the sections on installing external tools and databases. Predict protein structure, function and mutations using evolutionary sequence covariation.
Predicting functional long non-coding RNAs validated by low throughput experiments.
Epigenome-wide association study software.
A resource of DNA methylation array data and metadata.
A Python script for identifying protein complexes based on an edge weight algorithm and core-attachment structure.
EXPANDER (EXPression ANalyzer and DisplayER) is a comprehensive software package for analysis of expression data.
A validated web application suite to reveal the full details of HLA typing. Nomenclature for Factors of the HLA System. The WHO Nomenclature Committee for Factors of the HLA System comprises the following individuals:. EasyMatch-R is a tool designed to find unrelated donors in silico. We aim to improve efficiency by saving time and resources in HLA labs. From a patient’s HLA typing in input, Easymatch-R displays probability of finding a potential unrelated bone marrow donor according to the required matching level. In addition to the number of expected donors, Easymatch-R provides complementary typings recomendations. HLA-Upgrade uses the power of haplotypes to predict full high resolution HLA-A, B, C, DRB1, DQB1 genotypes.
An easy-to-use toolbox for MEG analysis. an easy-to-use software for MEG analysis based on FieldTrip and Matlab GUI. You can use the editor on GitHub to maintain and preview the content for your website in Markdown files
A user-friendly tool for building and analysis of simple mathematical models in systems biology
Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as well as the constituent RNA-binding domains (RBDs).
Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies.
Mapping the spatial distribution of pairwise gene expression intensities | This file details the different codes that we utlized to create the results for EdgeScaping
Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.
Program for neurofeedback that supports modularEEG. Uses fast Fourier transform to extract frequency bands from the raw signal.
Software tool to correct LC-MS data in isotope labeling experiments.
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning | Emap2sec is a computational tool to identify protein secondary structures | Emap2sec is a computational tool using deep learning that can accurately identify protein secondary structures, alpha helices, beta sheets, others (coils/turns), in cryo-Electron Microscopy (EM) maps of medium to low resolution
A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes | Abstract Background In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the number of cells profiled in individual scRNA-seq experiments, there is a demand for novel computational methods for classifying newly-generated scRNA-seq data onto annotated labels. Although several methods have recently been proposed for the cell-type classification of single-cell transcriptomic data, such limitations as inadequate accuracy, inferior robustness, and low stability greatly limit their wide applications. Results We propose a novel en semble approach, named EnClaSC, for accurate and robust cell-type cla ssification of s ingle- c ell transcriptomic data
R package for imputing dropout events in single cell RNA sequencing data via ensemble learning.
Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes.
EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.
Database to discover the regulate relationships in the context of enhancers.
Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
Library for working with Markov state models (MSMs) that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods.
Global genomic population structure of Salmonella, Escherichia/Shigella, Mycobacterium tuberculosis, Streptococcus, Clostridioides, Vibrio, Helicobacter, Yersinia, Moraxella
Python library to dynamically interact with the NCBI Entrez databases.
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. With Eoulsan, users can easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Working either on standalone workstations or cloud computing clusters, Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression.
Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context | Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum | EphaGen - a package to estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum
An approach of epistasis mining based on genetic Tabu algorithm and Bayesian network
Alignment-based bioinformatic tool for comparing chromatin state sequences.
Alignment of genomic regions with both sequence and epigenomic information.
Tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.
Improved inference of time-varying reproduction numbers during infectious disease outbreaks. This web application generates an estimate of infectious disease transmissibility throughout an outbreak. The time-dependent reproduction number (R) is inferred from disease incidence time series and patient data or estimates of the serial interval.
R package for large-scale integrated analysis in methylation hotspots linked to genetic regulation.
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation. Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels
Analysis of histone post-translational modifications by direct infusion mass spectrometry .
Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements | EpiSAFARI: Sensitive Detection of Valley Shaped Patterns in Epigenetic Signal Profiles | EpiSAFARI is a command line tool for detection, annotation, and characterization of the valley shaped patterns within the functional genomics signal profiles. It takes:
A robust classifier to determine smoking status from DNA methylation data | Aim: Smoking strongly influences DNA methylation, with current and never smokers exhibiting different methylation profiles. Methods: To advance the practical applicability of the smoking-associated methylation signals, we used machine learning methodology to train a classifier for smoking status prediction. Results: We show the prediction performance of our classifier on three independent whole-blood datasets demonstrating its robustness and global applicability. Furthermore, we examine the reasons for biologically meaningful misclassifications through comprehensive phenotypic evaluation. Conclusion: The major contribution of our classifier is its global applicability without a need for users to determine a threshold value for each dataset to predict the smoking status
Reproducible Epigenomics Analysis pipeline for the analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. The analysis workflow was originally designed to analyze Brassica rapa data.
Epigenomics Workflow on Galaxy and Jupyter
quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Episo-quantify Epitranscriptomal RNA m5c at isoform level. Episo is a probabilistic model to quantify Epitranscriptomal RNA m5C at the transcript isoform level. Episo consists of three tools, named mapper, quant and Bisulfitefq, for mapping, quantifying, and simulating RNA-BisSeq data, respectively. Episo needs a working version of Perl and it is run from the command line. Meanwhile, Bowtie, Tophat and Cufflinks need to be installed on your computer. First you need to download a transcript annotation file from the Ensembl or NCBI websites. Episo supports the reference trancriptom sequence files in FastA format, allowed file extensions are either .fa or .fasta. The details see the document Episo_User_Guide.pdf. This pakage is for estimating m5c level by using Kallisto in Episo
Tool for Model Discovery and Assembly with the Physiome Model Repository.
ModelExplorer is a metabolic model visualization package that can assist the user in finding blocked parts of the metabolic network as well as finding out why they are blocked.
A comprehensive database for eukaryotic RNA binding proteins. EuRBPDB is a comprehensive and user-friendly database for eukaryotic RNA binding proteins (RBPs). It contains 315,222 RBPs (forms 6,368 ortholog groups) from 162 eukaryotic species, including human, mouse, fly, worm and yeast. EuRBPDB provides precise and comprehensive list of RBPs of each eukaryote with annotations collected from various public databases
Open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.
EventEpi - A Natural Language Processing Framework for Event-Based Surveillance - is a tool to extract the most important entites from a epidemiological text and to analyze them.
A Literature Evidence-Based Miner for Human Microbial Associations. The importance of understanding microbe-microbe as well as microbe-disease associations is one of the key thrust areas in human microbiome research
Evidence Based Microbial Associations Miner (EviMass)
Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation | Ranking methodology of potential Driver genes using multi-view feature sets
The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
RNA 3D structure prediction guided by independent folding of homologous sequences and multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io.
Accurate and fast energy function for computational protein design. energy potential for protein design. EvoEF is a composite energy force field that contains two versions. The first version, EvoEF1, includes five energy terms with parameters optimized on two large sets of thermodynamics mutation data (ΔΔGstability and ΔΔGbind), while the second version, EvoEF2, includes nine energy terms and optimized based on recapitulation of protein sequence design. Extensive benchmark and analysis showed that the usefulness of energy functions is highly correlated with the parameter optimization processes. While EvoEF1 performs better than EvoEF2 on ΔΔG estimation, EvoEF2 significantly outperforms EvoEF2 on de novo protein sequence design. Therefore, we suggest users download the two versions according to their own needs.
Visualization of the Evolutionary Frequencies of Sequence and Model Data | Evolutionary frequency visualization tool of temporal data | Users have options ot install EvoFreq depending on if they want to use 'devtools'. Below we show two popular methods for installation. You will need a fully operational install of R (≥3.5.0) and, optionally, RStudio | Visualization Package for Evolutionary Dynamics from Sequence and Model Data. biorxiv pre-print here
EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species.
EvolClust predicts groups of genes that are conserved in terms of gene order across different species distinguishing it from the background gene order conservation found between species. We define a cluster as a group of homologous proteins that are found grouped together in at least two different genomes and which are more conserved than what is expected for the pair of genomes. The order of the genes inside the cluster is not necessarily conserved. Pairwise clusters are grouped into multi-species families.
EvryRNA platform is a web server providing various algorithms and bioinformatics tools developed in the laboratory IBISC of UEVE/Genopole, and dedicated to the prediction and the analysis of non-coding RNAs (ncRNAs).
Integrated Solution for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.
Tool for phylogenomic analyses on supercomputers.
Exact calculation of stationary solution and parameter sensitivity analysis of stochastic continuous time Boolean models. Abstract Motivation Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all asymptotic solutions. Moreover, these models have timescale parameters (transition rates) that the probability values of stationary solutions depend on in complex ways that have not been analyzed yet in the literature. These two fundamental uncertainties call for an exact calculation method for this class of models.
User-friendly tool for region-based rare variant association analysis (RVAA).
Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open reading frame (ORF) and noticed as therapeutic targets
Sequence-graph-based tool to analyze variation in short tandem repeat regions.
A computational method for locating known and novel repeat expansions in short-read sequencing data. A suite of tools for detecting expansions of short tandem repeats. ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.
Suite for single-cell alternative splicing analysis. Consists of outrigger, anchor and bonvoyage.
an image processing pipeline for multi-center ASL perfusion MRI studies. ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators. OSIPI ASL pipelines google forms. QUIZ: Presentation, QUIZ + IMAGES
An update incorporating candidate dietary biomarkers and dietary associations with cancer risk. database on biomarkers of environmental exposures. First database dedicated to biomarkers of exposure to environmental risk factors for diseases. BiomarkersConcentrationsAssociations with cancer risk. The database is being actively updated.
Easy interface for determining the Clermont 2013 phylotype of an E. coli isolate
A script for fast and consistent environmental DNA processing and identification. Scripts for executing a filtering, clustering and identification pipeline for eDNA samples. Fast And Consistent Environmental-DNA Processing And Identification (& Conversion and Preparation of Reference Sequences). Wahlberg, E. 2019. FACEPAI: a script for fast and consistent environmental DNA processing and identification. BMC Ecology 19: 51, doi:10.1186/s12898-019-0269-1
An interactive tool for geometric modeling of nerve fiber architectures in the brain | The fiber arcitecture constructor (FAConstructor) allows a simple and effective creation of fiber models based on mathematical functions or the manual input of data points. Models are visualized during creation and can be interacted with by translating them in the 3-dimensional space
Two real use cases of FAIR maturity indicators in the life sciences | This repository contains the results of the FAIR Metrics Group | FAIR Maturity Indicators and Tools | [Horizon 2020 Commission expert group on Turning FAIR data into reality](http://ec.europa.eu/transparency/regexpert/index.cfm?do=groupDetail.groupDetail&groupID=3464
FAIRDataPoint is a REST api for creating, storing and servering FAIR metadata. The metadata contents are in this api are generated semi-automatically according to the FAIR Data Point software specification document. In the current version of api we support GET, POST and PATCH requests.
The Data FAIRport includes FAIRifier and Metadata Editor (to create), FAIR Data Point (to publish), FAIR Search Engine (to find), ORKA (to annotate) FAIR data descriptions.
FAIR search engine, designed as a prototype for finding FAIR resources.
A general-purpose FAIRifier on the basis of the OpenRefine data cleaning and wrangling tool and the RDF plugin. This FAIRifier enables a post-hoc FAIRification workflow: load an existing dataset, perform data wrangling tasks, add FAIR attributes to the data, generate a linked data version of the data and, finally, push the result to an online FAIR data infrastructure to make it accessible and discoverable. Literal values in a dataset can be replaced by identifiers either manually or by embedded, customizable script expressions. The interoperability of the dataset can be improved by connecting these identifiers into a meaningful semantic graph-structure of ontological classes and properties using the integrated RDF model editor. A provenance trail automatically keeps track of each modification and additionally enables “undo” operations and repetition of operations on similar datasets. A FAIR data export function opens up a metadata editor to provide information about the dataset itself.
Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes | In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, natural products, agrochemicals, and cosmetics. FAME 3 was derived from the MetaQSAR database ( Pedretti et al. J. Med. Chem. 2018 , 61 , 1019 ), a recently published data resource on xenobiotic metabolism that contains more than 2100 substrates annotated with more than 6300 experimentally confirmed SoMs related to redox reactions, hydrolysis and other nonredox reactions, and conjugation reactions
A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics | Most biological systems are difficult to analyse due to a multitude of interacting components and the concomitant lack of information about the essential dynamics. Finding appropriate models that provide a systematic description of such biological systems and that help to identify their relevant factors and processes can be challenging given the sheer number of possibilities. Model selection algorithms that evaluate the performance of a multitude of different models against experimental data provide a useful tool to identify appropriate model structures
Fast And Robust DEconvolution of Expression Profiles (FARDEEP) - machine learning tool for enumerating immune cell subsets from whole tumor tissue samples.
Improved de novo Rosetta prediction of complex global RNA folds | ROSIE Rosetta server based on www.rosettacommons.org engine | Welcome to ROSIE Rosetta Online Server that Includes Everyone | Please cite the following article when referring to results from our ROSIE server: | Watkins, A. M.; Das, R. "An automated and customizable RNA fragment assembly protocol in Rosetta. bioRxiv 223305; doi: https://doi.org/10.1101/223305
FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison.
Sequence similarity searching against protein databases. FASTX and FASTY translate a DNA query. Optimal searches with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).
FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics.
a Perl module to parse FASTA/FASTQ files
Software to analyze Molecular Dynamics simulations of membranes.
FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells. FB5P-seq: FACS-based 5'-end single-cell RNA-seq. Copyright 2019: PMlab, Centre d'Immunologie de Marseille-Luminy This work is distributed under the terms of the GNU General Public License. It is free to use for all purposes. FB5P-seq is a computational pipeline to process single-cell RNA sequencing (scRNAseq) data produced with the FB5P-seq protocol designed by the Milpied lab at Centre d'Immunologie de Marseille-Luminy. The pipeline relies on 5 main softwares:
Fast Bayesian-bound tool to calibrate RNA-seq aligners.
Optical classification of inland waters based on an improved Fuzzy C-Means method. Water optical clustering based on water color information is important for many ecological and environmental application studies, both regionally and globally. The fuzzy clustering method avoids the sharp boundaries in type-memberships produced by hard clustering methods, and thus presents its advantages. However, to make good use of the fuzzy clustering methods on water color spectra data sets, the determination of the fuzzifier parameter (m) of FCM (fuzzy c-means) is the key factor. Usually, the m is set to 2 by default. Unfortunately, this method assigned some membership degrees to non-belonging water type, failing to obtain the unitarity of cluster structure in some cases, especially in inland eutrophic water.
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. Fully Convolutional Neural Network model. A demonstration of what can be accomplished visually through CSS-based design. If you want to visit this website, the google browser will be recommended !. The fully convolutional neural network (FCNN) model is a deep learning model based on traditional convolution neural network (CNN) model with a fully connected first layer and combines expression similarities and prior-knowledge similarities as the input
A calculator of conservation and allele frequency for variant pathogenic prediction.
Software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.
An Individualized Prediction Model for Long-term Lung Function Trajectory and Risk of COPD in the General Population
The FEniCS Project is a collaborative project for the development of innovative concepts and tools for automated scientific computing, with a particular focus on the solution of differential equations by finite element methods.
A Web Server for Transcription Factor and miRNA Feed Forward Loop Analysis in Human. FFLtool is a webserver for analyzing Feed Forward Loop (FFL) regulatory motifs among transcription factors (TFs), microRNAs (miRNAs) and genes. FFLs potentially regulate thousands of target genes in facilitating spatiotemporal avoidance or noise buffering and play important roles in biological processes and diseases (see Refs. PMIDs: 20157565 and 24307685 ). It integrated TF-target data from hTFtarget and miR-target data from several predicted and validated databases. Except for identifying FFLs, FFLtools can also be used to search miR-target and TF-target information
Analysis pipeline for FFPEcap-seq. A method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
A tool for quantitatively characterizing the morphology and growth of filamentous fungi. The FFT represents a user-friendly tool that automatically characterizes several fungal phenotypes using images that can be obtained using basic imaging devices. The FFT can be used to study different fungal species, conditions and image scales and resolutions. Relying on simple built-in image analysis functions, the FFT is able to quantitatively characterize conidiation, conidia morphology and different aspects of the mycelium, including the growth area, number of hyphal tips and total length of the hyphae. In addition, we developed a function within the FFT that can detect and count traps developed by nematode-trapping fungi.
Method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets.
FHIR is a standard for health care data exchange. It is a platform specification that defines a set of capabilities use across the healthcare process, in all jurisdictions, and in lots of different contexts.
FINET is a software to infer any network. Implemented by Julia with algorithms of stability selection and elastic-net, plus parameter optimization, finet can infer a network fast and accurately from a big data. Additionally, finet is user-friendly, only one single command line to complete all computational processes. Developed under Linux, but finet should work in any OS system. Installing and using finet becomes simple by using following instructions
finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. FInding REliable Variants without ArTifacts. FIREVAT (FInding REliable Variants without ArTifacts) is an R package that performs variant refinement on cancer sequencing data. FIREVAT uses mutational signatures to identify sequencing artifacts and low-quality variants
Framework for the Inference of In Situ Interaction Kinetics from Single-Molecule Imaging Data | Recent experimental and computational developments have been pushing the limits of live-cell single-molecule imaging, enabling the monitoring of intermolecular interactions in their native environment with high spatiotemporal resolution. However, interactions are captured only for the labeled subset of molecules, which tends to be a small fraction. As a result, it has remained a challenge to calculate molecular interaction kinetics, in particular association rates, from live-cell single-molecule tracking data. To overcome this challenge, we developed a mathematical modeling-based Framework for the Inference of in Situ Interaction Kinetics (FISIK) from single-molecule imaging data with substoichiometric labeling
Statistical modeling tool for transcriptome dynamics under fluctuating field conditions.
Integrative database around plant genomes.
A full-length mRNA sequencing reveals principles of poly(A) tail length control | Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs. We report a complementary DNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids and Caenorhabditis elegans we show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample
Full-Length Envelope Analyzer (FLEA) - tool for longitudinal analysis of viral amplicons.
A support tool for efficient and seamless experiment data processing to evaluate musculo-articular stiffness | FLEXOR is a multiplatform software tool to simplify traditional complex and manual procedures for MAS analysis
Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform | Web Server for Calculating Protein Second Virial Coefficients | PI2PE: Protein Interface/Interior Prediction Engine | FMAPB2 implements FMAP, a method based on fast Fourier transform (FFT), to calculate second virial coefficients ( B 2 ) for proteins represented at the all-atom level in implicit solvent. FMAP stands for F FT-based M odeling of A tomistic P rotein-protein interactions. In FMAPB2, we express terms of the protein-protein inteaction energy as correlation functions, and evaluate them by FFT. These terms include steric repulsion, nonpolar attraction (in the form of a Lennard-Jones potential), and electrostatic interactions (in the form of a Debye-H&#252ckel potential)
A 3-dimensional clustering package for single-molecule localization microscopy | Single-molecule localization microscopy (SMLM) yields an image resolution 1-2 orders of magnitude below that of conventional light microscopy, resolving fine details on intracellular structure and macromolecular organization. The massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Density based clustering algorithms, such as DBSCAN, can provide spatial statistics on protein nucleic acid aggregation or dispersion while explicitly identifying macromolecular clusters. The performance of DBSCAN, however, is typically dependent upon an arbitrary, or at least highly subjective, parametric tuning of the algorithm. Moreover, DBSCAN can be computationally expensive, which makes it arduous to evaluate on large image stacks
Computing the statistical significance of optimized communities in networks.
Fast Optimized Community Significance (FOCS)
Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks.
Tool for the systematic comparison of translational drug response modeling pipelines.
Tool for ranking variants and building an optimal graph genome.
A Python package automatic computed fusion of ontologies.
FP-LIMS is a LIMS solution specialized on mass spectroscopy measurement equipment. Primary compatible device manufacturers include: Spectro / Ametek,Agilent Technologies,Analytik Jena AG,Bruker,Hitachi / Oxford Instruments,Horiba Jobin Yvon GmbH,Malvern Panalytical,Microtrac GmbH,OBLF,PerkinElmer,Thermo Fisher,Zwick. FP-LIMS was first released in 1993. Its first version was based on spectroscopy-giant Spectro's(Ametek) in-house Laboratory data management solution. Its primarily used in metallurgy & foundry QM-laboratories where it is used for audit-trailing, certification, managing the passing of data from devices to an immutable data-store as well as upwards to systems such as the SAP QM module. FP-LIMS was formerly distributed as [DIA]/DIA2000/DIAPLUS.
Molecular featurizer for learning molecular properties.
Community-editable fluorescent protein database, cataloging an expanded range of proteins and parameters, including a new spectra viewer.
A parallel architecture for very high-speed assessment of sequencing quality metrics | BACKGROUND:High throughput DNA RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine but important task. Identification and elimination of low-quality sequence data is crucial for reliability of downstream analysis results. There is a need for a high-speed tool that uses optimized parallel programming for batch processing and simply gauges the quality of sequencing data from multiple datasets independent of any other processing steps. RESULTS:FQStat is a stand-alone, platform-independent software tool that assesses the quality of FASTQ files using parallel programming
Detection of aberrant splicing events in RNA-seq data with FRASER. FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is currently avaiable as preprint here. Accompanying analysis code for the FRASER manuscript. The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use our Colab tutorial at: http://tinyurl.com/RNA-ASHG-colab. This is based on a workshop we presented at ASHG 2019. FRASER: Find RAre Splicing Events in RNA-seq. This folder contains the FRASER paper and supplementary data. This project depends on the python package wBuild and the R package FRASER. Further, we use the Leafcutter adaptation used in the Kremer et al paper, which can be found here
Benchmarking machine learning models for the analysis of genetic data using FRESA.CAD Binary Classification Benchmarking | Feature Selection Algorithms for Computer Aided Diagnosis | Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization License: GPL-2, GPL-2.1 and/or GPL-3.
Food Spoilage and Safety Predictor (FSSP)
Topology-independent and global protein structure alignment through an FFT-based algorithm | Fast topology-independent and global structure alignment through an FFT-based algorithm
Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. MOTIVATION:The elucidation of dysfunctional cellular processes that can induce the onset of a disease is a challenging issue from both experimental and computational perspectives. Here we introduce a novel computational method based on the coupling between fuzzy logic modeling and a global optimization algorithm, whose aims are to (1) predict the emergent dynamical behaviors of highly heterogeneous systems in unperturbed and perturbed conditions, regardless the availability of quantitative parameters, (2) determine a minimal set of system components whose perturbation can lead to a desired system response, therefore facilitating the design of a more appropriate experimental strategy. RESULTS:We applied this method to investigate what drives K-ras induced cancer cells, displaying the typical Warburg effect, to death or survival upon progressive glucose depletion
A graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions. Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.
Create realistic 3D faces from photos or at random, edit with many controls, export for animation, rendering or 3D printing using a demographically diverse and customizable face space model
Open source framework for recording facial expressions with head-mounted cameras | The FaceSync toolbox provides 3D blueprints for building the head-mounted camera setup described in our paper. The toolbox also provides functions to automatically synchronize videos based on audio, manually align audio, plot facial landmark movements, and inspect synchronized videos to graph data
Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites. Faster parallel feature extraction from genome sequence. This is a tool for faster feature extraction from genome sequences and making efficient prediction. To build efficient prediction model, user can go through the following instructions step by step. If user only wants to predict query sequences from our built model, then just go to step Make prediction for query sequences. Currently, FastFeatGen supports text file as shown in dataset.txt file in datasets directory; however, fasta file can also be used with a simple preprocessing
Fast preprocessing of next-generation sequencing reads.
Tools to deal with fastq sequences and paired-end reads.
High-performance preprocessing tool for RNA-seq data.
An integrated Omics data warehouse for FAW, Spodoptera frugiperda
A Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs
a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies | HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes | Please see the Wiki page for introduction and tutorial on how to use this tool | git clone https://github.com/Arkadiy-Garber/FeGenie.git | Easy Installation (if you have Conda installed) | HMM-lib directory can be found within FeGenie's main repository -t 8 means that 8 threads will be used for HMMER and BLAST. If you have less than 16 available on your system, set this number lower (default = 1)
Software for feature selection based on machine learning approaches.
A web application for new bioactive peptides from food protein
Tool to extract data from the 1000 Genomes Project.
Identifying Fertility-Related Proteins by Incorporating Deep-Gated Recurrent Units and Original Position-Specific Scoring Matrix Profiles | Identifying fertility-related proteins by incorporating GRU and PSSM profiles
Numerical phantom for fetal cardiovascular magnetic resonance imaging.
Webserver for scoring the impact of single nucleotide variants in the dog genome.
Designing for Mobile and Immersive Visual Analytics in the Field | Abstract: Data collection and analysis in the field is critical for operations in domains such as environmental science and public safety
A quantitative method to analyse F-actin distribution in cells. ImageJ, with "Batteries Included". Fiji: A batteries-included distribution of ImageJ. Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating.
interpretable supervised contact prediction using inter-domain coevolution.
whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. FindSV is a structural variation pipeline written in nextflow and python. FindSV performs variant calling using TIDDIT and CNVnator. similar variants are merged, and the variants are annotated using VEP, frequency database, genmod, and custom annotation using the annotator script. FindSV outputs one unfilered vcf file per caller, a merged and unfiltered vcf file (_Combined.vcf), as well as an annotated and filtered vcf file "_FindSV.vcf". In addition, FindSV outputs a ploidy tab file, that describes the ploidy for each chromosome.
Repeat-aware tool for upgrading de novo assembly using long reads.
R package and GUI application for analysis of aquatic respirometry data.
Digital Filter Design, Viewing and Comparison tool.
Correcting reference bias from the Illumina Isaac aligner enables analysis of cancer genomes. Code to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file. Support code for NGS copy number algorithms. Takes a file of locations and a [cr:b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). Altered so that it clips all reads by n bases to reduce reference bias. python FixVaf.py [vcf file] [bam file] [fasta file]. The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. Requires python 3 with psam installed. The project previously contained 2 equivalent implementations of allele counting code in perl and C for BAM CRAM processing
Computing Persistent Homology of Directed Flag Complexes. Computing homology of directed flag complexes (based on https://github.com/Ripser/ripser). Three modified versions of flagser from luetge/flagser. flagser computes the homology of directed flag complexes. For a more detailed description consult the documentation under docs/documentation_flagser.pdf. Copyright © 2017–2018 Daniel Lütgehetmann. For more detailed instructions, see docs/documentation_flagser.pdf. The program flagser-memory is a variant of flagser storing the full directed flag complex in memory, speeding up parts of the computation but requiring more memory
Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data | Inference of microbial interaction networks from large-scale heterogeneous abundance data | FlashWeave predicts ecological interactions between microbes from large-scale compositional abundance data (i.e. OTU tables constructed from sequencing data) through statistical co-occurrence or co-abundance. It reports direct associations, with adjustment for bystander effects and other confounders, and can furthermore integrate environmental or technical factors into the analysis of microbial systems
A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well as therapeutic value. Flavonoids are often known for their effective antioxidant nature; however, their various other bioactivities are well established. These bioactivities mainly includes antibacterial, anti-cancer, cardio protective, promotion of immune system, anti-inflammatory and skin protection from ultra violet radiation; these properties are effectively reviewed by Tungmunnithum et al 2018.
Large scale microbiome profiling in the cloud | Main repository of the Flint project for Spark and Amazon EMR | This is the main repository of the Flint project for Amazon Web Services. Flint is a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark's built-in parallelism and streaming engine architecture to quickly map reads against a large reference collection of bacterial genomes
Flowsculpt is an open-source utility for solving the inverse problem in pillar programming. That is, given a fluid flow shape, what is the pillar sequence and inlet design that will produce such a shape? Our utility uses a customizable genetic algorithm to determine optimal pillar sequence and inlet flow design for a given fluid flow shape.
Tools for Influenza Activity and Surveillance. U.S. Influenza Surveillance System. Overview of Influenza Surveillance in the United States - CDC. Centers for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting People. FluNet is a global web-based tool for influenza virological surveillance first launched in 1997. The virological data entered into FluNet, e.g. number of influenza viruses detected by subtype, are critical for tracking the movement of viruses globally and interpreting the epidemiological data. The data at country level are publically available and updated weekly. The results are presented in various formats including tables, maps and graphs.
A database for the study of genomic reassortments among influenza viruses.
Tools for Influenza Activity and Surveillance. The Influenza Division at CDC collects, compiles and analyzes information on influenza activity year-round in the United States. FluView , a weekly influenza surveillance report, and FluView Interactive , an online application which allows for more in-depth exploration of influenza surveillance data, are updated each week. The data presented each week are preliminary and may change as more data is received
Algorithm for automated analysis of high-throughput droplet microfluidic data.
Automated analysis of mosaic imaginal discs in Drosophila | Fly-QMA: Quantitative Mosaic Analysis in Drosophila | Fly-QMA is part of the NU FlyEye platform for studying gene expression in the developing Drosophila eye. The package enables Quantitative Mosaic Analysis (QMA) - that is, it helps users compare expression levels between distinct clonal subpopulations within the eye epithelium
FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.
Formal model checking based pathway analysis (FoPA) - tool for identification of perturbed signaling pathways in clinical conditions using formal methods.
The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation
Data resource collecting taxonomic composition and related metadata of > 2300 food and food-related samples. Data were produced according to a standardized pipeline and each sample is identified according the FoodEx2 classification (developed by the European Food Safety Authority to facilitate the comparison among different studies).
Quality control on genetic variants from next-generation sequencing data using random forest. This classifier uses random forest model to identify good or bad variants from grey variants. $ conda install forestqc -c avallonking. To install the software. This software is compatible with OSX, 64-bit Linux and 64-bit Windows systems. If no HWE p-value file provided, HWE p-value would be computed by ForestQC. Or if ForestQC cannot find HWE p-value for some sites in the provided HWE p-value file, ForestQC would compute HWE p-value for those sites
A database for the late quaternary fossil records of Sahul along with data processing scripts.
FossilJ is a ImageJ plugin for fossil data acquisition and semi-automatic measurements by image analysis.
Message-oriented, horizontally scalable ETL system for scientific data integration and enhancement.
Automated tool for animal detection in camera trap images.
Graphical tool for assessing fractionation bias following polyploidy.
An efficient Python library to setup quantum chemistry calculations on peptides models. fragbuilder is a tool to create, setup and analyze QM calculations on peptides. FragBuilder will run with most versions of Open Babel, however there was bug in Open Babel which prevented some dihedral angles to be set accurately. If you experience this while using fragbuilder you will have to update your Open Babel
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. FreeHi-C pipeline for high fidelity Hi-C data simulation. FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation. FreeHi-C (v1.0) is short for Fragment interactions empirical estimation for fast simulation of Hi-C data. It is a data-driven Hi-C data simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating an interaction distribution of genome fragments and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data. FreeHi-C not only can be used to study and benchmark a wide range of Hi-C analysis methods but also boosts power and enables false discovery rate control for differential interaction detection algorithms through data augmentation
Frela is a web service for computing functional relationships of protein pairs based on Gene Ontology (GO) annotations. It allows very fast calculation of protein functional similarity based on their GO annotations for biological process (BP), molecular function (MF), and cellular component (CC) ontologies using various popular semantic similarity measures that can be combined arbitrarily with a set of widely used mixing strategies.
FrogCap is a modular sequence capture probeset for phylogenomics and population genetics for frogs
FullMeSH is a large-scale MeSH indexing method taking advantage of the recent increase in the availability of full text articles. The software is available upon request.
identification and prioritization of functional differential m6A methylation genes | A R package used to identify single base resolution m6A and differential m6A methylation site from MeRIP-seq data version 1.0
A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information. Functional potential of bacterial genomes and microbiomes from gene context information. This feature allows the user to input a newly sequenced genome and annotate it using gene context based modules generated using extensive literature mining and manual curation. Users can also carry out comparative analysis (synteny view using parallel coordinates) of the uploaded genome with genomes already sequenced in NCBI using interactive visualizations. This feature allows comparison of functional modules in sequenced genomes obtained from NCBI. Users can interactively select upto five genomes which are compared using a synteny based visualization (parallel coordinates) and circular genomic representations. Information about individual modules in all these genomes can also be viewed as tabular outputs
User-friendly graphical interface that allows to visualize and summarize the functional annotations of one or multiple molecular biology experiments at once.
A systematic pipeline to unravel the convergence patterns of genetic variants in ASD | A Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in Complex Diseases | FunVar (Functional annotation of Variants ) utilizes the existing resources to streamline and to improve the functional enrichment analysis of genetic variants disrupting genes in patients. FunVar, a semi-automated pipeline consist of three different and independent modules
Automated and interactive pattern recognition tool to integrate time with multi-omics assays.
The code which segment the retinal blood vessels accurately. The Kirsch's template is used for tracking the larger blood vessels; fuzzy c-means is used to segment smaller blood vessels. The region based active contour method is used for edge detection and Morphoplogical operations are used to remove the background from the foreground fundus image. This methodology is suitable for different fundus image databases captured using different fundus cameras.
Locating Retinal Blood Vessels on Fundus Images by Kirsch s Template and Fuzzy C-Means
R package for QTL mapping using longitudinal phenotypes.
An accurate prediction of fusion genes from RNA-Seq data. Homepage may be broken as of January 4th, 2021.
An interactive genomic graph viewer. G-Graph is a free-software graphical desktop application that allows you to perform efficient exploratory analysis of genomic copy number and other numeric datasets. G-Graph can be installed and runs under the Linux, Mac, and Windows operating systems. G-Graph's features include the ability to easily zoom and scroll the view, alter the visual display properties, display gene annotations, link genes to the UCSC genome browser, and save application views to image and pdf format. G-Graph is also very fast and therefore supports smooth scrolling and zooming of views even for millions of data points
Galaxy-based platform for collaborative annotation of eukaryotic genomes.
Assessing the performance of genome-wide association studies for predicting disease risk.
Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation.
R package to interactively visualize genetic mutation data using a lollipop-diagram.
A Python script for dividing genome annotation files into feature-based files. A python script for extracting genome features from GTF/GFF3.
Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data
A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction.
Online tool to build 3D models of GAG sequences from GlycoCT codes.
A Docker-based package for genome analysis and visualization.
GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations.
An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries | Geometry-preserving Adaptive Mesher | GAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others. GAMer has the following main features: | Geometry-preserving Adaptive Mesher — GAMer v2.0.5 documentation | Free document hosting provided by Read the Docs
Collection of commands for working with phylogenetic data.
a GPU accelerated sequence alignment library for high-throughput NGS data. GASAL2 - GPU-accelerated DNA alignment library. GASAL2 is an easy-to-use CUDA library for DNA/RNA sequence alignment algorithms. Currently it supports different kind of alignments:. A Linux platform with CUDA toolkit 8 or higher is required, along with usual build environment for C and C++ code. GASAL2 has been tested over NVIDIA GPUs with compute capabilities of 2.0, 3.5 and 5.0. Although lower versions of the CUDA framework might work, they have not been tested
Customizable computational tool included in Genome Analysis Toolkit (GATK) for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.
GBIF—the Global Biodiversity Information Facility—is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.
The Empusa code generator and its application to GBOL. GBOL; Genome Biology Ontology Language. To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). A group is a collection of several projects. If you organize your projects under a group, it works like a folder.
Screening populations for copy number variation using genotyping-by-sequencing | Detection of deletions and duplications from GBS data | delgbs is an R package which provides tools for detecting copy number variation from genotyping-by-sequencing (GBS) data. delgbs bases its CNV calls on the number of reads per sample in discrete bins (e.g. 1-kb bins) located along a reference genome
Galaxy workflow system for predictive model building for virtual screening.
Graph convolution for predicting associations between miRNA and drug resistance | IMPLEMENT FOR graph convolution for predicting associations between miRNA and drug resistance using raw data
Graph convolutional networks for inferring cell-cell interactions. using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions. GCNG for extracellular gene relationship inference. (A) GCNG model using spatial single cell expression data
Web tool for guanylyl cyclase functional centre prediction from amino acid sequence.
Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy. This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species. The gene sequence and genetic feature variation between different individuals are very important for natural variation research
GEnetic Antibiotic Resistance and Susceptibility Database.
Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification. graph embedding deep learning guide microbial biomarkers' identification.
Accurate Cell Type Quantification from Gene Expression Data | Abstract The cell type composition of heterogeneous tissue samples can be a critical variable in both clinical and laboratory settings. However, current experimental methods of cell type quantification (e.g. cell flow cytometry) are costly, time consuming and can introduce bias. Computational approaches that infer cell type abundance from expression data offer an alternate solution. While these methods have gained popularity, most are limited to predicting hematopoietic cell types and do not produce accurate predictions for stromal cell types. Many are also limited to particular platforms, whether RNA-Seq or specific microarray models. To overcome these limitations, we present the Gene Expression Deconvolution Interactive Tool, or GEDIT. Using simulated and experimental data, we demonstrate that GEDIT produces accurate results for both stromal and hematopoietic cell types
Lessons in Multi-Institution Teamwork Using Collaboration Software | Dashboard to view/download files from segregated Google Shared Drives | Center for Genetically Encoded Materials (C-GEM) | GEM-NET is the home of the Center for Genetically Encoded Materials (C-GEM), an NSF CCI (Center for Chemical Innovation) | Center for Genetically Encoded Materials | C-GEM seeks to establish a fundamentally new way to program chemical matter and transform the way we produce materials and medicines
a simple and fast global epistatic model predicting mutational effects | The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modelling inter-site dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present GEMME (www.lcqb.upmc.fr GEMME), an original and fast method that predicts mutational outcomes by explicitly modelling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods
GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae.
Extracting Views into Genome-scale Metabolic Models. The GEMtractor a platform for trimming and extracting genome-scale metabolic models (GEMs).
a shiny web application for gene expression normalization, analysis and visualization. GENAVi (Gene Expression Normalization Analysis and Visualization) is an rshiny web application that provides a GUI based platform for the analysis of gene expression data. GENAVi combines several R packages commonly used for normalizing, clustering, visualizing, and performing differential expression analysis (DEA) on RNA-seq data
Consortium identifying and classifying all gene features in the human and mouse genomes with high accuracy based on biological evidence, and releasing these annotations for the benefit of biomedical research and genome interpretation.
Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
An easy-to-use R pipeline for complete pre-processing of RNA-seq data | You're trying to access a page that requires authentication. × | Home: https://bitbucket.org/thomas_wolf/geo2rnaseq/overview | RNA-seq is a method that uses next-generation sequencing to quantify and analyze RNA. It can be used for finding significantly differentially expressed genes (DEGs) in well sequenced organisms. This package is a complete function library for analyzing read files, trimming of raw reads, mapping on reference genomes, counting reads per gene and finding significant DEGs | PRIVACY POLICY : EULA (Anaconda Cloud v2.33.29) © 2019 Anaconda, Inc. All Rights Reserved | Follow us on Twitter Tap To Close Find us on Facebook Tap To Close Follow us on Slideshare Tap To Close Find us on LinkedIn Tap To Close Follow us on Instagram Tap To Close Watch us on YouTube Tap To Close Follow us on GitHub Tap To Close
Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights into the question of how genes are regulated that governing a specific biological response. GREDB is a publicly available, manually curated biological database depositing the human gene expression regulation relationships (Links). To date, more than 39,000 Links have been contextual-ly annotated through the review of 53,000 plus abstracts. GREDB has the ability to analyze user-supplied gene expression data using the GEREA bioinformatics tool in a causal analysis oriented manner. The database can be searched use NCBI official gene symbol (eg. CDC42). The new version of GereDB is online for testing, please visit the following link: Run New GereDB online. Huang, Tinghua & Huang, Xiali & Shi, Bomei & Yao, Min. (2019)
GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.
Identification of transcriptional isoforms associated with survival in cancer patient. GESUR performs overall survival (OS) or disease free survival (DFS, also called relapse-free survival and RFS) analysis based on expression of a gene set. GESUR uses Log-rank test, a.k.a the Mantel–Cox test, for hypothesis test. Cohorts thresholds can be adjusted, and gene-pairs can be used. The cox proportional hazard ratio and the 95% confidence interval information can also be included in the survival plot.
Exploiting observations and measurement data standard for distributed LTER-Italy freshwater sites. Water quality issues. Geoinformation Enabling ToolkIT starterkit. Geoinformation Enabling ToolkIT starterkit ®. GET-IT allows you to easily share geospatial data on the web with simple actions. Share your maps, measurements, and sensors.
Gene expression based survival prediction for cancer patients. Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. This repository includes source code from the publication Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. You can find the code for the MTLR algorithm here http://pssp.srv.ualberta.ca/home/about.
An integrative machine learning approach to discovering multi-level molecular mechanisms of obesity using data from monozygotic twin pairs. We combined clinical, cytokine, genomic, methylation and dietary data from 43 young adult monozygotic twin pairs (aged 22 36, 53% female), where 25 of the twin pairs were substantially weight discordant (delta BMI > 3kg m2). These measurements were originally taken as part of the TwinFat study, a substudy of The Finnish Twin Cohort study. These five large multivariate data sets (comprising 42, 71, 1587, 1605 and 63 variables, respectively) were jointly analysed using an integrative machine learning method called Group Factor Analysis (GFA) to offer new hypotheses into the multi-molecular-level interactions associated with the development of obesity. New potential links between cytokines and weight gain are identified, as well as associations between dietary, inflammatory and epigenetic factors
Exact hypothesis testing for shrinkage based Gaussian Graphical Models.
Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.
Using Gauss Integrals to identify rare conformations in protein structures | Abstract The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general
GITAR (Genome Interaction Tools and Resources) is a standardized, easy to use and flexible solution to manage Hi-C genomic interaction data, from processing to storage and visualization, composed of two modules: HiCtool and a processed data library.
Charting the diversity of uncultured viruses of Archaea and Bacteria. Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. Perl script that automates the analyses to establish GL-UVAB (Genomic Lineages of Uncultured Viruses of Archaea and Bacteria). These include: 1) Identification of protein encoding genes with Prodigal. 2) All-versus-all protein search with Diamond. 3) Calculating Dice distances. 4) Building Dice tree using R 5) Identifying lineages based on the user defined criteria
A Python toolbox for investigating the association between gaze allocation and decision behaviour | A python toolbox for the Gaze Weighted Linear Accumulator Model (GLAM) | GLAMbox is a Python toolbox for investigating the association between gaze allocation and decision behaviour, and applying the Gaze-weighted Linear Accumulator Model (Thomas, Molter et al., 2019, full text available online)
Genomic loci annotation and enrichment tool.
Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Dimension Reduction of Non-Normally Distributed Data. Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.
16S subunit related sequences database, identified from metagenomic efforts as part of the Tara Oceans project. It includes a BLAST search tool. The analysis system incorporates the SILVA collection, allowing comparative analyses to identify unclassified sequences and their geographical distribution.
GLUE (Genes Linked by Underlying Evolution) is data-centric bioinformatics environment for virus sequence data, with a focus on variation, evolution and sequence interpretation.
Web-based tool to visualize, analyze, present and mine glycan microarray data.
Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies.
Predicting human lncRNA-disease associations based on geometric matrix completion. Recently, increasing evidences have indicated that dysregulations of long non-coding RNAs (lncRNAs) are implicated in various complex diseases. However, only a limited number of lncRNA-disease associations are experimentally verified. Prioritizing potential lncRNA-disease associations is beneficial not only for understanding disease mechanisms at lncRNA level, but also for disease diagnosis. Various computational methods have been proposed, but precise prediction and full use of data's intrinsic structure are still challenging. In this study, we propose a new method, named GMCLDA (Geometric Matrix Completion lncRNA-Disease Association), to infer potential lncRNA-disease associations based on geometric matrix completion.
Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers | A growth chamber sensing system using the Raspberry Pi as a platform | GMpi: A Growth Chamber Monitoring System Using the Raspberry Pi as a Platform | The GMpi is a cost-effective solution for monitoring the conditions of a growth chamber, greenhouse, or any other facility for which specific conditions (temperature, light, humidity, etc.) need to be maintained
a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries
transforming GO terms and proteins to vector representations via graph embeddings. BACKGROUND:Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content to estimate the semantic similarity between GO terms; recently some research exploited word embeddings to learn vector representations for GO terms from a large-scale corpus. In this paper, we proposed a novel method, named GO2Vec, that exploits graph embeddings to learn vector representations for GO terms from GO graph. GO2Vec combines the information from both GO graph and GO annotations, and its learned vectors can be applied to a variety of bioinformatics applications, such as calculating functional similarity between proteins and predicting protein-protein interactions
Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant Informatics and Computation Lab. Click on the link to learn more. Publicly available GOMAP Datasets. These datasets generated by GOMAP are new high-coverage and reproducible functional annotation sets of protein coding genes based on Gene Ontology (GO) term assignments. Follow the DOI link for more information, access, and download. Check out the main project page (Home on the left) to find out more about how they were generated and how you can use the pipeline yourself.
Generator of probes for capture Hi-C experiments at high resolution.
A Large High-Diversity Benchmark for Generic Object Tracking in the Wild. Generic Object Tracking Benchmark. A large, high-diversity, one-shot database for generic object tracking in the wild
Tool to navigate through branches of gene ontology hierarchy.
Advances in gene ontology utilization improve statistical power of annotation enrichment | Welcome to GOcats’ documentation! — GOcats 1.1.5 documentation
Tool for interactive Gene Ontology analysis.
GPCRmd uncovers the dynamics of the 3D-GPCRome. The online resource for GPCR simulations. GPCRmd is an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visualize, inspect, and analyse GPCR molecular dynamics.
Inherited glycophosphatidylinositol deficiency variant database.
a Gene PREDiction model accounting for 5 '- 3' GC gradient. a Gene PREDiction model accounting for 5'-3' GC gradient. A new hidden Markov model (HMM)-based ab initio. gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes.
A Docker-based Resource for Genomics, Proteomics and Systems biology. Welcome to GPSRdocker A resource for Genomics, Proteomics and Systems biology. GPSRdocker is a docker-based container that provides a resources on Genomics, Proteomics and System Biology
Implementation of the Molecular Electrostatic Potential over Graphics Processing Units.
A framework for querying General Feature Format (GFF) files and feature expression files in a compressed form”. This is the GPress, a framework for querying GTF, GFF3 and expression files in a compressed form. Here, we will use the test files to provide an example of how to use GPress. We will use GTF file for illustration since the GFF3 file is nearly the same except slight format variations. We will store the compressed GTF file and compressed expression file in a new folder gtf1
deconvolution of shared pseudo-profiles at single-cell resolution. Code for the GPseudoClust method, including pre- and postprocessing steps. Magdalena E Strauß, Paul DW Kirk, John E Reid, Lorenz Wernisch (2019); GPseudoClust: deconvolution of shared pseudo-trajectories at single-cell resolution
A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner | GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner
Generator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks.
GRANVIL (Gene- or Region-based ANalysis of Variants of Intermediate and Low frequency) - performs rare-variant analysis of binary or quantitative phenotypes. The method is based on accumulation of minor alleles of rare or uncommon markers discovered through dense genotyping or resequencing data. Association analyses are based on gene- or other pre-defined regions, determined by analyst.
Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes | Genome Relative Abundance to Sequencing Effort: a tool for planning MAG sequencing experiments | grase is a package that estimates the sequencing effort required to achieve a goal of MAG construction. This is based on a model presented in Royalty and Steen (2018)
From photo-geology to 3D geological models. An open source approach. GRASS GIS is a free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.
Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO) RNA-seq Data.
Guide RNA Identifier for Balancer Chromosome Generation (GRIBCG) - software for selection of sgRNAs in the design of balancer chromosomes.
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms | Abstract The gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. Reliable inference of GRNs is however still a major challenge in systems biology. To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard
GROMACS to LAMMPS (GRO2LAM) - converter for molecular dynamics software.
A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform genetic data on genes associated with the biological response to nicotine exposure and smoking related behaviors or diseases. By this database, we try to make such information easily accessible and interpretable for investigators in the smoking/nicotine addiction research community
Strategy for Intercorrelation Identification between Metabolome and Microbiome. Accumulating evidence points to the strong and complicated associations between the metabolome and the microbiome, which play diverse roles in physiology and pathology. Various correlation analysis approaches were applied to identify microbe-metabolite associations. Given the strengths and weaknesses of the existing methods and considering the characteristics of different types of omics data, we designed a special strategy, called Generalized coRrelation analysis for Metabolome and Microbiome (GRaMM), for the intercorrelation discovery between the metabolome and microbiome.
Gene Set Annotation - an alternative to enrichment analysis for annotating gene sets.
The Gender, Sex, and Sexual Orientation (GSSO) Ontology | GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior | Gender, Sex, and Sexual Orientation
Package for network-weighted gene-set clustering and network visualization.
GTA_Hunter is a 'support-vector machine' (SVM) classifier that distinguishes gene transfer agent (GTA) genes from their viral homologs | The classifier was developed to detect GTA genes that are homologous to 11 of the genes that encode the GTA in Rhodobacter capsulatus (RcGTA) (see Kogay et al, 2019). However, the classifier can be trained to detect other RcGTA genes, other GTAs, or even other virus-like elements, as long as there is training data available and the two classes have distinct amino acid composition
A User-Friendly Framework for Bacterial Comparative Genomics | Backend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | Frontend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | This project is the frontend part of the GTACG framework (Gene Tags Assessment by Comparative Genomics): a framework for comparative analysis of bacterial genomes | A proper execution of the GTACG pipeline requires at least genomic files (in fasta format) and coding sequences (CDS, faa, gbf, gb, gff) files. Additionally, you can define phenotypes groups. The following command lines can be used to download files with examples of these formats:
Annotation tool for providing image and text annotations to image-based datasets.
Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy | Toolkit for establishing, updating, and validating GTDB species clusters
a toolkit to classify genomes with the Genome Taxonomy Database. GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).
Unblended Disjoint Tree Merging using GTM improves species tree estimation. Abstract Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods
Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.
Multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles.
Expanding the capillary electrophoresis based glucose unit database of the GUcal app. GUcal 1.1c - Internal / bracketing standard approach with GlycoStore database
A GPU accelerated framework for efficient permutation based genome-wide association studies | GPU accelerated GWAS framework based on TensorFlow | GWAS-Flow was written and published in the hope that you might find it useful. If you do and use it for your research please cite the paper published alongside the software, which is currently publicly accessible on the BiorXiv preprint server. https://www.biorxiv.org/content/10.1101/783100v1 doi: 10.1101/783100
a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. A database for human genetic variants identified by genome-wide association studies. Enter a study id, dbSNP id, MeSH/HPO phenotype term, keywords, author names, HGNC gene symbols, chromosomal regions or PUBMED identifier. The NHGRI-EBI GWAS Catalog: a curated collection of all published genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. GWAS CENTRAL - INDIA : A Genotype - Phenotype Association Database. GWAS Central - India (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. GWAS Central provides a complete Study metadata file for use in data citation research, tracking researcher contributions, data discovery projects, etc
Non-local prior based iterative SNP selection tool for genome-wide association studies.
When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders | Grey-to-White matter Percent Contrast in Autism Spectrum Disorders | This repository contains the code used for the analyses described in our manuscript "Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders" (Preprint: https://doi.org10.1101/750117) | We used this code to analyse the grey-white contrast in Autism Spectrum Disorder using magnetic resonance imaging from ABIDE 1&2 datasets (http://fcon_1000.projects.nitrc.org/indi/abide/)
GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.
An online catalog that lists all the tools available on various Galaxy instances and thus allows through a simple web interface to quickly find on which instances a tool is usable.
A wide variety of tools from the Galaxy instance of Institut Pasteur, France.
We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a ‘visualise-filter-visualise’ paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data.
Tools for genotyping gall-causing phytopathogenic bacteria and identifying strains isolated from Agrobacterium or Rhodococcus-induced galls using MLSA and other methods.
Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways.
Efficient random sampling for constraint-based (COBRA) models.
Supervised classification enables rapid annotation of cell atlases | Garnett - Automated cell type identification
Development of Open-source Software and Gaze Data Repositories for Performance Evaluation of Eye Tracking Systems. Repository for GazeVisual performance evaluation software tools. The GazeVisual-Lib is a repository of software tools for practical evaluation of eye trackers and gaze data quality. All codes in this repository are released under GNU General Public License v3.0
A consensus Gene-disease Event Extraction System based on frequency patterns and supervised learning. Abstract Motivation The genetic mechanisms involved in human diseases are fundamental in biomedical research. Several databases with curated associations between genes and diseases have emerged in the last decades. Although, due to the demanding and time consuming nature of manual curation of literature, they still lack large amounts of information. Current automatic approaches extract associations by considering each abstract or sentence independently. This approach could potentially lead to contradictions between individual cases. Therefore, there is a current need for automatic strategies that can provide a literature consensus of gene-disease associations, and are not prone to making contradictory predictions
GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.
Genome-Phenome Explorer (GePhEx): A tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence.
GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
Program for gene presence-absence analysis for series of closely related bacterial genomes from annotated GFF files.
Read GenBank-formatted flat file into structure
Utilities for manipulations and visualization tasks on GenBank taxonomic information.
Genome exploration open source tool for variants generated from high-throughput sequencing projects.
A web application and database for gene family-based classification and functional enrichment analysis. Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query.
a python module for the simple generation and manipulation of genome graphs. A repository for the GenGraph toolkit for the creation and manipulation of graph genomes
Genome Integrative Explorer System. Genome Integrative Explorer System (GenIE-Sys). Website : Documentation : Demo : Users. Welcome to GenIE-Sys’s documentation! — GenIE-Sys 0.1 documentation. The Genome Integrative Explorer System(GenIE-Sys) based on a flat files Content Management System which is a dedicative in-house system to facilitate external groups in setting up their own web resource for searching, visualizing, editing, sharing and reproducing their genomic and transcriptomic data while using project raw data(gff3,fasta,fatsq) as an input. This is the Development and the latest version of GenIE-Sys. Our main goal is to add admin interface where users can easily create database plus integrate different types of data, create new pages and menus, configure tools and changing website layout by using Themes. Free document hosting provided by Read the Docs
Genomic Input Output (GenIO) identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner.
Integrated resource for analyzing the evolution and function of primate-specific coding genes.
Machine learning method that utilizes transcriptome-wide gene co-expression to generate a distributed representation of genes.
an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) provide effective methods for detecting DNMs and prioritizing candidate genes. However, it remains a challenge for scientists, clinicians, and biologists to conveniently access and analyse data regarding DNMs and candidate genes from scattered publications. To fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different degrees of statistical evidence, including 346 genes with false discovery rates <0.05. We then developed a database called Gene4Denovo (http: www.genemed.tech gene4denovo ), which allowed these genetic data to be conveniently catalogued, searched, browsed, and analysed
Identifying gene function and module connections by the integration of multispecies expression compendia. Integrative systems analysis identifying the associations between genes and biological process or modules. For analyzed results for a given gene or module/gene set, please visit https://systems-genetics.org/genebridge. Systems analysis toolkit containing Gene-Module Association Determination (G-MAD) and Module-Module Association Determination (M-MAD) to identify the associations between genes and biological process or modules, as well as associations between modules.
Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm (the set should be large enough to permit self-training). A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models. A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher).
Analysis of copy number variation using Illumina Infinium DNA methylation arrays.
Score for estimating gene pathogenicity in individuals using next-generation sequencing data.
A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss | GeneRax is a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss
Network-based identification of disease genes in expression data.
Ordering gene-expression and functional events in single-cell experiments. Data-driven Network Biology Group. The goal of GeneSwitches is to discover the order of gene-expression and functional events during cell state transitions at a single-cell resolution. It works on any single-cell trajectory or pseudo-time ordering of cells to discover the genes that act as on/off switches between cell states and importantly the ordering at which these switches take place.
Investigation of the background prevalence (rare, protein altering variants that could be classified as pathogenic) of exonic variation.
GeneWalk identifies relevant gene functions for a biological context using network representation learning | GeneWalk determines for individual genes the functions that are relevant in a particular biological context and experimental condition. GeneWalk quantifies the similarity between vector representations of a gene and annotated GO terms through representation learning with random walks on a condition-specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks
Tool for clinicians to make connections to share genetic data by being matched using phenotype data. It aims to create a portal for clinicians to enter phenotypic case data for individuals who have had exome sequencing without a genetic diagnosis.
Set of tools for assisting in highly precise genome editing and engineering.
Platform based on Artificial Intelligence Neural Network. Suggest the most probable gene (protein) based on deep learning on million of scientific papers. It also link the input+output to many free research tools to understand what the neural network suggested and why.
search engine for ranking genes from arbitrary text queries | Submit biomedical terms to receive ranked lists of relevant genes | Submit any search terms to Geneshot to receive prioritized genes that are most relevant to the search terms. Geneshot finds publications that mention both the search terms and genes. It then prioritizes these genes using various methods: 1) list of genes from publications; 2) predicted genes using gene-gene similarity matrices derived from a variety of resources ( ARCHS4 : Enrichr : Tagger : AutoRIF : GeneRIF ) | Examples: Wound healing : Hair loss : Trichostatin A : Glioblastoma : Diabetes
> LOW CONFIDENCE! | Uncovering missed indels by leveraging unmapped reads | Genesis-indel is a computational pipeline to explore the unmapped reads to identify novel mutations that are initially missed in the original alignment. The genes containing such mutations can be investigated to gain important biological insights
Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. A tool for genogeographic inference
GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces are heterogeneous, not interoperable, and with limited capabilities. GenoSurf provides access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of attributes are semantically enriched by making use of the most suited available ontologies. Users provide as input the search terms, set the desired level of ontological enrichment, and obtain as output the identity of matching data files at the various sources. We integrated about 40 million metadata of several major valuable data sources, including four providers of clinical and experimental data (TCGA, ENCODE, 1000 Genomes, and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq).
Database of genomic data related to marine species of biological interest. It allows analyses of reference genome annotations, organising the resources in an integrated way
integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Genome3D Annotating Genomes with Structures. Search Genome3D find structural annotations for your proteins. Tool to interact with the Genome3D API. Genome3D provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, THREADER, PHYRE. The tool genome3d-api aims to make communicating with the Genome3D API as convenient as possible. However, since the API has been defined using OpenAPI standards, you should be able to point any OpenAPI compatible client to the following specification:
Graphical tool for modeling and analyzing 3D genome structure.
Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo script. Generic Ensembl plugin for genomehubs sites. GenomeHubs is designed to make it easy to set up and host a core set of bioinformatics tools to help research communities share and access genomic datasets for non-model organisms. Sets up a GenomeHubs site hosting a mirror of the core database for the Glanville fritillary, Melitaea cinxia and imports the genome of the winter moth, Operophtera brumata, into a GenomeHubs site from FASTA and GFF.
A quality assessment tool for genome assemblies and gene structure annotations. GenomeQC generates descriptive summaries with intuitive graphics for genome assembly and structural annotations. It also benchmarks user supplied assemblies and annotations against the publicly available reference genomes of their choice. It is optimized for small and medium sized genomes (<2.5 Gb) and has pre-computed results for several maize genomes.
A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome. About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety Test new features.
Using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes | # 2019 Bioinformatics Methods / GenomicGPS | GenomicGPS is a software package for applying multilateration to genomic data
Advancing clinical cohort selection with genomics analysis on a distributed platform. Highly performant data storage in C++ for importing, querying and transforming variant data with Java/Spark. Used in gatk4. Sparse Array Storage for Genomics. GenomicsDB, originally from Intel Health and Lifesciences, is built on top of a fork of htslib and a tile-based array storage system for importing, querying and transforming variant data. Open source project providing a collaboration to optimizing sparse array storage for genomics. Using high-level APIs provided in C++, Java*, and Spark*, users can both write and read variant records to and from GenomicsDB shared-nothing instances in parallel using multiple processes in a Single Process Multiple Data (SPMD) manner.
Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.
Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (https://www.aniseed.cnrs.fr) database.
A multigenome platform with information on genomes and gene annotations from different tomato cultivars. This platform includes genomes from Heinz 1706, Lucariello and Corbarino (tomato landaraces) with related genome browsers and transcriptomic data. It gives free access to the recently sequenced Italian tomato varieties and offers tools for their comparative analysis. (Tranchida-Lombardo et al., ‎2017; https://doi.org/10.1093/dnares/dsx045)
A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all protein and RNA structures deposited in the PDB. This database presents also various statistics and extensive information about biological function of analyzed biomolecules. Moreover, users can analyze their own structures
Open source tools to support Integrated Coastal Management and Maritime Spatial Planning. Geospatial tools to support Maritime Spatial Planning. GeoNode is a web-based application and platform for developing geospatial information systems (GIS) and for deploying spatial data infrastructures (SDI). Tools4MSP is a python-based Free and Open Source Software (FOSS) for geospatial analysis in support of Maritime Spatial Planning (MSP) and marine environmental management. Tools4MSP implements models for Cumulative Effects Assessment (CEA), Maritime Use Conflict (MUC) Analysis and Marine Ecosystem Services Threat (MES-Threat) analysis. The package can be used as stand-alone library or as integrated GeoNode Plugin providing additional functionalities to geospatial CMS and enhancing usability through a graphical user interface (GUI). Gallery Quick Start Try the Demo Blog. The webtools (GeoNode integration) analysis workflow follows a four step approach:
database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes | Gephebase compiles genotype-phenotype relationships, i.e. associations between a mutation and a phenotypic variation. Gephebase consolidates data from the scientific literature about the genes and the mutations responsible for phenotypic variation in Eukaryotes (mostly animals, yeasts and plants). We plan to include non Eukaryote species in the future. For now, genes responsible for human disease and for aberrant mutant phenotypes in laboratory model organisms are excluded and can be found in other databases ( OMIM , OMIA , FlyBase , etc.). QTL mapping studies that did not identify single genes are not included in Gephebase | If you use Gephebase for your publication, please cite: Martin, A., & Orgogozo, V. (2013). The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution, 67(5), 1235- 1250
German Obstetric Surveillance System (GerOSS) - project to improve the treatment of obstetric rare diseases and complications using a web based documentation and information platform.
A versatile neuroimaging encoder for extracting deep features from multisequence brain MRIs
The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.
A fast and memory-efficient tool for rare cell type identification. Rare cell identification tool for single cell datasets. GiniClust is a clustering method specifically designed for rare cell type detection.
Fast and accurate interpretation of nonlinear gapped k-mer SVMs | Accompanying repository for GkmExplain paper | GkmExplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines | This repository accompanies Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer SVMs by Shrikumar*†, Prakash* and Kundaje† (*co-first authors †co-corresponding authors).
Tool for generating structural ensembles of partly disordered proteins from chemical shifts.
Glycan Microarray Database and Analysis Toolset.
Software for automated interpretation of N -glycan profiles after exoglycosidase digestions.
Conversion tool for translating the complexities of glycans.
a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | Glyco-DIA is a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | The Glyco-DIA library consists of sublibraries obtained from human cell lines and human serum, and it currently covers 2,076 O-glycoproteins (11,452 unique glycopeptide sequences) and the five most common core1 O-glycan structures. Applying the Glyco-DIA library to human serum without enrichment for glycopeptides enabled us to identify and quantify 269 distinct glycopeptide sequences bearing up to 5 different core1 O-glycans from 159 glycoproteins in a singleshot analysis. The DIA method is expandable and widely applicable to different glycoproteomes, and it may represent a first step towards direct and comprehensive approach to glycoproteomics
a Python framework for the rapid modeling of glycans. Framework for the rapid modeling glycans and glycoproteins. Glycosylator is a Python framework for the identification, modeling and modification of glycans in protein structure. It can be used directly in a Python script through its API or through its Graphical User Interface (GUI). The GUI provides a straightforward 2D rendering of a glycoprotein that allows for a quick visual inspection of the gylcosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific 3D glycans on a protein structure using a library of predefined templates. Glycosylator has been implemented in a generic way allowing the user to expand the library to incorporate other polymers
Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.
Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data.
The Golden Gate cloning technique has been proven to be a highly efficient toolbox for a variety of cloning setups. Based on its modular concept it is particularly suitable for the use in multiple-site mutagenesis approaches. In this technical note we developed a protocol termed Golden Mutagenesis for the rapid, easy, reliable and cheap formation of mutagenesis libraries. One to five positions could be altered in parallel or simultaneously within two days. To facilitate the implementation of this technique, this R-library has been developed for the automated primer design and the graphical evaluation of sequencing results to determine the quality of the library.
a Julia package for approximate Bayesian computation with Gaussian process emulation | GpABC provides algorithms for likelihood - free parameter inference and model selection using Approximate Bayesian Computation (ABC). Two sets of algorithms are available:
A comprehensive tool for plasmid analysis using short-read graphs. gplas: Binning plasmid-predicted contigs using short-read graphs
An integrated database for grapevine data
Rapid and Versatile Sequence-to-Graph Alignment. Seed-and-extend program for aligning long error-prone reads to genome graphs. For a description of the bitvector alignment extension algorithm, see https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz162/5372677.
Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. A pipeline for structural clustering of RNA secondary structures. GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow.
Tool for calling transcription factor peaks on graph-based reference genomes using ChIP-seq data.
Biomedical Informatics Research Group (BMI)
Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | GraphMap2 - A highly sensitive and accurate mapper for long, error-prone reads | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and | GSNAP: Genomic Short-read Nucleotide Alignment Program | Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget
Publicly available novel algorithm and software for discovering and genotyping sequence variants.
A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BACKGROUND:Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients. Relapsing Remitting Multiple Sclerosis (RRMS) is one of the most common form of MS in adults and is characterized by a series of neurologic symptoms, followed by periods of remission. Recently, many treatments were proposed and studied to contrast the RRMS progression. Among these drugs, daclizumab (commercial name Zinbryta), an antibody tailored against the Interleukin-2 receptor of T cells, exhibited promising results, but its efficacy was accompanied by an increased frequency of serious adverse events.
Web-based tool that rapidly designs custom CRISPR screens targeting sets of genes defined by the user.
Predicting gene regulatory interactions based on spatial gene expression data and deep learning | Gene regulatory interaction prediction through Deep Learning | Gene regulatory interaction prediction through Deep Learning By Qingwei Fang, 2018
A model for studying living resources through digestive efficiency | The neural computational model GrowthEstimate is introduced with focusing on new perspectives for the practical estimation of weight specific growth rate (SGR, % day-1). It is developed using recurrent neural networks of reservoir computing type, for estimating SGR based on the known data of three key biological factors relating to growth
Comprehensive biological interpretation of gene signatures using semantic distributed representation. GsVec (Gene signature Vector) is an analysis method that supports the biological interpretation of Gene signature obtained by gene expression analysis of Bioinformatics. The association between the gene signature to be interpreted and the gene signature of the Pathway / Gene Ontology data base is performed by natural language processing
Program for preparing small-molecule libraries for structure-based virtual screening.
The ML Glossary developed by H3ABioNet The machine learning glossary for Bioinformaticians | Ready to get started? Build your own site from scratch or generate one for your project | Code repository for the RefGraph project
Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. calculate haplotype-derived allele frequencies for pool-seq samples. HAF-pipe is a bash- and R-based pipeline to calculate haplotype-inferred allele frequencies from pool-seq data and founder SNP profiles. To simulate recombination and pooled sequencing data from a panel of sequenced founders, see the scripts HAFpipe-sim.run_forqs.sh and HAFpipe-sim.simulate_poolseq.sh in the simulations folder
HAMR (High-throughput Annotation of Modified Ribonucleotides) - web application that allows you to detect and classify modified nucleotides in RNA-seq data.
Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma using Large-scale Transcriptomics Data | A webserver to predict Hepatocellular carcinoma (HCC) | Pipeline Differential Expression Analysis | HCCpred is a web-bench for the prediction of tumorous and non-tumorous Hepatocellular Carcinoma (HCC) patients. Our major prediction modules based on the robust biomarkers such as 3-Gene HCC Biomarker, 4-Gene HCC Biomarker, 5-Gene HCC Biomarker. These HCC biomarkers identified using gene expression profiles of a total of 3,961 samples include 2,306 HCC and 1,655 non-tumorous samples. The datasets derived from various profiling platforms such as Affymatrix, Illumina, High-througput and Agilent. The user can also analyse the expression pattern of any of 26 "core genes of HCC" in cancerous vs normal conditions
Automated brain extraction of multisequence MRI using artificial neural networks | Brain extraction is a critical preprocessing step in the analysis of neuroimaging studies conducted with magnetic resonance imaging (MRI) and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy brains and thus frequently fail in the presence of pathologically altered brain or when applied to heterogeneous MRI datasets. Here we introduce a new, rigorously validated algorithm (termed HD-BET) relying on artificial neural networks that aim to overcome these limitations
Gaussian Mixture Copulas for High-Dimensional Clustering and Dependency-based Subtyping | MOTIVATION:The identification of sub-populations of patients with similar characteristics, called patient subtyping, is important for realizing the goals of Precision Medicine. Accurate subtyping is crucial for tailoring therapeutic strategies that can potentially lead to reduced mortality and morbidity. Model-based clustering, such as Gaussian mixture models, provides a principled and interpretable methodology that is widely used to identify subtypes. However, they impose identical marginal distributions on each variable; such assumptions restrict their modeling flexibility and deteriorates clustering performance. RESULTS:In this paper, we use the statistical framework of copulas to decouple the modeling of marginals from the dependencies between them. Current copula-based methods cannot scale to high dimensions due to challenges in parameter inference
Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats | Data package containing high-dimensional cytometry data sets in SummarizedExperiment and flowSet formats | R code to reproduce example in Figure 1 in our HDCytoData paper | The HDCytoData package is an extensible resource containing a set of publicly available high-dimensional flow cytometry and mass cytometry (CyTOF) benchmark datasets, which have been formatted into SummarizedExperiment and flowSet Bioconductor object formats. The data objects are hosted on Bioconductor's ExperimentHub platform
New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform | Essential genes are those whose loss of function compromises organism viability or results in profound loss of fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic and regulatory characteristics of human essential genes. First, we found that essential genes act as 'hubs' in protein-protein interaction networks, chromatin structure and epigenetic modification. Second, essential genes represent conserved biological processes across species, although gene essentiality changes differently among species. Third, essential genes are important for cell development due to their discriminate transcription activity in embryo development and oncogenesis
Aims to bring together geographically dispersed medical personnel in order to share a common workspace where they can collaborate over medical images in real-time.
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures. Hypermap Registry, remote map services made easy for your SDI. Hypermap Registry is a platform that manages OWS, Esri REST, and other types of map service harvesting, and orchestration and maintains uptime statistics for services and layers. Check Hypermap Registry documentation.
A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. The Hearing Impairment Ontology (HIO) is a collaboratively developed resource by a group of experts in different aspects of hearing impairment (HI) to provide a common controlled HI terminology and concepts. The HIO will allow researchers and clinicians alike to readily access standardised HI-related knowledge in a single location and promote collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic information. It is worth noting, this ontology provides an illustration of the adaptability of the Sickle Cell Disease Ontology framework for use in developing a disease-specific ontology.
Inferring Chromosome Radial Organization from Hi-C Data. The included Python scripts (mat2net.py, and predictCTpos.py) contain an implemention of the HIRAC computational technique described in the following manuscript.
Detection of novel HIV-1 drug resistance mutations by support vector analysis of deep sequence data and experimental validation. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV/SIV vaccine trials. Each of these topics are available through a dedicated database, extensively annotated and with many specialized search and analysis tools. The HIV databases are supported by the NIH and DOE and maintained at the Los Alamos National Laboratory. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes.
Online, Educational, Clinical Decision Support Tool to Guide Patient-Centered ARV Regimen Selection | HIV-ASSIST (HIV Antiretroviral Selection Support and Interactive Search Tool) is a web-based platform designed at Johns Hopkins University to assist and educate clinicians in personalizing ART regimens for their patients | HIV-ASSIST is an online, interactive, educational tool to inform clinical decision-making for ARV selection
A tool for detecting linked HIV-1 drug resistance mutations in next generation sequencing data. A script detect and calculate Linked HIV drug resistant mutations on single HIV genomes. HIV-DRLink_github.pl is a script that detects and calculates Linked HIV drug resistant mutations on single HIV genomes. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV SIV vaccine trials. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes
Optimal allocation of HIV resources among geographical regions.
Web server for predicting HIV-1 CRF01_AE coreceptor usage.
Massively parallel sequencing solutions for two common forensically used platforms | HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool | 8px 9px 10px 11px 12px 13px 14px 15px 16px 17px 18px | With the advancement of DNA phenotyping as a tool in Forensic and Anthropological usage, we now provide an easy to use interactive website to predict eye, hair and skin colour from DNA using the IrisPlex, HIrisPlex and HIrisPlex-S systems
Human kinase pocket database for drug design. BACKGROUND:The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot be directly used in the kinase drug study. Therefore, a comprehensive database of human kinase protein pockets is urgently needed to be developed. RESULTS:Here, we have developed HKPocket, a comprehensive Human Kinase Pocket database. This database provides sequence, structure, hydrophilic-hydrophobic, critical interactions, and druggability information including 1717 pockets from 255 kinases. We further divided these pockets into 91 pocket clusters using structural and position features in each kinase group. The pocket structural information would be useful for preliminary drug screening
Using RNA Sequencing to Characterize the Tumor Microenvironment | Using k-mers to call HLA alleles in RNA sequencing data | HLAProfiler uses the k-mer content of next generation sequencing reads to call HLA types in a sample. Based on the k-mer content each each read pair is assigned to an HLA gene and the aggregate k-mer profile for the gene is compared to reference k-mer profiles to determin the HLA type. Currently HLAProfiler only supports paired-end RNA-seq data
The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues | The HLA Ligand Atlas is a comprehensive, tissue and HLA allele specific collection of HLA ligands, generated from more than 1,000 MS experiments | This website uses cookies to ensure you get the best experience on our website. Learn more | Warning The HLA Ligand Atlas is currently in a beta test phase . Please notice that the data and interface design might undergo frequent changes. You are welcome to contact us at
A machine learning-based model to identify the hidden labels of m6A candidates. HLMethy: Machine learning-based model to identify the hidden labels of candidate m6A modifications
Older version of the HMMER3 program (https://bio.tools/hmmer3) used for searching sequence databases for sequence homologs, and for making sequence alignments.
Collection of workflows that handle processing several different data types assocaited with the IBDMDB (Inflammatory Bowel Disease Multi’omics Database) project.
Nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures.
Lab of Bioinformatics and Molecular Modeling
Integrated Gene and Drug Database for Head and Neck Cancer.
A new software tool for interpreting the cellular and network origin of human MEG/EEG data | The Human Neocortical Neurosolver (HNN) is a software tool that gives researchers/clinicians the ability to develop/test hypotheses on circuit mechanisms underlying EEG/MEG data | Click here to join our Google Group | Human Neocortical Neurosolver (HNN) is a user-friendly software tool that provides a novel solution to this challenge | Electro- and magneto-encephalography (EEG MEG) are among the most powerful technologies to non-invasively record human brain activity with millisecond resolution
HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification.
A quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases. Allows to compute the HOrizontal Pleiotropy Score (HOPS) from summary statistics. HOPS (HOrizontal Pleiotropy Score). The HOPS package allows to compute the horizontal pleiotropy score (HOrizontal Pleiotropy Score) from summary statistics. The package includes a shiny visualization tool to visualize and download the full set of HOPS results computed using UK Biobank summary statistics
Examining the basis of high-occupancy target regions.
An R package that facilitates the retrieval and analysis of the Human Protein Atlas data | To access this site please go to: http://alexdussaq.info/jsHPAanalyze | A Bioconductor package to retrieve and analyze data from the Human Protein Atlas | Results: HPAanalyze is an R package for retreiving and performing exploratory data analysis from HPA. It provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as download all staining images of interest. The package is free, open source, and available via Github | Background: The Human Protein Atlas program aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics
Collision Cross Section Calculations Using HPCCS. The High Performance Collision Cross Section (HPCCS) is a new software for fast and accurate calculation of CCS for molecular ions. Based on the Trajectory Method (TM), HPCCS was parallelized and optimized to be an user-friendly program. High Performance Collision Cross Section Calculation – HPCCS
Prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences. Mapping between HPO and GO terms. If you find HPO2GO useful, please consider citing this publication:. Mapping between Human Phenotype Ontology (HPO) and Gene Ontology (GO) terms for the prediction of gene/protein - function - phenotype - disease associations. In this study, a novel approach is proposed for the identification of relationships between biomedical entities by automatically mapping phenotypic abnormality defining HPO terms with biomolecular function defining GO terms, where each association indicates the occurrence of the abnormality due to the loss of the biomolecular function expressed by the corresponding GO term
Discovery of novel helix binding sites at protein-protein interfaces. Helix Positioner a program for locating helix binding sites at protien-protein interfaces.
The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas
Image-Based Quantitation of Host Cell-Toxoplasma gondii Interplay Using HRMAn. Host Response to Microbe Analysis. HRMAn enables you to automatically analyse parameters of host-pathogen interaction derived from immunofluorescent experiments
Model-free biomarker detection for ultra-high dimensional data | Versatile Nonlinear Feature Selection Algorithm for High-dimensional Data | Supervised, nonlinear feature selection method for high-dimensional datasets | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a black box (nonlinear) feature selection method considering the nonlinear input and output relationship. HSIC Lasso can be regarded as a convex variant of widely used minimum redundancy maximum relevance (mRMR) feature selection algorithm | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a nonlinear feature selection method considering the nonlinear input and output relationship
Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts. Code for our work developing and characterizing the HSMRF priors for birth-death processes. This repository contains code for analyses from "Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts" (Magee et al. 2019). In the directory 1_simulation_study is code for simulating a number of trees under a time-dependent birth-death process, inferring diversification rates under the HSMRF-based and GMRF-based models, and processing those results. In the directory 2_empirical_analyses is code for the empirical analyses presented in the manuscript. Both directories contain more extensive readme files.
A computational method to perform the integrated analysis of multiple heterogeneous time-series data. This program was designed for integrating analysis of multiple heterogeneous time-series gene expression data to identify response genes.
Histosketching Using Little Kmers (HULK) - tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
A pan-genome analysis pipeline for human genomes | Human pan-genome analysis pipeline | HUman PAN-genome analysis toolkit | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. It encourages us to build the pan-genome of human population. Previously, our team developed a "map-to-pan" strategy, EUPAN, specific for eukaryotic pan-genome analysis. However, due to the large genome size of individual human genome, EUPAN is not suit for pan-genome analysis involving in hundreds of individual genomes. Here, we present an improved tool, HUPAN (HUman Pan-genome ANalysis), for human pan-genome analysis | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions | We propose HUPAN strategy primarily in the 185 deep sequencing and 90 assembled Han Chinese genomes
R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean | Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity | Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer, Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis | The goal of hagis is to provide analysis tools for plant pathogens with gene-for-gene interactions in the R programming language that the original Habgood-Gilmour Spreadsheet, HaGiS, (Herrmann, Löwer and Schachtel) provided
A modular pipeline for high-throughput sequencing data analysis. High-throughput sequencing pipeline software. HaTSPiL is a a Python pipeline for High-Throughput Sequencing analysis. It has been designed to be used inside our laboratory, the Salvatore Oliviero lab within the HuGef institute, TO (IT). Whoever find it useful or a good starting point to develop his own pipeline is encouraged to use and hack the code
R package for power and sample size calculations in genetic association analyses of family triads and unrelated controls.
Association between DIO2 polymorphism and the risk of Kashin-Beck disease in the Tibetan population | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation
a variant-calling pipeline for phased genomes. This is the Haplotypo repository. This repository contains the Haplotypo pipeline. HaploTypo is a pipeline suited to map variants into haplotypes in genetic variation analyses. After mapping and variant calling on a phased reference genome, HaploTypo infers the haplotype correspondence for each heterozygous variant. It also generates two independent FASTA files for each reconstructed haplotype
Tool for visualizing haplotype diversity, based on a cluster-based model for haplotype variation
it is an easy-to-use and reliable bioinformatics tool that provides B-cells clonality assessment and MRD monitoring over time analyzing data from Next-Generation Sequencing (NGS) technique. The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database.
Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.). This is a repository for a analysis of avocado GBS data in R. This is a repository for a analysis of GBS data in R. The R packages used in this repository are shown below:.
Web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences. R package that provide interactive graphical interface for metabolic profiling. If you find it useful, please cite this work. to convert R variables into a JSON object and save it as a file. hastaLaVista is developed and tested using Chrome, although it is known to work with other browser. In the case that a feature is not working as expected please try using Chrome before filling an issue
Web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
R package for an Ultra-Fast and Comprehensive Gene Annotation in Plants.
A deep learning predictive model for multi-type biological dataset | HetEncs: A Deep Learning Classifier for Integrated Gene Expression Analysis
A genetic resource database for rubber tree genomic study | Molecular & Genetic Resources for Hevea tree
Building blocks for efficient handling of large Hi-C datasets. Framework for Storing and Accessing Hi-C Data Through HDF Files. HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization
Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line. An analytical and visualization tool for CNV discovery and contact map correction of Hi-C/3C-seq data of cancer cell lines. HiCNAtra is a MATLAB-based tool that accepts HDF5 files, the output of hiclib after applying the iterative-mapping technique, as input. HiCNAtra pipeline is divided into three modules: 1) computation of the read depth (RD) signal from Hi-C or 3C-seq reads (RD calculator), 2) RD-based detection of copy number events based on CNAtra approach (CNV caller) and 3) bias correction of chromatin interaction matrix introduced by CNVs and other systematic biases (Contact map corrector)
Computational method for resolution enhancement of Hi-C data. It uses a very deep convolutional neural network to learn the mapping between low-resolution and high-resolution Hi-C contact matrices.
A Novel Shiny App for Hi-C Data Analysis. R package that allows easily performing a complete Hi-C data analysis through a Graphical User Interface. HiCeekR is a novel Shiny based R package for Hi-C data analysis
An Online Application to Aid Matching Peptide Pairs with Isotopically Labelled PTMs | MOTIVATION:Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy light pair are assigned. In such cases, having a pair of MS MS spectra that differ due to an isotopic label can assist in identifying the relevant m z values that support the correct peptide annotation or can be used for de novo sequencing. RESULTS:We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra
Gradient-based, GPU-accelerated, high-precision contour-segmentation algorithm with application to cell membrane fluctuation spectroscopy.
Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data. High-dimensional mass cytometry (Cytometry by Time-Of-Flight; CyTOF) is a multiparametric single-cell approach that allows for more than 40 parameters to be evaluated simultaneously, opening the possibility to dissect cellular heterogeneity and elucidate functional interactions between different cell types. However, the complexity of these data makes analysis and interpretation daunting. We created High-throughput Population Profiler (HiPPO), a tool that reduces the complexity of the CyTOF data and allows homogeneous clusters of cells to be visualized in an intuitive manner. Each subpopulation is mapped to the Population Analysis Database (PANDA), an open-source, manually curated database containing protein expression profiles for selected markers of primary cells, allowing for cell type abundance in the analyzed samples to be monitored.
Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances.
Collaborative intra-tumor heterogeneity detection | An algorithm for collaborative intra-tumor heterogeneity detection | We introduce a method called Hintra for intra-tumor heterogeneity detection | Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult
Hippocampal segmentation for brains with extensive atrophy using three-dimensional convolutional neural networks. Welcome to HippMapp3r’s documentation! — HippMapp3r documentation. Free document hosting provided by Read the Docs
A human immunosuppression gene database. HisgAtlas is the first database that stores a list of immunosuppression genes collected by literature mining and manual curation. 995 human immunosuppression genes and 260 associated diseases are collected in this database. The user needs to log in for the curation. Please refer to our FAQ for detail. HisgAtlas is a manual curation database for human immunosuppression genes.
A practical guide for analysis of histone post-translational modifications by mass spectrometry. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0 or Skyline software. Raw data and example scripts can be found at: doi:10.25345/C5ZQ0F.
A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curated database offering variability and pathogenicity information about mtDNA variants. Data are gathered from HmtVar's twin database HmtDB, and further integrated with pathogenicity predictions as well as additional information from several online resources focused on mtDNA, such as MITOMAP, 1000 Genomes Project, MutPred, SNPs&GO and many others.
Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes. Phylogenetic profiling with orthology data. HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient
Detecting fabrication in large-scale molecular omics data | Fraud is a pervasive problem and can occur as fabrication, falsification, plagiarism or theft. The scientific community is not exempt from this universal problem and several studies have recently been caught manipulating or fabricating data. Current measures to prevent and deter scientific misconduct come in the form of the peer-review process and on-site clinical trial auditors. As recent advances in high-throughput omics technologies have moved biology into the realm of big-data, fraud detection methods must be updated for sophisticated computational fraud | In the financial sector, machine learning and digit-preference are successfully used to detect fraud | See our pre-press article at: https://www.biorxiv.org/content/10.1101/757070v1
Graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.
A first prototype Python plugin enabling exploratory spatial data analysis into QGIS. A QGIS plugin for hotspot analyis. Hotspot Analysis Plugin for QGIS.
Redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Web-based tools to search tissue specific housekeeping genes.
Housekeeping and Reference Transcript Atlas
Improved representation of sequence Bloom trees | Sequence Bloom Tree, supporting determined/how split filters | Jellyfish (Version 2.2.0 or later)
Manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites.
HumanMine integrates many types of data for Homo sapiens and Mus musculus
Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression | A Hurdle model is a modification of a distribution at zero. This package provides routines to estimate and sample from multivariate Hurdle models on a Normal density. These are distributions that are conditionally Normal, but with singularities along the coordinate axes, so generalize a univariate zero-inflated distribution
HyAsP (Hybrid Assember for Plasmids) - tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm.
Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.
A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery | Hybrid Molecules is defined as the design of new chemical molecule that hybridizes two or more pharmacophoric moieties from known identical or non-identical bioactive molecules, or two or more known identical or non-identical bioactive molecules directly into a single molecule to obtain better affinity and efficacy or to improve the properties of the parent molecules or to interact with two or multiple targets or to reduce undesirable side effects or to decrease in drug-drug interactions or reduce emergence of drug resistance | Hybrid Molecule Database (HybridMolDB) provides a versatile resource for the display, search, and analysis of the structure, manual-annotated design protocol, the pharmacological data, some physicochemical and ligand efficiency and druglike and ADMET characteristics and the proﬁle of targets of the well-known hybrid molecules
Joint Estimation of Gross Recharge, Groundwater Usage, and Hydraulic Properties within HydroSight. A toolbox for data-driven hydrogeological insights. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. Websites for you and your projects. HydroSight is a highly flexible statistical toolbox for quantitative hydrogeological insights. It comprises of a powerful groundwater hydrograph time-series modelling and simulation framework plus a data quality analysis module. Multiple models can be built for one bore, allowing statistical identification of the dominant processes, or 100’s of bores can be modelled to quantify aquifer heterogeneity. This flexibility allows many novel applications such as:.
An integrated data warehouse for the Hymenoptera Genome Database
Two hundred million combinatorially complete datasets from a single experiment | Generate all combinatorially complete datasets from the given genotype list | python3 HypercubeME.py -g test_complete_03.txt | Run in the command line following examples: | See the file 'test_complete_03.txt' for input example. Columns are tab-separated, first line is a header which is ignored by HypercubeME. First column (example: '0C:2T') is a column-separated mutation list of a particular mutant variant. Each mutation consists of mutated position and the variant (amino acid residue or RNA/DNA base) where it is mutated. For wild-type HypercubeME uses '0Z', where 'Z' means wild-type variant (amino acid residue or RNA/DNA base); however, in the genotype file wild-type can also be denoted as empty string as in the file 'test_complete_03.txt'. All other columns are ignored by HypercubeME
Method to construct module-level three-way interaction networks. The method is able to present integrative uniform hypergraphs to reflect the global dynamic correlation pattern in the biological system, providing guidance to down-stream gene triplet-level analyses.
A Deep Learning-Based Approach for High-Throughput Hypocotyl Phenotyping. A deep learning-based approach for high throughput plant phenotyping. This repository is the companion for the paper A deep learning-based approach for high throughput plant phenotyping, Dobos et al.. The dataset used in the article can be found at this page. Using a trained model for measuring hypocotyls. The pretrained model used in the research article can be downloaded here.
A Scalable Exploratory Framework for Analyzing Complex Phenomics Data. A header only software library helps to visually discover the insights of high dimensional complex data set. We can represent the category of points in a cluster using a pie chart. In our Hyppo-X framework, we have capability to define a category of a point using single or multiple columns of the dataset. Pie chart shows the percentage distribution of points among all categories. For instance, for the above sample dataset, we can define the locaion column named Loc as the category of all the points then we will get following graphs. Here, blue color indicates points those belong in location N and red color indicates points those belong in location K. This graph with pie chart node helps us to understand the behavior of points with respect to two locations. This software library is built to delve the insights of a complex high dimensional dataset
A self-consistent method to impute single cell RNA sequencing data | I-Impute is a “self-consistent” method method to impute scRNA-seq data. I-Impute leverages continuous similarities and dropout probabilities and refines the data iteratively to make the final output "self-consistent". I-Impute exhibits robust imputation ability and follows the “self-consistency” principle. It offers perspicacity to uncover the underlying cell subtypes in real scRNA-Seq data
A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data. Intuitive Integrative Interpretation (I3) of complex genetic data. 3 Interpreting genetics of gene expression in brains. 1 State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
A MATLAB framework for efficient microscopy image analysis development, applied to quantifying intracellular transport of internalized peptide-drug conjugate | IA-Lab: a MATLAB-based framework for high throughput custom image analysis | This is the central repo for the IALab software, including parsers of various microscopy experiments, into multidimensional and multichannel images, and core code for segmentation, measurement, export of results and display of images and results . Some example workflows are stored in the Examples directory
Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE) - web server designed for network-based genotype-phenotype mapping of clonal populations that display the same focal phenotype.
iLASH - IBD Estimation Using Locality Sensitive Hashing | iLASH: Ultra-Rapid Detection of IBD Tracts | iLASH divides the genotype data in consecutive slices and then runs LSH algorithm over each slice. Slices (windows) are, thus, the building blocks of IBD tracts. The following parameters control different properties of these slices
Attacks on genetic privacy via uploads to genealogical databases. Create figures for "Attacks on genetic privacy via uploads to genealogical databases" by Michael D. Edge and Graham Coop. README for gedmatch figures & emails. The files marked GEDmatch_*_Redacted.pdf are printouts of the display of the GEDmatch 1-to-1 match genome browser.
Tool for integrated sequence and 3D structure analysis of large macromolecular complexes.
Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets | ICA-in-Cancer-research-review-materials | Jupyter Notebook containing example of Independent Component Analysis (ICA) accompanying the review in Internal Journal of Molecular Sciences (IJMS) | "Independent Component Analysis of BIg Omics Data" | BIODICA: Independent Component Analysis for BIg Omics Data | Deconvolution of transcriptome through Immune Component Analysis | BIODICA is a user-friendly pipline for high-performant computation of independent components for omics data, using stability analysis and computing the optimal number of the components from their stabilities, and performing analyses for interpreting the results of ICA application | You can install deconICA from GitHub with: | AN R PACKAGE FOR IDENTIFYING IMMUNE-RELATED SIGNALS IN TRANSCRIPTOME THROUGH DECONVOLUTION OR UNSUPERVISED SOURCE SEPARATION METHODS
Nanoscale Distribution of Nuclear Sites by Super-Resolved Image Cross-Correlation Spectroscopy. User-fiendly code for image cross-correlation specroscopy (ICCS) analysis based on the following article:
Integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset. BACKGROUND:Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with genome-wide distributed SNPs instead of pedigree. The key step of it is to construct genomic relationship matrix (GRM) via genome-wide SNPs; however, usually the calculation of GRM needs huge computer memory especially when the SNP number and sample size are big, so that sometimes it will become computationally prohibitive even for super computer clusters. We herein developed an integrative algorithm to compute GRM.
Automated electroencephalographic independent component classifier, dataset, and website.
Accurate and reproducible prediction of ICU readmissions. The code in this repository was used to produce the results of this paper (awaiting acceptance, link will be updated). A walkthrough can be found in this notebook.
Web server for adult age estimation of human skeletal remains.
A MALDI bioinformatics platform for analyzing protein and small molecule MALDI-TOF MS data (with a particular focus on mic organism analysis )
Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. IDDomainSpotter – Section for Biomolecular Sciences. IDDomainSpotter is a sequence-based approach to assess and visualize domain organisation in long intrinsically disordered proteins based on compositional biases
An independently validated nomogram for isocitrate dehydrogenase-wild-type glioblastoma patient survival. Background:In 2016, the World Health Organization reclassified the definition of glioblastoma (GBM), dividing these tumors into isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant GBM, where the vast majority of GBMs are IDH-wild-type. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a nomogram for IDH-wild-type patients with newly diagnosed GBM.
Large-scale directed network inference with multivariate transfer entropy and hierarchical statistical testing | The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory. IDTxl provides functionality to estimate the following measures:
Predicting virus-receptor interactions based on similarity and semi-supervised learning. BACKGROUND:Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicting virus-receptor interactions are limited. RESULT:In this study, we propose a new computational method (IILLS) to predict virus-receptor interactions based on Initial Interaction scores method via the neighbors and the Laplacian regularized Least Square algorithm. IILLS integrates the known virus-receptor interactions and amino acid sequences of receptors. The similarity of viruses is calculated by the Gaussian Interaction Profile (GIP) kernel. On the other hand, we also compute the receptor GIP similarity and the receptor sequence similarity.
Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion. Kernelized Logistic Matrix Factorization based on Similarity Network Fusion for Predicting Virus-host Association. Xingpeng Jiang, xpjiang@mail.ccnu.edu.cn Dan Liu, liudan@mails.ccnu.edu.cn.
The ImmunoDataAnalyzer (IMDA) pipeline provides various methods for analysing immunological next-generation sequencing (NGS) data.
An update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. The public IMG/ABC site has limited features and tools.
IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, "IDENTIFICATION", "CLASSIFICATION", "DESCRIPTION", "NUMEROTATION", "LOCALIZATION", "ORIENTATION" and "OBTENTION". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized.
IMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI). Annotation is based on the IMGT-ONTOLOGY concepts.
IMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences.
IMGT/CloneSearch is the IMGT® tool allowing the search of a clone in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts.
IMGT/Collier-de-Perles is the IMGT® tool to draw standardized IMGT 2D graphical representations, or IMGT Colliers de Perles, of variable (V), constant (C), groove (G) domains, starting from the user own domain amino acid sequences. IMGT Colliers de Perles are based on amino acid sequences gapped according to the IMGT-ONTOLOGY concept of IMGT unique numbering.
IMGT/DomainDisplay is the IMGT® tool for the display of the amino acid sequences of the variable (V), constant (C) and groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/DomainGapAlign is the IMGT® tool for the analysis of amino acid sequences of variable (V), constant (C) or groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/DomainSuperimpose is the IMGT® tool to superimpose 3D structures of two domains from IMGT/3Dstructure-DB. Domain 3D structures are numbered according to the IMGT-ONTOLOGY concept of IMGT unique numbering.
IMGT/GENE-DB is the IMGT® database for immunoglobulin (IG) and T cell receptor (TR) genes and alleles (international nomenclature). Annotation is based on the IMGT-ONTOLOGY concepts.
IMGT/GeneFrequency is the IMGT® tool providing the frequency usage of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D) and joining (J) genes in Homo sapiens and Mus musculus rearranged sequences from IMGT/LIGM-DB. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/GeneInfo is the IMGT® tool providing combination (V-J and V-V) information for the human and mouse T cell receptor (TR) loci. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/GeneSearch is the IMGT® tool allowing the search of a gene in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts.
IMGT® tool providing the view of a gene in IMGT/LocusView. Display is based on the IMGT-ONTOLOGY concepts.
IMGT/HighV-QUEST is the IMGT® portal for NGS high-throughput nucleotide sequence analysis of immunoglobulins (IG) and T cell receptors (TR) variable domains, integrates IMGT/JunctionAnalysis and IMGT/Automat. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/JunctionAnalysis is the IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR). Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/LIGM-DB is the IMGT® database for nucleotide sequences with translation of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.
IMGT/LocusView is the IMGT® tool providing a view of immunoglobulin (IG), T cell receptor (TR) and major histocompatibility (MH) loci. Display is based on the IMGT-ONTOLOGY concepts.
IMGT/PRIMER-DB is the IMGT® database for oligonucleotides (primers) of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.
IMGT/PhyloGene is the IMGT® tool to compute and draw phylogenetic trees for immunoglobulin (IG) and T cell receptor (TR) V-REGION nucleotide sequences. Analysis is based on the IMGT-ONTOLOGY concepts.
IMGT/StatClnotype is the IMGT® tool for statistical analysis of sets from IMGT/HighV-QUEST output. IMGT/StatClonotype uses a generic statistical procedure for identifying significant changes in IG and TR differences of proportions of IMGT clonotypes (AA) diversity and expression. It uses the IMGT gene and allele nomenclature and it is based on IMGT-ONTOLOGY concepts.
IMGT/StructuralQuery is the IMGT® tool to retrieve IMGT/3Dstructure-DB entries using amino acid structural criteria for variable (V), constant (C) or groove (G) domains. Annotation is based on the IMGT-ONTOLOGY concepts.
IMGT/mAb-DB is the IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA). IMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.
Extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. IUPHAR Guide to IMMUNOPHARMACOLOGY. The IUPHAR/BPS Guide to IMMUNOPHARMACOLOGY. Description.
Aligner for mapping noisy long reads to the reference genome.
Inferring MiRNA Targets based on Restricted Boltzmann Machines (IMTRBM) for prediction of miRNA-target interactions (MTIs).
R package for network based differential expression analysis.
Interactive pathway modeling using natural language with automated assembly.
Flexible modelling of spatial variation in agricultural field trials with the R package INLA | This is the site for the INLA approach to Bayesian inference within the R project for Statistical Computing | "Bayesian inference with INLA" by Virgilio Gómez-Rubio Another book from Virgilio is soon here. While we're waiting for the printed one, the current version is available as a github book; see the book section. May be ..
Discovering nuclear targeting signal sequence through protein language learning and multivariate analysis. Nuclear localization signals (NLSs) are peptides that target proteins to the nucleus by binding to carrier proteins in the cytoplasm that transport their cargo across the nuclear membrane. Accurate identification of NLSs can help elucidate the functions of nuclear protein complexes. The currently known NLS predictors are usually specific to certain species or largely dependent on prior knowledge of NLS basic residues. Thus, a more general predictor is highly desired to reduce the potentially high false positives or false negatives in discovering new NLSs. Here, we report a new method, INSP (Identification Nucleus Signal Peptide), to effectively identify NLS mainly based on statistical knowledge and machine learning algorithms.
Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions.
Biomedical Applications of Magnetic Resonance research group
A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships | Integrated Probabilistic Annotation (IPA) - A Bayesian annotation method for LC/MS data integrating biochemical relations, isotope patterns and adduct formation
R package for iterative pruning to capture population structure.
A centralised resource for the study of polymorphism in genes of the immune system. The Immuno Polymorphism Database. IPD was developed in 2003 to provide a centralised system for the study of polymorphism in genes of the immune system. The IPD project was established by the HLA Informatics Group of the Anthony Nolan Research Institute in close collaboration with the European Bioinformatics Institute.
Software tool to identify prokaryotic and eukaryotic virus-derived sequences in virome using deep learning. Used to calculate a set of scores that reflect the probability that input sequence fragments are prokaryotic and eukaryotic viral sequences.
Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis | Abstract We provide a single cell atlas of Idiopathic Pulmonary Fibrosis (IPF), a fatal interstitial lung disease, focusing on resident lung cell populations. By profiling 312,928 cells from 32 IPF, 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we demonstrate that IPF is characterized by changes in discrete subpopulations of cells in the three major parenchymal compartments: the epithelium, endothelium and stroma. Among epithelial cells, we identify a novel population of IPF enriched aberrant basaloid cells that co-express basal epithelial markers, mesenchymal markers, senescence markers, developmental transcription factors and are located at the edge of myofibroblast foci in the IPF lung
An XGBoost model for prediction of internal ribosome entry sites | BACKGROUND:Internal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5' cap-dependent translation initiation mechanism. IRES usually function when 5' cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool. RESULTS:This paper systematically examines the features that can distinguish IRES from non-IRES sequences
the database of immunologically relevant non-coding RNAs | git clone git@github.com:sschmeier/irndb2.git irndb2 | IRNdb - Database of immunologically relevant non-coding RNAs | // © Massey University 2014-2018 // v1.5.8
Image System Engineering Toolbox for Biology (ISETBIO) is a Matlab toolbox designed for calculating the properties of the front end of biological visual systems.
Semi-Automated Data Analysis for Ion-Selective Electrodes and Arrays Using the R Package ISEtools. Tools for Ion Selective Electrodes. Characterisation and calibration of single or multiple Ion Selective Electrodes (ISEs); activity estimation of experimental samples. Implements methods described in: Dillingham, P.W., Radu, T., Diamond, D., Radu, A. and McGraw, C.M. (2012) <doi:10.1002/elan.201100510> and Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) <doi:10.1109/ICSENS.2017.8233898>
Hep G2 cell culture confluence measurement in phase-contrast micrographs. Phase-contrast micrographs are often used for confirmation of proliferation and viability assays. However, they are usually only a qualitative tool and fail to exclude with certainty the presence of assay interference by test substances. The complexity of image analysis workflows hinders life scientists from routinely utilizing micrograph data. Here, we present an open-source software-based, combined ilastik segmentation ImageJ measurement of area (ISIMA) approach for cell monolayer segmentation and confluence percentage measurement of phase-contrast micrographs of Hep G2 cells. The aim of this study is to test whether the proposed approach is suitable for quantitative confirmation of proliferation data, acquired by the 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay.
Visually interpretable deep learning for mortality prediction inside the ICU | To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they have been shown by several studies to offer sub-optimal performance. Alternatively, Deep Learning offers state of the art capabilities in certain prediction tasks and research suggests deep neural networks are able to outperform traditional techniques. Nevertheless, a main impediment for the adoption of Deep Learning in healthcare is its reduced interpretability, for in this field it is crucial to gain insight into the why of predictions, to assure that models are actually learning relevant features instead of spurious correlations
Modeling methylation dynamics with simultaneous changes in CpG islands.
Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries. GENERATING AND TESTING MIMOTOPE LIBRARIES. Proof of pricniple diagnostic use with feature selection and predictor construction. comparison between IgM reactivity with different peptide libraries.
Software for Biomolecular Illustration | The small program Illustrate generates non-photorealistic images of biological molecules for use in dissemination, outreach, and education. The method has been used as part of the "Molecule of the Month," an ongoing educational column at the RCSB Protein Data Bank (http: rcsb.org). Insights from 20 years of application of the program are presented, and the program has been released both as open-source Fortran at GitHub and through an interactive web-based interface
An open-source computational platform for the deep learning era. ImJoy -- Deep Learning Made Easy!
A multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. A deep learning model for protein subcellular localization based on immunohistochemistry images
R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data. R package to quantify CDR3 data for immune repertoire diversity. Author and Maintainer: Martijn Cordes. devtools::install_github("martijn-cordes/ImSpectR"). We also used ImSpectR to score CDR3 data from human TCR sequencing data sequenced with the ImmunoSeq platform. The CDR3 data scored by ImSpectR was data from CMV+ PBMCs published by Suessmuth et al. (Blood, 2015). Tab seperated (tsv) files were dowloaded from the Adaptive Biotech database for immunoSEQ data: https://clients.adaptivebiotech.com/pub/b4ac7a84-1e69-4d60-8254-845720454d7d
ImaGEO is a web tool for gene expression Meta-Analysis that implements a complete and comprehensive meta-analysis workflow starting from Gene Expression Omnibus (GEO) dataset identifiers. The application integrates GEO datasets, applies different meta-analysis techniques and provides functional analysis results in an easy-to-use environment. ImaGEO is a powerful and useful resource that allows researchers to integrate and perform meta-analysis of GEO datasets to lead robust findings for biomarker discovery studies.
A convolutional neural network to quantify natural selection from genomic data. ImaGene implements a supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Specifically, it uses a convolutional neural network (CNN) which takes as input haplotypes for a population and locus of interest. It outputs confusion matrices as well as point estimates of the selection coefficient along with its posterior distribution and various metrics of confidence
A Tool To Extract and Quantify Data from Microscopy Images. Extract relevant images using ChemDataExtractor. Identify regions corresponding to individual particles
New Software for Viewing Dynamic PET Scans and Extracting Radiomic Parameters from PET Data | Extensive research is currently being conducted into dynamic positron emission tomography (PET) acquisitions (including dynamic whole-body imaging) as well as extraction of radiomic features from imaging modalities. We describe a new PET viewing software known as Imager-4D that provides a facile means of viewing and analyzing dynamic PET data and obtaining associated quantitative metrics including radiomic parameters. The Imager-4D was programmed in the Java language utilizing the FX extensions. It is executable on any system for which a Java w FX compliant virtual machine is available. The software incorporates the ability to view and analyze dynamic data acquired with different types of dynamic protocols. For image display, the program maintains a built-in library of 62 different lookup tables with monochromatic and full-color distributions
Characterization of inner shell colour variations in Pinctada margaritifera assessed by HSV colour quantification.
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets.
Data repository with analysis tools that is mainly focused on cytometry and immunology.
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. Welcome to the Immcantation Portal! — Immcantation documentation. Free document hosting provided by Read the Docs
A unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Copyright © Guo Lab , College of Life Science and Technology , HUST , China. Any comments and suggestions, please contact us
Web-based tool for identifying human immune regulatory elements.
Structural Modeling of Lymphocyte Receptors and Their Antigens
Tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.
Development, application, feasibility and preliminary evaluation of the implementation science research development (ImpRes) tool and guide | BACKGROUND:Designing implementation research can be a complex and daunting task, especially for applied health researchers who have not received specialist training in implementation science. We developed the Implementation Science Research Development (ImpRes) tool and supplementary guide to address this challenge and provide researchers with a systematic approach to designing implementation research. METHODS:A multi-method and multi-stage approach was employed. An international, multidisciplinary expert panel engaged in an iterative brainstorming and consensus-building process to generate core domains of the ImpRes tool, representing core implementation science principles and concepts that researchers should consider when designing implementation research
Python package for writing data analysis workflows to interpret microbial physiology.
Laboratory for Metabolic Systems Engineering
Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices | We introduce two highly accurate machine learning based distance imputation techniques. One of our approaches is based on matrix factorization (MatrixFactorization.py), and the other one is an autoencoder based deep learning technique (Autoencoder.py). We evaluate these two techniques on a collection of simulated and biological datasets, and show that our techniques are more accurate and robust than the best alternate technique for distance imputation. Moreover, our proposed techniques can handle substantial amount of missing data, to the extent where the best alternate method fails | (See the imports in both of the python files) | -python 3.5+ -easygui -pandas -numpy -matplotlib -seaborn -tensorflow -keras
MATLAB script for importing images and metadata using the LOCI Bioformats package.
Imread for multiple life science image file formats
Database and software for mitochondrial imperfect interspersed repeats annotation.
INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.
Python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports | Genome scale copy number inference from discrete reports of gene-level amplifications on somatic cancer NGS testing reports | InferAMP - inferring genome-wide amplicon boundaries from cancer NGS reports | Optimized for Foundation One reports from Foundation Medicine | A working version of the web implementation is at http://inferamp.org
InfernoRDN can perform various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation.
Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. R package for DNA methylation analysis. R package for DNA methylation analysis The proposition of cancer cells in a tumor sample, named as tumor purity, is an intrinsic factor of tumor samples and has potentially great influence in variety of analyses including differential methylation, subclonal deconvolution and subtype clustering. InfiniumPurify is an integrated R pa ckage for est imatin g and accoun ting for tum or puri ty based on DNA methylation Infinium 450 k array data. InfiniumPurify has three main functions getPurity, InfiniumDMC and InfiniumClust, which could infer tumor purity, differential methylation analysis and tumor sample c luster accounting for estimated or user-provided tumor purities, respectively. The InfiniumPurify package provides a comprehensive analysis of tumor purity in cancer methylation research.
Multi-model inference of non-random mating from an information theoretic approach. Non-random mating and Information Theory. mate choice, assortative mating, jmating, sexual selection, akaike. Relying on the informational partition of the non-random mating effects, and by modeling mate choice and competition by the mutual propensity parameters, it is possible to identify the necessary and sufficient conditions of random mating and from here, develop and connect different kinds of models producing different effects. These models can be used to generate inferences on the parameters of interest. The software InfoMating implements the methodology to do so
Comprehensive genetic resource and analysis platform of insects.
Platform-integrated mRNA Isoform Quantification. Integrated model for RNA-Seq based transcript quantification. IntMTQ is an integrative method combining isoform expressions from NanoString/Exon-array platforms to provide better quantification of RNA-Seq based transcript abundances. We provide the source code of paper Platform-integrated mRNA Isoform Quantification for bioinformatics submission
Deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data. Intelli-NGS:Intelligent NGS, a deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data Preprint: DOI https://doi.org/10.1101/2019.12.17.879403
Global Peptide-Protein Docking with Structural Templates. Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming, and because of the disordered nature of the ligand, the interactions are especially difficult to predict through software, requiring specialized solutions. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide-protein interactions. We have previously shown that structural templates can be used to accurately predict peptide-protein binding sites, and that using templates from regular protein-protein interactions will increase the number of sites found
Integrated Supportive Webtools for Low- and High-Field NMR Analyses Toward Molecular Complexity | Description SpinLIMS Contact Others | Integrated supportive webtools for low- and high-field NMR analysis toward molecular complexities | SENsitivity improvement with Spectral Integration
Adding Circumstances Of Mortality CATegories (COMCATs) to deaths investigated by verbal autopsy. files relating to evaluation of InterVA-5 software. Resources relating to InterVA-5 verbal autopsy software. Software for WHO verbal autopsy standards. InterVA provides the leading public-domain resources for interpreting verbal autopsy data. InterVA is a suite of computer models to facilitate interpreting VAs, and the latest versions and information are available on a public-domain basis from this site. This research is based at the Umeå Centre for Global Health Research, in northern Sweden, which also hosted the World Health Organization Collaborating Centre for Verbal Autopsy from 2012 to 2016.
The Case for Sensible Extraction of Interactions in the Era of Machine Learning. Extract meaningful interactions from machine learning models to obtain machine-learning performance with statistical model interpretability. Welcome to InteractionTransformer. Welcome to the InteractionTransformer wiki!. What our package does not do: extract transformations in the data to add them to the design matrix. For those capabilities, please see the SAFE Transformer package (https://github.com/ModelOriented/SAFE). Our package does have an experimental feature that will iteratively call InteractionTransformer and SAFETransformer to develop multi-layer interactions/transformation models, but this is still under development.
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues | Spatial Dirichlet Gaussian Mixture Model for single ion images | run W_matrix.R GMM.R k_DGMM.R S_DGMM.R first | run CpG_Sal_mouse brain.R to get results of CpG and Sal preconditioned mouse brain data
IsoCor is a scientific software dedicated to the correction of low- and high-resolution mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
Another look at the eigenvalues of a population matrix model. Theoretical Population Modeling for Understanding Growth Rates. Visualizing how the growth rates responds to alterations in life history traits. Hanley B, Connelly P, & Dennis B. 2019. IsoPOPd: Interactive software to understand how elements in a population matrix model influence the asymptotic population growth rate [Software]. Cornell University Library eCommons Repository. doi: https://doi.org/10.7298/bcmg-7w08
IsobariQ is a program designed for use in quantitative mass spectrometry based proteomics. It is a novel tool for accurate quantification of IPTL, iTRAQ and TMT data, and currently, it is the only freely available tool to analyse IPTL data. It allows the user to examine proteomic data in detail and interactively through a graphical user interface. In addition, it provides the user with advanced statistical analysis, including recently published variance stabilising normalisation (VSN).
“C++”-program simulating the dynamics of metabolites and their isotopic isomers in the central metabolic network using a corresponding kinetic model. Supports the final step of 13C assisted the fluxomic analysis: evaluation of metabolic fluxes consistent with a given mass isotopomer distribution. The previous steps are supported by Ramid, Midcor, Isoform.
R-program that prepares the corrected mass spectra (supposed to be provided by Midcor) to the final step of the workflow of fluxomic analysis: simulation of dynamics of mass isotopomer distribution in a kinetic model.
An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs | MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs
Analysis package for processing counts from genome-wide CRISPR/Cas9 screens.
JACOBI4 software for multivariate analysis of biological data. JACOBI4 является проектом, разработанным для автоматизации статистического многомерного анализа биологических данных. Д.А. Полунин, И.А. Штайгер, В.М. Ефимов Разработка программного комплекса JACOBI 4 для многомерного анализа микрочиповых данных // Вестник НГУ т.12 Вып. 2. – Новосибирск: Редакционно-издательский центр НГУ, 2014. С. 90-98
Characterization of Hydration Properties in Structural Ensembles of Biomolecules.
Assessing intraspecific genetic diversity from community DNA metabarcoding data. Estimating intraspecific genetic diversity from community DNA metabarcoding data. JAMP - Just Another Metabarcoding Pipeline. JAMP is a modular metabarcoding pipeline, integrating different functions from USEARCH, VSEARCH, CUTADAPT and other programs. The pipeline is run as an R package and automatically generates the needed folders and summary statistics
Joint Overlap Analysis (JOA) of multiple genomic interval sets. Takes n interval sets and finds overlapping intervals with no constraints on the given intervals.
A Python Program of Joback and Reid Method | Python GUI program for a quick estimation of physicochemical properties of molecules | A brief description of JRgui program: | By using the modern object-oriented programming language Python (e.g. tkinter and pandas modules) and a chemoinformatics open source library (RDKit), the classic Joback and Reid group contribution method was revisited and written into a graphical user interface program JRgui
Bioinformatics Pipeline using JUDI. This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!. JUDI - Bioinformatics Pipeline: Just Do It.
Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics | protein docking using a density-based descriptor for atoms charge and dynamics | JabberDock provides a mechanism to dock two protein STID maps together in conjunction with the POW engine and BioBox | Shipped with this version of JabberDock is a heavily stripped version of biobox containing the functions JabberDock requires. Please move the biobox folder into whatever directory you like (e.g. your home), just make sure it's in your pythonpath There is a readme file in the biobox folder containing instructions on requirements and installation instructions
Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients. Calculate statistical significance of Jaccard/Tanimoto similarity coefficients for binary data.
Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
Extensible open-source software package for adaptive quantum mechanics/molecular mechanics (QM/MM) Methods.
a Java pipeline for isomiR characterization in miRNA-Seq Data. MOTIVATION:The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences. RESULTS:We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations
Joint Multi-Modal Longitudinal Regression and Classification for Alzheimer's Disease Prediction. Code for Joint Multi-Modal Longitudinal Regression and Classification. Joint Multi-Modal Longitudinal Regression and Classification (JMMLRC) Estimator. This repository contains the code for performing a classification and a regression task at the same time on longitudinal data. This work has been applied to the ADNI dataset and has shown state-of-the-art performance in predicting patients with and without Alzheimer's Disease.
Joint Multi-Modal Longitudinal Regression Classification
Aeschynomene evenia genomic data from the Legume Information System
General approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes.
In vitro and in silico PCR analysis tool for high-throughput SNP genotyping.
a universal framework for multi-omics data integration and biological discoveries. Towards this, we have expanded our in-house developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean to other organisms via Knowledge Base Commons (KBCommons) without the need for reinventing the wheel. Advancement of next generation sequencing and high-throughput technologies has resulted in generation of multi-level of 'OMICS' data for many organisms
A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding | KBbox is developed to be of use to researchers interested in applying these methods in their work. To help with this, KBbox provides an updated list of examples of published work, along with detailed tutorials to guide less experienced researchers
Novel computational framework for systematic uncovering hidden gene interactions underlying known drug-disease associations | A computational framework for uncovering hidden gene interactions underlying Known Drug-Disease Associations (KDDAs) | To use KDDANet, please refer to the instructions in manual.txt in this subdirectory | This software identifies the hidden gene interactions and modules underlying KDDAs through implementing minimum cost optimization and graph clustering on a unified flow network model
A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services. BACKGROUND AND OBJECTIVE:To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment. METHODS:The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data
new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interactions between DNA, RNA, proteins and chemical compounds. All datapoints were manually annotated and reviewed based on open source articles available on Europe PMC
Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. The first Korean Reference Genome. KOREF_S means KOREF_Single.
KPDGUI (Kidney Paired Donation Graphical User Interface) - interactive application for optimization and management of a virtual kidney paired donation program.
Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes.
Online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas.
Defining and targeting adaptations to oncogenic KRASG12C inhibition using quantitative temporal proteomics | ABSTRACT Covalent inhibitors of the KRAS G12C oncoprotein have recently been developed and are being evaluated in clinical trials. Resistance to targeted therapies is common and likely to limit long-term efficacy of KRAS inhibitors (KRASi). To identify pathways of adaptation to KRASi and to predict drug combinations that circumvent resistance, we used a mass spectrometry-based quantitative temporal proteomics and bioinformatics workflow to profile the temporal proteomic response to KRAS G12C inhibition in pancreatic and lung cancer 2D and 3D cellular models. We quantified 10,805 proteins across our datasets, representing the most comprehensive KRASi proteomics effort to date. Our data reveal common mechanisms of acute and long-term response between KRAS G12C -driven tumors
Kinase-Substrate Enrichment Analysis (KSEA) App - web-based tool for kinase activity inference from quantitative phosphoproteomics.
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Kaptive reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies. You can also run a graphical version of Kaptive via this web interface (source code). Given a novel genome and a database of known loci (K, O or OC), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:. Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. It takes one or more pre-assembled genomes and for each finds the best matching locus from a reference database. References for Klebsiella pneumoniae species complex and Acinetobacter baumannii are available in Kaptive's web interface
Multiregion whole-genome sequencing depicts intratumour heterogeneity and punctuated evolution in ovarian clear cell carcinoma. An R package for detecting and visualizing Kataegis events. KataegisPortal is an R package that provides utilities to detect and visualize the Kataegis events from single nucleotide variants (SNVs)
De Novo Pathway Enrichment with KeyPathwayMiner. (17E1EF77D1E66C1CFE344BDA3D7945B0). Given a biological network and a set of case-control studies, KeyPathwayMiner efficiently extracts all maximal connected sub-networks. These sub-networks contain the genes that are mainly dysregulated, e.g., differentially expressed, in most cases studied.
Visualization tool to detect cryptic relatedness in genetic datasets.
Efficient Manipulation and Generation of Kirchhoff Polynomials for the Analysis of Non-equilibrium Biochemical Reaction Networks. Efficient manipulation and compact generation of expressions of Kirchhoff polynomials
KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome.
Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity.
A tool for assessing complex sequence space in plant species. Kmasker - a tool for masking and exploring of sequences from plant species. a versatile tool for masking and exploring of sequences from plant species. Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity. The installation instructions are available at: INSTALL.md. There, you find our list of requirements of external tools. Please make sure, that these are in your PATH environemnt if you installed from source. If not please specify them in the 'etc/kmasker.config' file. Kmasker uses an interal repository for reuse of kindex structures.
A comprehensive human gene expression profile database with knockdown/knockout of transcription factors. We develop a comprehensive human gene expression profile database with TF knockdown/knockout (KnockTF), which provides a large number of available resources of human gene expression profile datasets associated with TF knockdown/knockout and annotates TFs and their target genes in a tissue/cell type-specific manner
Knot_pull-python package for biopolymer smoothing and knot detection | Python module for knot-like structure detection in biological molecules | KnotPull - a simplifier for 3D structures | KnotPull reduces a user provided 3D structure, to simplify it, while preserving the topology of the chain. It has been successfully used for knot detection in proteins and chromatin chains
Tool to study the entanglement of open protein chains using the concept of knotoids.
A Web-Resource Focused on Diversity Data for Pulse Crop Improvement | Welcome to the Public Portal for the University of Saskatchewan Pulse Crop Research Group | ◼ View other species of interest | ◼ View other bioinformatics tools
Rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings.
KEGG ortholog assignment based on profile HMM and adaptive score threshold. KofamKOALA - KEGG Orthology Search. K number assignment based on KO-dependent scoring criteria. KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.
Identification and quantitation of clinically relevant microbes in patient samples.
Matlab implementation of the Kronecker Regularized Least Squares with multiple kernels algorithm.
Deep learning software for automated kymograph analysis | The AI that analyses your kymographs | The AI that analyses your kymograph | Easy drag and drop software under http://kymobutler.deepmirror.ai | Download KymoButler.nb and open it in Mathematica. Run the first cell to download the necessary neural networks and the KymoButler package. The use the function KymoButler[] to analyse your kymographs
A tool for accurate locus specific LINE-1 RNA quantification. Estimate locus specific human LINE-1 expression. git clone https://github.com/wmckerrow/L1EM. git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git). anaconda (https://docs.anaconda.com/anaconda/install/). If necessary, you can specify the path for bwa and samtools in the run_L1EM.sh script. You must use samtools >=1.0. Early version of pysam will not work. I highly recommend that you use bwa 0.7.17. Earlier versions may differ in how they write the XA tag. This will lead to inaccurate results without throwing an error
A new database designed specifically for Lactic Acid Bacteria bacteriocins | Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicrobial peptides (AMPs) is scattered through the literature and databases. Therefore, we developed the LABiocin database, a specialized database on LAB bacteriocins. The database was stored and compiled using MySQL with NetBeans IDE as the platform. Important data are compiled, including bacteriocin name, class, amino acids and nucleic acid sequences, if available. Target microorganisms, origin, status of the producing strains and their culture conditions and extraction and purification methods are also included in this new database. A phylogenetic tree for the mature peptide bacteriocin sequences has also been created
Integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics
Liege Acromegaly Survey (LAS) database includes anonymous historical and prospective data on liege acromegaly patients, pathophysiology, clinical features, responses to therapy and long term outcomes of acromegaly.
Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using Multi-Contrast MRI | LASHiS was loosely adapted from the ANTs Longitudinal Cortical Thickness pipeline https://github.com/ANTsX/ANTs/ The ASHS_TSE image slice direction should be z. In other words, the dimension of ASHS_TSE image should be 400x400x30 or something like that, not 400x30x400
A lattice model for simulating phase transitions of multivalent proteins. Many biomolecular condensates form via spontaneous phase transitions that are driven by multivalent proteins. These molecules are biological instantiations of associative polymers that conform to a so-called stickers-and-spacers architecture. The stickers are protein-protein or protein-RNA interaction motifs and or domains that can form reversible, non-covalent crosslinks with one another. Spacers are interspersed between stickers and their preferential interactions with solvent molecules determine the cooperativity of phase transitions. Here, we report the development of an open source computational engine known as LASSI (LAttice simulation engine for Sticker and Spacer Interactions) that enables the calculation of full phase diagrams for multicomponent systems comprising of coarse-grained representations of multivalent proteins.
a streamlined visualization tool for longitudinal analysis of viral alleles. LAVA: Longitudinal Analysis of Viral Alleles. LAVA analyzes and visualizes minor allele variants in longitudinal sequence data. LAVA takes a reference fasta (normally representing the first sample in your longitudinal analysis), fastq files (for every sample in your analysis), and a metadata sheet (providing information on what day or passage each sample was collected). Output will be displayed as an interactive graph in your web browser. LAVA will only work on Mac and Linux machines
Label Ambiguous Domain Adaptation (LAmbDA) - species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets.
LBEEP (Linear B-Cell Exact Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell epitopes. Please refer the article tilted "Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-based Feature Descriptor" for more deatils.
Learning Cascade Attention for fine-grained image classification. Code for paper "Learning Cascade Attention for Fine-grained Image Classification", which currently under review at Elsevier Journal of Neural Networks(NN). Train/test split for CUB-200-2011 dataset. Rotate training set for data augmentation.
A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes. Practical program to annotate candidate polymorphism using annotations for genes in genetic linkage in the specific experiment. A bioinformatics tool to automatically provide annotations for genes included in DNA blocks in linkage disequilibrium with candidate SNPs. LD-annot estimates experiment-specific linkage disequilibrium to delineate regions genetically linked to each genetic markers from a list of polymorphisms (most often candidate SNPs from GWAS) and provide coordinates and annotations for genes included or overlapping such regions. Email: jprunier.1@gmail.com or arnaud.droit@crchudequebec.ulaval.ca
A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Documentation : Forum : Contact. "2,8-Dimethyl-5,7-dimethoxychromone". "5,7-Dihydroxy-2,6,8-trimethylchromone".
Improved read/write cost tradeoff in DNA-based data storage using LDPC codes | LDPC codes for Illumina sequencing-based DNA storage
Tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation.
Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs. Source code for LD motif detection. In this repository, we uploaded the necessary files to set up and environment to predict the LD motif from input sequence. We also have a server for LD motif predition : https://www.cbrc.kaust.edu.sa/ldmf/. Users need to run scripts after changing the value of input parameters. The deatils of each parameter is also provide. The code is shared in the folder "src". All external jars are shared in the folder "ExternalJar_Required" There are two files that should be used for Amino Acid index. These files are also shared.
A method to construct the local strains at horizontal gene transfer sites in gut metagenomics. It is a software to reconstruct the HGT inserted local strain. It is a software takes use of existing shotgun NGS datasets to detect HGT breakpoints, identify the transferred genome segments, and reconstructs the inserted local strain. usage: python LEMON/Scripts/get_raw_bkp.py [options]. git clone --recursive https://github.com/lichen2018/hgt-detection.git
Local event-based analysis of alternative splicing using RNA-Seq data. Local Event-based analysis of alternative Splicing using RNA-Seq. The Local Event-based analysis of alternative Splicing using RNA-Seq (or LESSeq) is a Linux-based processing pipeline for analyzing alternative splicing events from RNA-Seq data
Algorithm for label-free absolute protein quantification, which can correct the biased MS intensities using the predicted peptide quantitative factors for all identified peptides.
An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant. A tool for analysing label-free quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. LFQ-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative proteomic datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result output graphics and tables to facilitate statistical and exploratory analysis of label-free quantitative datasets
A lossless non-reference-based FASTQ compressor. Contribute to sya12005/LFastqC development by creating an account on GitHub. You can’t perform that action at this time
Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort. An automated script for extracting the scar area, entropy, components, transmurality, radiality and interface length from short axis late gadolinium enhanced cardiac MRI images in nifti format. This repository provides a script that creates a list of metrics quantifying a scar pattern seen in a cardiac short axis late gadolinium enhanced MRI image. The metrics provided are. area - The total area of the scar. radiality - The angular extent of the LGE pattern, with values between 0 and 1. A score of 1 indicates that scars are present in a full 360 degree pattern with respect to the centre of the blood pool, wheras 0 indicates no angular extent of scar.
An independently validated survival nomogram for lower grade glioma. BACKGROUND:Gliomas are the most common primary malignant brain tumor. Diffuse low-grade and intermediate-grade gliomas, which together comprise the lower-grade gliomas [LGG] (WHO grades II and III), present a therapeutic challenge to physicians due to the heterogeneity of their clinical behavior. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a survival nomogram for patients with newly diagnosed LGG. METHODS:Data were obtained for newly diagnosed LGG patients from The Cancer Genome Atlas (TCGA) and the Ohio Brain Tumor Study (OBTS) with the following variables: tumor grade (II or III), age at diagnosis, sex, Karnofsky Performance Status (KPS), and molecular subtype (IDH mutant with 1p 19q codeletion [IDHmut-codel], IDH mutant without 1p 19q codeletion [IDHmut-non-codel], IDH wild-type [IDHwt])
LIBR Methamphetamine and Opioid Cue Database (LIBR MOCD) | Repository for the LIBR Meth Opioid Cue Reactivity Database | This project contains two folders:
Standardized representation of the LIDC annotations using DICOM. Scripts for converting TCIA LIDC-IDRI collection derived data into standard DICOM representation from project-specific XML format. This repository contains the script used to convert the TCIA LIDC-IDRI XML representation of nodule annotations and characterizations into the DICOM Segmentation object (for annotations) and DICOM Structured Reporting objects (for nodule characterizations). pylidc is an Object-relational mapping (using SQLAlchemy) for the data provided in the LIDC dataset. This means that the data can be queried in SQL-like fashion, and that the data are also objects that add additional functionality via functions that act on instances of data obtained by querying for particular attributes.
Toolkit for Simulating Lignin Biosynthesis.
A tool for comparing species partition. We are pleased to announce the launch of Limes!.
A Web service for genome-based identification of microbes as members of crowdsourced taxa | Abstract The development of next generation and third generation DNA sequencing technologies in combination with new efficient algorithms allows scientists to economically, quickly, and precisely identify microbes at all taxonomic levels and even attribute pathogen isolates to specific disease outbreaks. However, current taxonomic practice has not kept up with the sequencing revolution and continues to rely on cumbersome journal publications to describe new species. Here we introduce a Web service that allows any user to genomically circumscribe any monophyletic group of bacteria as a taxon and associate with each taxon a name and short description. Any other user can immediately identify their unknown microbe as a member of any of these crowdsourced taxa using gene or genome sequences. The Web service is called LINbase
Web-based ontology enrichment tool for lipidomic data analysis.
Software for identifying lipids in LC-MS/MS-based lipidomics data.
Longitudinal linear combination test for gene set analysis. LLCT is a two-step self-contained gene-set analysis method which is developed to handle multiple longitudinal outcomes. Analysis of within-subject variation in the first step is followed by examining the between-subject variation utilizing Linear Combination Test (LCT) in the second step. This method is also applicable in analysis of time-course microarray data
A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections | LM-GlycomeAtlas v.1.0 is a web tool visualizing the data from Lectin Microarray analyses using 45 lectins by the Kuno Laboratory at AIST | This work was supported by a project for utilizing glycans in the development of innovative drug discovery technologies in the project focused on developing key technology for discovering and manufacturing drugs for next-generation treatment and diagnosis from the Japan Agency for Medical Research and Development (AMED) | CFG(Consortium for Functional Glycomics) Glycan Profilling data | Mapping data of human serum data was from Dr. Shunji Natsuka of Niigata University, Japan
An environment to design bioimage analysis workflows for large and complex fluorescence microscopy data. SUMMARY:Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation & Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory.
Annotation tool that recommends candidate Human Phenotype Ontology (HPO) terms to a LOINC (Laboratory Observation Identifier Names and Codes) test based on lexical matching between HPO term definitions and the name of a laboratory test.
LOMETS (Local Meta-Threading Server) is meta-threading method for template-based protein structure prediction.
A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data | LONI Quality Control (LONI QC) is an imaging data review and assessment platform for human neuroimaging research studies involving one or more centers. LONI QC allows users to anonymously download imaging data from the LONI IDA and run a standardized quality control check via an automated pre-processing system specifically designed to generate a range of vector statistics and derived images
A single- and multitask machine learning algorithm for the prediction of cancer driver genes. LOTUS is an algorithm for cancer driver gene prediction. This page provides in particular codes to reproduce simulation results. We propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types
Combining pre-clinical drug structures and post-market safety reports. Code and Datasets for paper "Towards early detection of adverse drug reactions: combining pre-clinical drug structures and post-market safety reports". This repository contains source code for paper "Towards early detection of adverse drugreactions: combining pre-clinical drug structuresand post-market safety reports" (accepted by BMC Medical Informatics andDecision Making). Please kindly cite the paper if you use the code, datasets or any results in this repo or in the paper:.
A latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations. LPM (Latent Probit Model), is an efficient statistical approach to characterize relationship among complex traits using summary statistics from multiple GWASs and functional annotations. 'LPM' package provides model parameter estimation as well as statistical inference
Tool for evaluating Long Reads Correction methods.
Improving draft genomes using long noisy reads. Hybrid assembly strategy is a reasonable and promising approach to utilize strengths and settle weaknesses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologies. According to this principle, we here present a new toolkit named LRScaf (Long Reads Scaffolder) by applied TGS data to improve draft genome assembly. The main features are: short running time, accuracy, and being contiguity. To scaffold rice genome, it could be done in 20 mins with minimap mapper. In human, LRScaf could improve the draft assembly NG50 from 127.5 Kb to 10.4 Mb on 20x PacBio CHM1 dataset and NG50 from 115.7 Kb to 17.4 Mb on ~35x Nanopore NA12878 dataset
Assessment of human diploid genome assembly with 10x Linked-Reads data. A program to simulate linked reads sequencing from 10X Chromium System. LRTK-SIM: Linked read simulator for 10X Chromium System. line2 and line3: Path_Fastahap1 and Path_Fastahap2, the two haploid reference serquences. LRTK-SIM allows one or two fasta files to perform haploid and diploid simulation. The diploid reference sequences can be generated by gen_fasta.py that inserting variants to the reference genome (only SNVs for this version). You can remove Path_Fastahap2=XXX in line3 and set Hap=1 in line33 for haploid simulation.
Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimer's disease.
Progressive Object Transfer Detection | LSTD: A Low-Shot Transfer Detector for Object Detection | Specifically, SSD acts as the region proposal network (RPN) in LSTD. Additionally, we propose Transfer Knowledge (TK) and Background Depression (BD) modules for transfer detection task. More details can be found in LSTD
Predicting microRNA sequence using CNN and LSTM stacked in Seq2Seq architecture | sequence-prediction-using-CNN-and-LSTMs | microRNA sequence prediction using CNN and LSTM
Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Large-Scale Transcriptome Analysis Pipeline-Lite on credit card-sized ARM computer. If you use LSTrAP-Lite in your research, please cite: Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Tan and Mutwil, 2019. (https://doi.org/10.1101/661058).
Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference | A script in R to run the LS³ and LS⁴ phylogenetic data subsampling algorithms for reducing lineage rate heterogeneity | LSX is a script in R that runs the LS³ and LS⁴ algorithms of data subsampling for multigene phylogenetic inference
Webpage dedicated to the visualization and management of environmental and planktonic data collected at the LTER-MC station in the Gulf of Naples.
A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data | This repository contains the R codes which could reproduce the results of "LTMG: A statistical model of transcriptional regulatory states in single cell RNA-Seq data" by Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Sha Cao, Melissa L. Fishel, Qin Ma, and Chi Zhang
Scripts and Data associated with our publication on genomic signatures to discriminate LUAD and LUSC lung cancer types using TCGA data | Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark | Repository associated to the publication: | Different molecular signatures in lung cancer types from integrative bioinformatic analyses of RNASeq data Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo*, bioRxiv, doi: https://doi.org/10.1101/501569
A Latent Unknown Clustering Integrating Multi-Omics Data (LUCID) with Phenotypic Traits | Latent Unknown Clustering with Integrated Data | An implementation for the 'LUCID' method to jointly estimate latent unknown clusters/subgroups with integrated data. An EM algorithm is used to obtain the latent cluster assignment and model parameter estimates. Feature selection is achieved by applying the regularization method
A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding | r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding) | The purpose of LULU is to reduce the number of erroneous OTUs in OTU tables to achieve more realistic biodiversity metrics. By evaluating the co-occurence patterns of OTUs among samples LULU identifies OTUs that consistently satisfy some user selected criteria for being errors of more abundant OTUs and merges these. It has been shown that curation with LULU consistently result in more realistic diversity metrics. The required input of LULU is an OTU table and a corresponding matchlist with all the internal matches of OTUs | A r-package for distribution based post clustering curation of amplicon data
Using Transcriptional Signatures to Find Cancer Drivers with LURE | LURE (Learning UnRealized Events)
The open data geoportal of the Lamma Consortium. In questa categoria sono immagazzinati i dati relativi a bollettini,... In attuazione del decreto legge D. Lgs n. 33 del 14 marzo 2013, che sancisce...
Diverse traits contribute to salinity tolerance of wild tomato seedlings from the Galapagos Islands. Analyzing natural variation in Galapagos tomatoes. La_isla_de_tomato App user guide. The manuscript is currently undergoing submission / revision, but this App is available to explore the data freely. The App can be accessed here or run locally from your machine, by typing the following: library("shiny") shiny::runGitHub("mmjulkowska/La_isla_de_tomato", "mmjulkowska").
Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.
A web application for interactive genomic summary visualization. Download and Check the official demo input. Additional demo files from the References are provided in the GitHub project. The 'LandScape' visualization is frequently utilized to provide a systematic illustration of integrative data from multiple layers of batch samples, which are always compared to each other on certain attributes, such as genes and biological pathways mutated in cancers. This online 'LandScape' visualization is designed as a fixed part (histogram and gene-panels) with additional panels (e.g., age, gender, and histology). To visualize data, upload a CSV file in the required format and use sidebar options to customize the display
Laniakea is a complete software solution to set up a “Galaxy on-demand” Platform as a Service (PaaS). Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance, and to the underlying virtual machine (VM).
Deep Lasso-Selection of 3D Point Clouds | Zhutian Chen, Wei Zeng, Zhiguang Yang, Lingyun Yu, Chi-Wing Fu, and Huamin Qu IEEE VIS 2019 | Selection is a fundamental task in exploratory analysis and visualization of 3D point clouds
An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate
MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging.
Open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research.
A QGIS plugin for automated landscape ecology analysis.
Estimating population history from genetic data. Estimate population history parameters from site pattern frequencies. Legofit is a computer package that uses counts of nucleotide site patterns to estimate the history of population size, subdivision, and gene flow.
Multi-organism mine integrates data from legume species: string bean, soybean, peanut and barrel medic
A Computational Method for the Detection and Classification of Ligand-Gated Ion Channels. LiGIoNs: Prediction of Ligand Gated Ion Channels. LiGIoNs is a profile Hidden Markov Model based method capable of predicting Ligand-Gated Ion Channels utilizing their special topological information. The method consists of a library of 35 pHMMs, built from the alignment of transmembrane segments of representative LGIC sequences. In addition, 14 Pfam pHMMs are used to further annotate and correctly classify unknown protein sequences into one of the 10 LGIC subfamilies
Towards gene regulatory network predictions of high-certainty | Abstract Motivation Reverse engineering of gene regulatory networks has for years struggled with high correlation in expression between regulatory elements. If two regulators have matching expression patterns it is impossible to differentiate between the two, and thus false positive identifications are abundant. Results To allow for gene regulation predictions of high confidence, we propose a novel method, LiPLike, that assumes a regression model and iteratively searches for interactions that cannot be replaced by a linear combination of other predictors. To compare the performance of LiPLike with other available inference methods, we benchmarked LiPLike using three independent datasets from the previous DREAM5 challenge
Scalable k-mer-based tool for massive all-vs-all metagenome comparisons.
LiceBase is a genomics database for sea lice (Lepeophtheirus salmonis and Caligus spp.), which are major pathogens affecting the global salmon farming industry. The database contains the genome annotation of the Atlantic salmon louse (L. salmonis) and is designed to help researchers, industry professionals, and other interested parties access and share information about these parasites, with the goal of developing new treatment methods and tools to ensure a sustainable salmon farming industry. LiceBase provides annotated genome reports, genome browsing, RNA interference (RNAi) experiment browsing for several additional species, BLAST search, and in-situ images. The database homepage posts news updates and recent publications related to sea lice and salmonid species.
Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc.
Multi-view CpG sites detection on single-cell whole genome sequence data.
Tool to determine DNA profile weight of evidence.
R package for personalized pathway-based classification modeling using metabolomics data.
LinX is a Java language-based program designed for fast assignment, evaluation, and validation of mass spectrometric datasets from chemical cross-linking.
Linclust is the first clustering algorithm whose runtime scales linearly. With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.
linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search | The new source code of the LinearFold, linear-time prediction for RNA secondary structures | This codebase replaces the now deprecated version: https://github.com/abentu0101/LinearFold. This version fixes many bugs and design problems in the old version | Add a sequence Paste or type your sequence here (length < 100,000): | GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGG | Choose model(s) LinearFold-C (using CONTRAfold v2.0 machine-learned model, Do et al 2006) | * Liang Huang, **He Zhang, **Dezhong Deng, Kai Zhao, Kaibo Liu, David Hendrix, and David H. Mathews (2019). LinearFold: Linear-Time Approximate RNA Folding by 5’-to-3’ Dynamic Programming and Beam Search. Bioinformatics, Volume 35, Issue 14, July 2019, Pages i295–i304. ISMB 2019
a versatile framework to explore and integrate heterogeneous microbial communities. a versatile approach to integrate heterogeneous datasets. LinkHD: a versatile framework to explore and integrate heterogeneous data. Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. Laura Zingaretti & Yuliaxis Ramayo Caldas. Laura M Zingaretti, Gilles Renand, Diego P Morgavi, Yuliaxis Ramayo-Caldas, Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz862
Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is timeconsuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model.
Publicly available portal that includes multi-omics data from all 32 TCGA Cancer types. It also includes mass spectrometry-based proteomics data generated by the Clinical Proteomics Tumor Analysis Consortium (CPTAC) for TCGA breast, colorectal and ovarian tumors.
Connects rare diseases patient registries through a Semantic Web Layer.
Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance. Matlab Script for automated LC-MS/MS phospholipid analysis. LipMat script is a set of tools for automated LC-MS/MS phospholipid analysis. Paper is in preparation and this section will be updated when it will be published. Matlab Script for automated LC-MS/MS lipid analysis.
The modular structure of α/β-hydrolases | The BioCatNet Database System aims to collect and present comprehensive information about biocatalysators: sequence, structure, educts, products, environmental conditions and kinetics | The Lipase Engineering Database (LED) version4.0.0 | Widmann M., Juhl PB. & Pleiss J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics 11: 123
Deposit and classification of lipolytic enzymes based on the proposed classification system in Hitch and Clavel (TBP).
The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Questions: zhouzw AT sioc.ac.cn, jiangzhu AT sioc.ac.cn. © Zhu lab , Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Chinese Academy of Sciences (CAS). All Rights Reserved.
R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.
Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values.
Lipid Mining and Ontology (Lipid Mini-On) - mining and ontology tool for enrichment analysis of lipidomic data.
A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ceRNA regulation. e.g. NEAT1, TP53, hsa-let-7b-5p, rs3825071, COSN13341324, BRCA
ab initio lncRNA identification and functional annotation tool based on deep learning.
LncBook accommodates a high-quality collection of human lncRNA genes and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts.
A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species. LncTarD provides key lncRNA-target regulations, their influenced functions and lncRNA-mediated regulatory mechanisms in human diseases. Quick Search, start typing keywords, press ESC to close suggestions
Database of genetic variations associated with long noncoding genes.
Automated eukaryotic genome annotation based on long-read cDNA sequencing.
Integrating protein localization with automated signaling pathway reconstruction. Are you sure you want to delete this graph?
An integrated Omics data warehouse for Locust, Locusta migratoria
Beautiful sequence logos in python | Software for the visualization of sequence-function relationships | beautiful sequence logos in Python — logomaker 0.8 documentation | Logomaker can be installed from PyPI by executing | Software for creating highly customized sequence logos | Free document hosting provided by Read the Docs
de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models.
A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA. git clone https://github.com/kaizhao86/loxodontalocalizer. Loxodonta Localizer maps the localities from which mitochondrial DNA sequences have been reported for African elephants, Loxodonta africana and L. cyclotis, using the dataset described in Ishida et al., 2013, updated with additional sequences. #first, install Python 2.7, pip and git
A comparison of alveolar formation and maturation within mouse and human lung. Anatomic Ontology for Mouse Lung Maturation. Cell Ontology for Mouse Lung Maturation. Anatomic Ontology for Human Lung Maturation. Cell Ontology for Human Lung Maturation. Search BREATH to explore the developing lung. LungMAP provides users with a tool to annotate images within the website. This webpage provides instructions on how to annotate an image using the tool. Image annotation to convey specific information about an image, importantly, in the context of the image increases its value exponentially, especially with resolution on the molecular level. LungMAP human and mouse ontologies reference page provides links to the LungMAP Ontology Browser, Release Notes, and text files for the scientific community to view the ontologies.
White and narrow-leaf lupin data from the Legume Information System
Digital key for Brazilian sand flies (Diptera, Phlebotominae) within an Android App. Here we present an Android mobile application (app) for the identification of Brazilian phlebotomine sand fly species. The app, which is named LutzoDex™, relies on information included in a data source with morphological and morphometrical characters. This tool can present up to seven answer options to a question. Images of morphological structures can be referenced to make identification easier, and users can see a list of possible species based on the features they report. Maps are also used to determine the geographical distribution and whether the species is incriminated or suspected as a vector of Leishmania spp. in Brazil. The app is available free of charge in both English and Portuguese in the Google Play Store at https: play.google.com store apps details?id=max.com.lutzodexhl=pt_BR.
Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. FileUtil.pm - perl helper module for loading files reformatFasta.pl - perl script the cleans and reformats multi-fasta files findOverlaps.pl - perl script to identify sets of overlapping peaks for Venn diagram getPeakAnno.pl - perl script to add annotation information to Macs2 peaks getGenePeakAnno2.pl - perl script to add peaks to gene information findClosest2.pl - perl script to produce table relating luxR peaks to H-NS double peaks.
An Open-Source Lyophilization Process Optimization Tool. This work presents a new user-friendly lyophilization simulation and process optimization tool, freely available under the name LyoPRONTO. This tool comprises freezing and primary drying calculators, a design-space generator, and a primary drying optimizer. The freezing calculator performs 0D lumped capacitance modeling to predict the product temperature variation with time which shows reasonably good agreement with experimental measurements. The primary drying calculator performs 1D heat and mass transfer analysis in a vial and predicts the drying time with an average deviation of 3% from experiments. The calculator is also extended to generate a design space over a range of chamber pressures and shelf temperatures to predict the most optimal setpoints for operation.
Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes | *This document is under developement. Your ideas and suggestions are always welcome! | M-GCTA is an user-friendly software package, which can be used to estimate the proportion of phenotypic variance due to tagged maternal (or paternal) and offspring genetic effects on offspring phenotypes using large studies where genome-wide genotype data are available on mother- (or father-) offspring pairs
A platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data. M-TRACK is a live cell imaging analysis tool
Web server for the analysis of large-scale microbial genomics data.
A comprehensive model selection for multi-modal single-cell RNA sequencing data. M3S: A user-friendly tool for comprehensive evaluation of multi-modality and statistical model selection for single-cell RNA sequencing data. A large number of single-cell RNA sequencing (scRNA-seq) data set was recently generated to characterize the heterogeneous in cell types or states in a complex tissue or biological process
A web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared.
Analyzing Machupo virus-receptor binding by molecular dynamics simulations. Code and data for Meyer et al, Analyzing Machupo virus-receptor binding by molecular dynamics simulations, PeerJ 2:e266 (2014). This file is meant to explain each of the top level directories. There should be a similar readme in the relevant folders. eq_analysis - contains the scripts used to generate the equilibration rmsf plots as well as the plot themselves. fep_config - contains everything necessary to run the dual topology fep.
An ultra-fast approach for large-scale protein structure similarity searching. Protein similarity search in PDB. Ultra-fast and Large-Scale Protein Structural Neighbor Searching. MADOKA, a webserver features on searching similar protein structures by aligning input structure with the whole PDB library implemented by MADOKA, an algorithm for matching protein structures by two phases.
Robust detection of mosaic loss of chromosome Y from genotype-array-intensity data | R package to detect mosaic loss of Y events in SNP array and NGS data | R package to detect mosaic loss of Y events (LOY) from SNP array data
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
Multiple alignment program for amino acid or nucleotide sequences.
High speed multiple sequence alignment program.
Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Seed-centric method to identify gene modules of similar interaction and co-expression characteristics. Merge A ffected G enes into I ntegrated networks.
Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes. Microbial species play important roles in different environments and the production of high-quality genomes from metagenome datasets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units
Discovering Subclones in Tumors Sequenced at Standard Depths. MAGOS: Model-based Adaptive Grouping of Subclones
Microbial Assessment by Genome-wide Tn-Seq Analysis (MAGenTA) - Galaxy implemented tool for complete Tn-Seq analysis and data visualization.
Web-tool to interrogate classical and complex splicing variations from RNA-Seq data.
Supervised machine learning for diagnostic classification from large-scale neuroimaging datasets. Machine Learning in NeuroImaging (MALINI) is a MATLAB-based toolbox used for feature extraction and disease classification using resting state functional magnetic resonance imaging (rs-fMRI) data. 18 different popular classifiers are presented. With slight modifications, it can also be used for any classification problem using any set of features
Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online resource that integrates data from KEGG, SCOP and structural phylogenomic reconstruction. The database, which was introduced in 2006, traces the deep history of the structural domains of enzymes in metabolic pathways. Here we release version 3.0 of MANET, which updates data from KEGG and SCOP, links enzyme and PDB information with PDBsum, and traces evolutionary information of domains defined at fold family level of SCOP classification in metabolic subnetwork diagrams.
Model-based analysis of proteomic data to detect proteins with significant abundance changes. MAP (Model-based Analysis of Proteomic data), is designed to statistically compare the proteomic profiles generated from different biological samples using the isotope labeling based mass spectrometry (MS) technique and directly identify proteins with significant abundance changes. Unlike many existing tools for this purpose, it does not require parallel/additional technical replicates to fathom technical variations; instead, MAP uses a novel step-by-step regression analysis to directly model technical variations from the profiles under comparison. Therefore, experimental designs and their expenses can be simplified and reduced for more practices
MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.
MARGO (Massively Automated Real-time GUI for Object-tracking). Fast object tracking in real time allows convenient tracking of very large numbers of animals and closed-loop experiments that control stimuli for many animals in parallel. We developed MARGO, a MATLAB-based, real-time animal tracking suite for custom behavioral experiments. We demonstrated that MARGO can rapidly and accurately track large numbers of animals in parallel over very long timescales, typically when spatially separated such as in multiwell plates. We incorporated control of peripheral hardware, and implemented a flexible software architecture for defining new experimental routines. These features enable closed-loop delivery of stimuli to many individuals simultaneously. We highlight MARGO's ability to coordinate tracking and hardware control with two custom behavioral assays (measuring phototaxis and optomotor response) and one optogenetic operant conditioning assay.
Predicting HLA class II antigen presentation through integrated deep learning. MARIA is a machine learning tool developed by Chen et al. to predict likelihood of HLA-II peptide ligand presentation given cell HLA alleles, peptide sequences, and source genes of the peptides.
Extracting Publication-ready Mass Spectrometry Metadata from RAW Files.
Novel tool for virtual phenotyping of maize root system hydraulic architectures. How to use MARSHAL from the R environment. install_github("MARSHAL-ROOT/marshal"). MAize Root System Hydraulic Architecture soLver. MARSHAL is a maize root system hydraulic architecture solver that combines the root architecture model CRootBox (Schnepf et al. 2018) with the method for solving water flow in RSHA of Meunier et al. (2017) and with the method for computing macroscopic parameter of Couvreur et al. (2012). To load the package, you can use the command:
The leading software package for protein identification and characterisation using mass spectrometry data.
Improved linking of motifs to their TFs using domain information. Improved motif enrichment analysis using protein domain type information. MASSIF - motif association with domain information. MASSIF is a novel method to improve the performance of existing tool that link motifs to TFs relying on TF-associated sequences.
an ultra fast algorithm for solving the single individual haplotype assembly problem. Abstract Background Human genomes are diploid, which means they have two homologous copies of each chromosome and the assignment of heterozygous variants to each chromosome copy, the haplotype assembly problem, is of fundamental importance for medical and population genetics. While short reads from second generation sequencing platforms drastically limit haplotype reconstruction as the great majority of reads do not allow to link many variants together, novel long reads from third generation sequencing can span several variants along the genome allowing to infer much longer haplotype blocks
Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology. bionomics.cpp: fast functions in C++ to calculate summary statistics of interest from simulation output. trivial-simulation.R: run MBITES on a very simple landscape (used for model comparison) and generate plots to compare with MBDETES. bionomics.R: takes output generated by peridomestic-simulation.R and generates output to make figures
An integrated omics knowledgebase for molecular breeding in rice. Rice Phenotype Search and Summary. Rice Genotype Search and Summary. Molecular Breeding Knowledge Database. Created with the Personal Edition of HelpNDoc: News and information about help authoring tools and software. For example: Locus (OsG00048223), RAP Locus (Os03g0407400), MSU Locus (LOC_Os02g44360),. For example(case sensitive): HD, TGW. MBK Nip Locus (OsNipG0313111200.01), MBK R498 Locus (OsR498G0203315700.01). For example(case sensitive): Drought Tolerance, Blast Resistance. Project: All Rice3k MBK Japan174 SubTree Sample >= 20 30 40. Molecular Breeding Knowledgebase (MBKbase) is an integrated database for population next-generation sequencing, germplasm resources, phenotypic and various othergenomics data.
Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions | MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. added a link to the publication · 92cb2e86. 3rd_party/jemalloc_win_x64_5.1.0
Minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks | Codes and data of competitive methods for finding minimal cut sets of a metabolic network | Files for the work on metabolic networks with Leonid, Tamon, Cedric, Reza, Hooman, and Nafiseh | You need to have licensed MATLAB before running the scripts | There are implemenations of four approaches for enumerating MCSs here. You can run either of them by running its script followed by model name followed by target reaction followed by 1 or 0 which indicates prior network reduction. -1 stands for all reactions
This software provides a clustering module for viewing the relationship of colinear segments in multiple genomes (or heavily redundant genomes). It takes the predicted pairwise segments from dynamic programming (DAGchainer in particular) and then try to build consensus segments from a set of related, overlapping segments.
A reference-free, whole genome profiling system to address cytosine/adenine methylation changes. Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6 mA) at an affordable price. Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6 mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing.
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees | Algorithms for summarizing cancer phylogenies using multiple consensus trees | MCT-Solver - Multiple Consensus Tree Solver | Multiple Consensus Tree (MCT) is a problem that takes a set of input trees on the same set of vertices and an integer k as input, find k consensus trees and a k-clustering of the input trees such that the sum of the distance of each input tree to its corresponding consensus tree is minimized. MCT-Solver contains 3 approaches to this problem, Brute Force, MILP, and Coordinate Ascent
When global and local molecular descriptors are more than the sum of its parts. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming. …methods and tools for Chem-Bio-Med-Informatic Studies. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming language
A Computational Model to Predict the Causal miRNAs for Diseases. miRNA-disease causal association predictor. /main.py used for calculate causal miRNA-disease association potential score. /crossvalidation.py used for 10-fold cross validation.
Web server for identifying glutarylation sites.
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. This is a Python implementation of the molecular dynamics fingerprints (MDFP) methodology for building predictive models for phys-chem properties as delineated in our publication. This toolkit is described and applied to the SAMPL6 logP prediction challenge, with the results published here. Visit our documentation to learn details about installation, example workflow and API references.
Software Facilitating Performing Molecular Dynamics Simulations. MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins. MDMS: Molecular Dynamics Made Simple. The idea behind MDMS design is that the beginnings should be easy - not exhausting. That is why this program accommodates everything that is required for getting realistic insights about protein/protein-ligand complexes through MD simulations
MDPbiome is a software developed in R that uses Markov Decision Processes to create "policy prescriptions" for microbiome engineering. MDPbiome performs a variety of analysis describing the robustness of the prescription, as well as a variety of visualizations to assist in manual interpretation of the state transitions and biological understanding of a microbiome's dynamics.
A model to estimate differential co-occurrence networks in microbiome studies. (Note: This package is currently in development) Microbiome Differential Network Estimation (mdine) allows the estimation of OTU co-occurrence networks within two separate groups, where the networks are defined through precision matrices. The difference between the two precision matrices is also estimated, along with corresponding interval estimates. This work was developed in the Greenwood Lab at McGill University.
Minimum Energy Path Surface Analysis over n-dimensional surfaces | Molecular Modelling Group. Grupo de Modelado Molecular. Centro de Biologia Molecular 'Severo Ochoa' CBMSO, CSIC-UAM | bioweb: molecular modelling group / grupo de modelado molecular | [ http://www.cbm.csic.es/bioweb ] [ http://bioweb.cbm.uam.es ] | n-dimensional energy surfaces are becoming computationally accessible, yet interpreting their information is not straightforward. We present MEPSAnd, an open source GUI-based program that natively calculates minimum energy paths across energy surfaces of any number of dimensions. Among other features, MEPSAnd can compute the path through lowest barriers and automatically provide a set of alternative paths. MEPSAnd offers distinct plotting solutions as well as direct python scripting
Visualising molecular epidemiology data combining genetic markers and drug resistance profiles. Molecular epidemiology uses genetic information from bacterial isolates to shed light on the population structure and dynamics of pathogens. Bacterial pathogens can now be studied by whole genome sequencing, but for some well-studied pathogens such as Mycobacterium tuberculosis a wealth of information is also available from other sources such as spoligotyping and multi-locus variable-number-tandem-repeats (VNTR). Isolates are also frequently tested for susceptibility to antibiotics. Methods of analysis are available for each type of data but it would be informative to combine multiple sources of information into a single analysis or visualisation. Here, we propose and implement a simple way to visualise genotypes along with drug resistance profiles for multiple drugs.
Reconstructing complex lineage trees from scRNA-seq data using MERLoT | Reconstruct the lineage topology of a scRNA-seq differentiation dataset | MERLot: A MEthod for Reconstructing Lineage tree Topologies using scRNA-seq data | Benchmark and plotting scripts for the MERLoT paper | MERLot is a tool that can reconstruct the lineage tree topology that explains the emergence of different cell types from a progenitor population. MERLot is an R package than can reconstruct complex lineage tree topologies using coordinates for cells in a given manifold(like diffusion maps) as input | A collection of scripts that was used to generate and benchmark the simulations provided with the tool MERLoT. Download the expression matrices and parameter files via the GWDG FTP server. These will be used as examples for the various scripts | merlot_prosstt_deep_20190424.tar.gz
Web server to prepare and run coarse-grained membrane protein dynamics.
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA | MEta-Server for protein Sequence Analysis (MESSA) is a tool that facilitates widespread protein sequence analysis by gathering structural (local sequence properties and three-dimensional structure) and functional (annotations from SWISS-PROT, Gene Ontology terms, and enzyme classification) predictions for a query protein of interest. MESSA uses multiple well-established tools to offer consensus-based predictions on important aspects of protein sequence analysis. Being freely available for noncommercial users and with a user-friendly interface, MESSA serves as an umbrella platform that overcomes the absence of a comprehensive tool for predictive protein analysis. This article reveals how to access MESSA via the Web and shows how to input a protein sequence to analyze using the MESSA web server
Despite the increasing importance of non-targeted metabolomics to answer various life science questions, extracting biochemically relevant information from metabolomics spectral data is still an incompletely solved problem. Our framework captures potential relationships between spectral features and substructures learned from public spectral libraries. These associations are used to recommend substructures for any unknown mass spectrum. Our method does not require any predefined metabolite candidates, and therefore it can be used for the partial identification of unknown unknowns.
MESSAR (MEtabolite SubStructure Auto-Recommender)
R package for context-specific expression analysis of metabolic gene clusters.
Mutual Exclusion and Coverage Based Random Walk to Identify Cancer Modules | This is the original repository for the MEXCOwalk paper | The evaluation file can also be run with multiple models and compared to MEXCOwalk. Simply store the models in 'out/connected_components_isolarge/model_x' and add the model name to the evaluations section in the evaluation file as follows:
An on-ramp for RESTful query composition. an on-ramp for learning to use the MG-RAST API. MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server provides upload, quality control, automated annotation and comparative analysis for shotgun and amplicon metagenomic samples as well as metatranscriptomes. MG-RAST API Explorer -- an on-ramp for learning to use the MG-RAST API. An object store for scientific data. MG-RAST provides a RESTful API at https: api.mg-rast.org. workflow and resource management system for bioinformatics data analysis.
Mobile Genetic Elements Retrieving Tool Pipeline (MGERT) for retrieving coding sequences of mobile genetic elements from genome assemblies.
A probabilistic model to recover individual genomes from metagenomes. MGLEX - MetaGenome Likelihood EXtractor. This Python Package provides a probabilistic model to classify nucleotide sequences in metagenome samples. It was developed as a framework to help researchers to reconstruct individual genomes from such datasets using custom workflows and to give developers the possibility to integrate the model into their programs. MGLEX – A Python Package for Probabilistic Modeling and Binning of Metagenomes. We recommend to create a Python virtual installation enviroment for MGLEX. In order to do so, install the venv package for your Python version (e.g. the Debian package python3.4-venv), if not included (or use virtualenv). The following command will make use of the installed system packages
Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data.
The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae | The Methylotroph Gene Order Browser (MGOB) is an online tool for visualising the syntenic context of any gene from several yeast genomes - Copyright Kevin Byrne - ygob@ucd.ie - Wolfe Laboratory, Conway Institute, University College Dublin, Dublin 4, Ireland
The microbiome analysis resource in 2020. MGnify (http: www.ebi.ac.uk metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility.
Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach. IEDB recommended 2.22 IEDB recommended 2.18 Consensus 2.22 Consensus 2.18 NetMHCIIpan 3.2 NetMHCIIpan 3.1 NN-align 2.3 (NetMHCII 2.3) NN-align 2.2 (NetMHCII 2.2) SMM-align (NetMHCII 1.1) Combinatorial library Sturniolo Help on prediction method selections. Enter protein sequence(s) in FASTA format. Or select file containing sequence(s). or as whitespace-separated sequences.
Deep neural network model for universal Major Histocompatibility Complex (MHC) binding prediction.
Computational Molecular Biology Group, Chulalongkorn University
Automated and Reproducible Data Analysis for Immunopeptidomics. MHCquant: Identify and quantify peptides from mass spectrometry raw data.
Microsatellite instability detection on NGS amplicons data. Workflow for detecting microsatellite instability by next-generation sequencing on amplicons. MIAmS: Microsatellites Instability by AMplicon Sequencing.
Variable transformation and model selection for species distribution models. A reproducible paper describing the MIAmaxent R package. Read our open-access paper in Ecology and Evolution introducing MIAmaxent: https://doi.org/10.1002/ece3.5654. Maxent software for modeling species niches and distributions. The file 'miamaxent-ms. MIAmaxent is intended primarily for maximum entropy distribution modeling (Phillips et al., 2006; Phillips et al., 2017), and provides an alternative to the standard methodology for training, selecting, and using models. Use this site to download Maxent software for modeling species niches and distributions by applying a machine-learning technique called maximum entropy modeling.
A novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy. The dataset for MIC_Locator can be downloaded from the website (https://pan.baidu.com/s/1dvvyT9OuJUcQYkCxidABDw)
An interactive web tool for microRNA-target enrichment and network-based analysis. BACKGROUND:miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS:We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis
Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.
Multiple Instance Prediction of Amyloid Proteins | Software and Data Downloads — Personal Webpage documentation | Note: This page will be discontinued. Please visit my new webpage HERE and update your bookmarks | Link to my GitHub profile: HERE Here is a list of the software developed in my lab | AMAP: Antimicrobial activity prediction | MILAMP: Multiple Instance Learning of Amyloid Proteins. Webserver available HERE. Code available HERE
De-identified publicly available database of chest radiographs with free-text reports. If you use the MIMIC-CXR Database in your work, please cite the following publication:. MIMIC-CXR: A large publicly available database of labeled chest radiographs. Johnson AEW, Pollard TJ, Berkowitz S, Greenbaum NR, Lungren MP, Deng C-Y, Mark RG, Horng S. arXiv.. Available from: https://arxiv.org
Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression | Using Multiple Measurements of Tissue to Estimate Subject- And Cell-Type-Specific Gene Expression via Deconvolution | MIND (Multi-measure INdividual Deconvolution) | MIND is a method to glean insights from bulk gene expression. It borrows information across multiple measurements of the same tissue per subject, such as multiple regions of the brain, using an empirical Bayes approach to estimate subject- and cell-type-specific gene expression via deconvolution
The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource. The MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.
Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution. (m)6A (I)dentification Using (N)anopor(E) (S)equencing. Tombo(v1.4) Commands Prior to MINES:. python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa.
A webserver for statistical, visual and meta-analysis of RNA editing data in mammals. BACKGROUND:Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS:Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages.
A myocardial infarction risk knowledge base. Myocardial Infarction Risk Knowledge Base. MIRKB (the Myocardial Infarction Risk Knowledge Base) is a database that collected single factors, combined factors, and risk models which are article-supported to be associated with the risk assessment, diagnosis, prognosis, and treatment of MI in human. The goal of MIKB was to improve the efficiency of MI research. MI is a common cardiovascular disease and a leading cause of death worldwide. It can be classified into many types according to the disease phase, lesion range, ECG expression, infarction location, and clinical type
Fast in-silico MIRU-VNTR typing directly from long sequencing reads. In-silico MIRU-VNTR typing using long reads. Identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). Also work on assembled genome.
Generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI.
Inferring features from microbiota time-series data linked to host status | The Microbiome Interpretable Temporal Rule Engine | Input code and results from simulations supporting the MITRE paper | Supporting files for the Microbiome Interpretable Temporal Rule Engine manuscript | MITRE learns predictive models of patient outcomes from microbiome time-series data in the form of short lists of interpretable rules | This repository includes the configuration files used to set up simulations for the MITRE manuscript, and results from those simulations, with a few useful auxiliary files | MITRE will load data from Bokulich, N. A., et al., "Antibiotics, birth mode, and diet shape microbiome maturation during early life." Science Translational Medicine 8(343): 343ra82, which is packaged with MITRE
Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. MOTIVATION:The use of human genome discoveries and other established factors to build an accurate risk prediction model is an essential step towards precision medicine. While multi-layer high-dimensional omics data provide unprecedented data resources for prediction studies, their corresponding analytical methods are much less developed. RESULTS:We present a multi-kernel linear mixed model with adaptive lasso (MKpLMM), a predictive modeling framework that extends the standard linear mixed models widely used in genomic risk prediction, for multi-omics data analysis. MKpLMM can capture not only the predictive effects from each layer of omics data but also their interactions via using multiple kernel functions.
Potential based, spatial simulation of dynamically nested particles. Source repository for the publication "Potential based, spatial simulation of dynamically nested particles" in BMV Bioinformatics. ML-Force source code added · 1e971b94.
A Fast, Accurate and General Approach for Automated Detection and Landmarking of Biological Structures in Images | Machine-learning-based morphometrics | Machine-learning tools for landmark-based morphometrics | Porto & Voje (2019) A fast, accurate and general model for automated landmarking of biological images. Submitted | Also note that while ml-morph can handle multiple image file formats, some care is needed with regards to the presence of special characters in image filenames. So far, we have only had problems with &, but it is possible that other special characters might lead the software to throw out an error
Metric Learning on Expression Data for Gene Function Prediction.
A Fast and Memory Efficient MLCS Algorithm by Character Merging for DNA Sequences Alignment. This is a fast MLCS algorithm for DNA sequence
An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis | An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
Morais-Lima-Martin (MLM) algorithm for data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach.
R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions.
Automatic multilocus and core genome sequence typing in R. An easy way of MLSTyping your genomes in R. This R package allows you to easily determine the Multi Locus Sequence Type (MLST) of your genomes. It also works as an interface between PubMLST through their RESTful API, so you don't have to bother downloading and collecting files: the application does it automatically. Today the package works in Unix-based systems. If you use MLSTar in your publications, please cite:. Note: cgMLST and wgMLST are not yet fully supported since the RESTful API interphase for theses cases is a little different than the one for the standard 7 loci schemes. See issues#11 for more details
Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae. python-dev (sudo apt-get install python-dev),. regex (https://launchpad.net/ubuntu/+archive/primary/+files/python-regex_0.1.20170117.orig.tar.gz).
Microbiome Learning Repo (ML Repo) - public repository of microbiome regression and classification tasks
Program package for quantum chemical research assisted by machine learning.
Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ML for insightful data analysis and enhance research outcomes. By simplifying and automating various stages of the ML workflow, it enables researchers to allocate more time to their core research tasks, thereby enhancing efficiency and productivity.
Evaluation of algorithms for Multi-Modality Whole Heart Segmentation | Multi-Modality Whole Heart Segmentation Challenge | MM-WHS: Multi-Modality Whole Heart Segmentation | Accurate computing, modeling and analysis of the whole heart substructures is important in the development of clinical applications. Segmentation and registration of whole heart images is however challenging and still relies heavily on manual work, which is time-consuming and prone to errors | For evaluation of the test data, the participants should prepare a brief description of their algorithm and email with the segmentation results of the test datasets to the organizers
Mother machine image analysis with MM3. Version 3 of Python mother machine analysis code. MM3 at University of California, San Diego. MM3 at University of California, San Diego for Fall 2019 on Piazza, a free Q&A platform for students and instructors. mm3 is a image analysis pipeline for mother machine experiments. It takes as input raw timelapse images and produces as output cell objects containing information such as elongation rate, birth size, etc. There is support for fluorescent planes. Segmentation and tracking software for mother machine experiments. The name Piazza comes from the Italian word for plaza--a common city square where people can come together to share knowledge and ideas. We strive to recreate that communal atmosphere among students and instructors
GPU-accelerated mesh-based Monte Carlo photon transport simulations. ===============================================================================. = Mesh-based Monte Carlo (MMC) =. = Supporting both OpenCL and Multi-threading with SSE4 =. A GPU-accelerated photon transport simulator. Download v2019.4 or Nightly-build. "mmc -L" or "mmclab('gpuinfo')" to list). Designing MATLAB-streamlined MC-based analysis using MCXLAB and MMCLAB.
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.
Software and resources for experiments and data analysis of MEG and EEG data | Installation — contents — MNE 0.19.1 documentation | The official home of the Python Programming Language | Notice: While Javascript is not essential for this website, your interaction with the content will be limited. Please turn Javascript on for the full experience | MNE-Python is an open-source Python module for processing, analysis, and visualization of functional neuroimaging data (EEG, MEG, sEEG, ECoG, and fNIRS) | Python is a programming language that lets you work quickly and integrate systems more effectively | Join the official 2019 Python Developers Survey Start the survey!
Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing.
Efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model
Automated Annotation of MOB Relaxases. Please, fill the submission form below and select the FASTA file containing the amino acid sequences. Your data is being processed. Please be patient as, depending on the number of sequences uploaded, it could take a few minutes
Web-application to collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills.
Multi-omics late integration with deep neural networks for drug response prediction | MOTIVATION:Historically, gene expression has been shown to be the most informative data for drug response prediction. Recent evidence suggests that integrating additional omics can improve the prediction accuracy which raises the question of how to integrate the additional omics. Regardless of the integration strategy, clinical utility and translatability are crucial. Thus, we reasoned a multi-omics approach combined with clinical datasets would improve drug response prediction and clinical relevance. RESULTS:We propose MOLI, a multi-omics late integration method based on deep neural networks. MOLI takes somatic mutation, copy number aberration and gene expression data as input, and integrates them for drug response prediction
Toolbox integrating top-performing methods for NEtwork MOdularisation.
Design and assembly of DNA molecules using multi-objective optimisation | A DNA design and assembly method based on multi-objective optimization | MOODA: Multi-Objective Optimization for DNA sequence Design and Assembly | A manufacturing-aware sequence optimizer | Write a MOODA configuration file. A .yaml file defining operators, objective functions, assemblies strategy and their parameters, this is how a MOODA configuration file looks like:
Mathematical explOration of 'Omics data on a MetabolIc Network | MOOMIN is a tool for analysing differential expression data | MOOMIN (Mathematical explOration of Omics data on a MetabolIc Network) is a tool for analysing differential expression data. It takes as its input a metabolic network and the results of a DE analysis: a posterior probability of differential expression and a (logarithm of a) fold change for a list of genes. It then forms a hypothesis of a metabolic shift, determining for each reaction its status as "increased flux", "decreased flux", or "no change". These are expressed as colours: red for an increase, blue for a decrease, and grey for no change. See the paper for full details: https://doi.org/10.1093/bioinformatics/btz584
Multi-Omic and Survival pathway analysis for the identification of survival associated gene and module.
Software for producing automated textbook-style maps of genome-scale metabolic networks.
Mobile training and support (MOTS) service-using technology to increase Ebola preparedness of remotely-located community health workers (CHWs) in Sierra Leone. As in many African countries, the Community Health Worker (CHW) is the backbone of the healthcare system, and the focus and objective of the Mobile Training and Support (MOTS) project will be strengthening this network to ensure preparedness for Ebola vaccine campaigns and outbreak response. The project will set up a MOTS service that is the veh….
A standalone GUI-based package for maximum entropy model inference. Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters. MPF-BML: A standalone GUI-based cross-platform package for maximum entropy model inference. MPF-BML-GUI is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the input data (protein sequence data or data of multiple configura-tions of a complex system with large number of variables) and returns the maximum entropy model parameters inferred using the MPF-BML method
Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation. Molecular Prognostic Indicators in Cirrhosis. Database for clinical context-specific in silico prognostic biomarker validation. This is a system that enables quick and easy assessment of user’s prognostic gene signature in various liver disease patient cohorts for a specific clinical outcome
Statistical framework for massively parallel reporter assays | Statistical Analysis of MPRA data | MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes
Web-based tool for the design of massively parallel reporter assay experiments.
Robust and non-parametric analysis of massively parallel reporter assays | MPRAscore: Robust and non-parametric analysis of massively parallel reporter assays (MPRA) | MPRAscore infers allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.
Language workbench user interfaces for data analysis. The Domain-Specific Language Creator by JetBrains. Use MPS platform to create your own domain-specific language that speak to your business needs. Use non-textual notation with projectional editing. BDVal for MPS is an MPS plugin designed to help you configure BDVal projects. BDVal for MPS makes it easier to develop and validate predictive models in high-throughput datasets. When the product is highly complex and the developers aren’t experts in your business domain. MPS helps even unfamiliar developers understand the system immediately
Applications of the Microphysiology Systems Database for Experimental ADME-Tox and Disease Models | The MPS-Db aggregates MPS data with linked preclinical and clinical databases for analysis in the context of human exposure. Built in tools enable the assessment of the reproducibility and transferability of MPS models, while computational models are being developed to enhance the value of MPS models for understanding disease mechanisms, compound toxicity, and prediction of drug pharmacokinetics (PK)
Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes | This repository contains the case studies associated with the manuscript "Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes" | 2-sample Mendelian Randomisation | MR-base is a database and analytical platform for Mendelian randomization being developed by the MRC Integrative Epidemiology Unit at the University of Bristol
Clustering of genetic variants in Mendelian randomization with similar causal estimates. R package for investigating clustered heterogeneity in Mendelian randomization (MR) analyses. mr_clust_em - performs expectation-maximisation (EM) based model fitting of the MR-Clust mixture model. Genetic variants which recover similar estimates of the causal effect of the risk-factor on the outcome - i.e. their ratio-estimates are similar in direction, magnitude and precision - can form distinct clusters in MR analyses. We call this `clustered heterogeneity'. Each cluster might represent a distinct pathway with which the risk-factor is related to the outcome and hence clustered heterogeneity is interesting to investigate as the identity of the genetic variants in the clusters may reveal information about the risk factor and how it relates to the outcome
MR-MEGA (Meta-Regression of Multi-Ethnic Genetic Association) - tool to detect and fine-map complex trait association signals via trans-ethnic meta-regression.
Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification.
Neural Correlates of Urinary Retention in Lateral Medullary Infarction. MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.
Tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.
Tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.
A fast, flexible and open software framework for medical image processing and visualisation | MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software
Tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps (CPMs) or in general terms circular plots with a non-genomic basis.
Predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. Under construction, we will update it soon. MS2CNN compilation requires the following tools installed on your system Python, Keras==2.0.4 and Tensorflow==1.1.0. Predicting MS/MS spectrum based on protein sequence by Deep Convolutional Neural Networks. Lin YM, Chen CT, Chang JM. MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. BMC Genomics. 2019;20(Suppl 9):906
MS²PIP is a tool to predict MS² peak intensities from peptide sequences. This makes it possible to generate in silico predicted spectral libraries for full proteomes. MS²PIP employs the XGBoost machine learning algorithm and is written in Python.
A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacterial Microsatellites. MICAS: Microsatellite Analysis Server 3.0. An Online Repository of All Prokaryotic Microsatellites. with a focus on Viruses of Microbes and Molecular Epidemiology of bacterial pathogens. CRISPRCasdb: database for CRISPRs and associated Cas genes. MICAS: Microsatellite Analysis Server.
Modular within and between score for drug response prediction in cancer cell lines. Drug response prediction in cancer cell lines is vital to discover new anticancer drugs. However, it's still a challenging task to accurately predict drug responses in cancer cell lines. In this study, we presented a novel computational approach, named as MSDRP (modular within and between score for drug response prediction), to predict drug responses in cell lines. The method is based on a constructed heterogeneous drug-cell line network with multiple information. Compared with other state-of-the-art methods, MSDRP acquired better predictive performance, and identified potential associations between drugs and cell lines, which have been confirmed by the published literature. The source code of MSDRP is freely available at https: github.com shimingwang1994 MSDRP.git
Tool to visualize biological indices from mass spectrometry imaging data.
Python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine.
Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure. Computational Selection of MSMS to Include in Library (MSMS-Chooser). Open-source Protocol for Community-created Public MS/MS Reference Library (MSMS-Chooser). MSMS-Chooser is a GNPS workflow and open-source protocol to empower the community to collect MS/MS reference data and contribute to the public MS/MS reference library.
MTB Genome to Test (MTBGT) tool transforms WGS-derived data into laboratory-validated results of the primary RDTs – Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II.
Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data. MTGO applied to Single Cell analysis. MTGO analysis applied to Single Cell data version 0.2.0 from GitHub. MTGO-SC is an adaptation for single cell RNA-sequencing (scRNA-seq) of MTGO, a biological network module detection algorithm. MTGO-SC integrates external gene annotations, such as the Gene Ontology terms or Reactome pathways with the gene expression networks obtained from single-cell DGE matrices. This package integrates MTGO (Module detection via Topological information and Gene Ontology (GO) knowledge) to single cell analysis. Effort is made to seamless integration of Seurat results, together with visualization and filtering functions. ne1s0n/MTGOsc: MTGO analysis applied to Single Cell data. Extracting gene modules from single cell RNA-seq cell clusters
A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. Code and sequence files used in MTK manuscript
Multi-Task Deep Model with Margin Ranking Loss for Lung Nodule Analysis | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | This is the pytorch implementation for 《MTMR-Net: Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 Project
Docking into a user-defined binding site or blind docking using AutoDock 4.2.
Automated virtual screening with AutoDock Vina.
Multivariate analysis application for streamlined data analysis and curation.
Multi-view based integrative analysis of gene expression data for identifying biomarkers | This repository provides some codes for this paper | The widespread applications in microarray technology have produced the vast quantity of publicly available gene expression datasets | If you are interested in it but have doubts about the content, please feel free to contact me | Communication: yangziyi091100@163.com
Myelin Water Fraction and Intra/Extracellular Water Geometric Mean T2 Normative Atlases for the Cervical Spinal Cord from 3T MRI | Normative atlases for the spinal cord using myelin water imaging | Myelin water imaging was applied in 20 healthy spinal cords to create T2 metric healthy population atlases that depict the mean and variation of myelin water fraction (MWF), and intra- and extra-cellular water mobility as described by geometric mean T2 (IEGMT2). The created atlases demonstrated structural variations in the spinal cord consistent with well-known anatomical characteristics. These atlases (in PAM50 space from Spinal Cord toolbox) can be used as a reference to demonstrate areas of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400
A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses
A functional genomics hub for Malvaceae plants. Pipelines of data analysis for MaGenDB
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning. MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces. MaSIF- Molecular Surface Interaction Fingerprints: Geometric deep learning to decipher patterns in protein molecular surfaces. MaSIF is a proof-of-concept method to decipher patterns in protein surfaces important for specific biomolecular interactions
A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI (Mycobacterium ABscessus modELLing INItiative) is a database available to anyone that wishes to know in detail the structural proteome of Mycobacterium abscessus. It contains thousands of models, generated with an unique domain-based methodology and thoroughly annotated with information from UniProt, CATH, SCOP and many more resources. These models are readily available for download, either individually or in bundles. To access them, simply use one of the many available queries or explore the data using our hierarchical interactive sunbursts
Maize Database of Images and Genomes | MaizeDIG - Maize Database of Images and Genomes. This tool allows users to tag phenotypes in images and link them to specific genes | MaizeDIG the Maize Database of Images and Genomes, a genotypic-phenotypic database, for maize based on BioDIG | There are some prerequisites to set up MaizeDIG system such as installation of Django framework, Database system, Python and related libraries, and other dependencies | The Maize Genetics Executive Committee is reaching out to the global maize genetics, genomics, and breeding research communities to encourage researchers to become a maize cooperator (What is a maize cooperator?) Regions currently underrepresented within the maize cooperators are Africa, Asia, Europe, and Latin America
An integrated data warehouse for MaizeGDB
A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used in the system command line with R installed in the system or be used in the R enviroment. test.snp.RData is the input data to this R script. test.snp.RData is an R data file contained the genotype data of 1210 maize lines across 1000 SNP sites in character matrix. The content of this R data can be viewed in the R enviroment as shown below. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The genotypes of 1210 maize lines at 35,370,939 SNP sites are stored using Sparse Matrices in R. MaizeSNPDB is idle until you activate it by accessing the URL. After running the R script, a new R data file named as test.snp. Mat.
Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm. The cytoplasm of a cell is sometimes jestingly called a Soup, since it contains many different ingredients. Indeed there is quite a bit of salt and glutamate, the well known flavour enhancing compoud that is used a lot in asian kitchen but also in broth. Read more here: https://en.wikipedia.org/wiki/Glutamate_flavoring. In order to study the cytoplasm of a cell one can use a variety of experimental biochemistry techniques, but also computer simulations, which is the focus of this page. Here we thererfore provide information and python scripts to run computer simulations using http://www.gromacs.org of (quite) realistic models of the cytoplasm. The main work is done here by a few scripts, located in the aptly named scripts directory. They are described briefly in the README.md in that directory
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo credit: Genome Research Limited. We're working with researchers in malaria-endemic countries to generate large-scale genetic and genomic data on all three malaria genomes: human, parasite, and mosquito. The Plasmodium falciparum Community Project supports groups around the world to integrate parasite genome sequencing into clinical and epidemiological studies of malaria. Our projects provide a framework for malaria researchers around the world to work together on large-scale studies that combine epidemiology with the analysis of genome variation to better understand the evolutionary battle between human hosts, malaria parasites, and the mosquito vector
An open-source web application for increasing access to malaria information. Preventable diseases still cause huge mortality in low- and middle-income countries. Research in spatial epidemiology and earth observation is helping academics to understand and prioritise how mortality could be reduced and generates spatial data that are used at a global and national level, to inform disease control policy. These data could also inform operational decision making at a more local level, for example to help officials target efforts at a local regional level. To be usable for local decision-making, data needs to be presented in a way that is relevant to and understandable by local decision makers. We demonstrate an approach and prototype web application to make spatial outputs from disease modelling more useful for local decision making.
Displaying genome-wide association summary statistics with multiple annotation layers. A useful way to summarize genome-wide association data is with a Manhattan plot. This type of plot has a point for every SNP or location tested with the position in the genome along the x-axis and the -log10 p-value on the y-axis
Tool for automatically detecting and characterizing peaks from GWAS output files (Manhattan Plots).
MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data | MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes | MapCaller: An efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data | MapCaller aligns every NGS short read against a reference genome and collects all the alignment information to deduce sequence variants
Lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments.
The opendata geoportal of the Lamma Consortium.
Topological gene expression networks recapitulate brain anatomy and function | Code for reproducing results in the paper "Topological gene-expression networks recapitulate brain anatomy and function" | TDA summary for gene-expression: Mapper Algorithm in 2D | Understanding how gene expression translates to and affects human behaviour is one of the ultimate aims of neuroscience
Enhancer prediction in the human genome by probabilistic modeling of the chromatin feature patterns. This package is a PRobabilistic Enhancer PredictIoN Tool PREPRINT. Clone the project to the desired directory, this will be your path_to_dir. https://github.com/MariaOsmala/RFECS_BUG_FIXES.git.
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. We aimed to design a hybrid system for systematic entity recognition and ranking to identify poten-tial biomarkers for liver cancer
Mascot Daemon is a Microsoft Windows client application that automates the submission of data files to Mascot server.
Mascot Distiller Workstation offers a single, intuitive interface to a wide range of native (binary) mass spectrometry data files. A unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists. This core functionality can be extended by adding one or more toolboxes. These are optional collections of tools for specific tasks, such as Mascot search result review, automatic and manual de novo sequencing, quantitation, and batch processing. There is also a developer’s package that provides access to the API of the underlying COM library.
Mascot Parser provides an object-oriented Application Programmer Interface (API) to Mascot result files and configuration files, making it easy for programs written in C++, C#, Java, Perl or Python to access Mascot results.
An extensible, vendor-agnostic application for mass spectrometry analysis. Current analysis packages include protein-protein crosslinking (XL), hydrogen/deuterium exchange (HX), covalent labelling quantification and normalization (CLEAN).
A Package for Constructing Master Equation Models of Molecular Dynamics | Python package for generating Markov state models | MasterMSM is a Python package for generating Markov state models (MSMs) from molecular dynamics trajectories. We use a formulation based on the chemical master equation. This package will allow you to:
Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA). Please read the documentation here: https://biocorecrg.github.io/master_of_pores/. Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing. This is a joint project between CRG bioinformatics core and Epitranscriptomics and RNA Dynamics research group.
Comprehensive annotation of mature peptides from polyproteins in five virus families. Annotate a viral polyprotein by projecting reference mature peptide annotation through global alignment. The United States Government Department of Health and Human Services, National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases, owns the copyright to the accompanying software under FAR 52.227-14 (c).
Supervised Learning for High-dimensional Matched Case-Control Studies. This code implements Matched Forest algorithm which aims to find important variables in high-dimensional matched case-control data sets. Please refer to our papers for more details:
General Analysis Utilities for Dynamic Omics Datasets. MathIOmica is a package for bioinformatics, written in the Wolfram language, that provides multiple utilities to facilitate the analysis of longitudinal data generated from omics experiments, including transcriptomics, proteomics, and metabolomics data, as well as any generalized time series. MathIOmica uses Mathematica's notebook interface, wherein users can import longitudinal datasets, carry out quality control and normalization, generate time series, and classify temporal trends. MathIOmica provides spectral methods based on periodograms and autocorrelations for automatically detecting classes of temporal behavior and allowing the user to visualize collective temporal behavior, and also assess biological significance through Gene Ontology and pathway enrichment analyses. MathIOmica's time-series classification methods address common issues including missing data and uneven sampling in measurements.
We propose MatrixMotif(MM), a new combinatorial hybrid algorithm allowing qualitative and quantitative analysis of TFBS (Transcription Factor Binding Site) motifs using NGS data originated from DNA extraction and enrichment techniques. MM allows de novo motifs discovery and motifs iteration employing enumerative and probabilistic models based on several types of matrixes. MM primarily utilizes set of sequences from NGS in fasta format as a template for mathematical and statistical modeling. Fasta format can be generated from fastq format (Illumina platform) set of individual enriched sequences. MM generates final motifs as PPM, PWM or TFFM allowing visualization of de novo computed motifs.
An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the citation details for MaveDB. MaveDB is a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning (DMS) or massively parallel reporter assay (MPRA) experiments. Welcome to our table of Multiplexed Assay of Variant Effect (MAVE) studies. To contribute a study or amend/expand an existing entry, please use the GitHub issue tracker or create a pull request
An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis | Minimum Error Calibration and Normalization for Copy Number Analysis | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It’s crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale | Mecan4CNA (Minimum Error Calibration and Normalization for Copy Number Analysis) uses an algebraic method to estimate the baseline and the distance between DNA levels (referred to as level distance). It can be used for both single file analysis and multi-file normalization | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It's crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale
Applying knowledge-driven mechanistic inference to toxicogenomics | Mechanistic inference of toxicity from gene expression time series and knowledge graphs | Mechanistic inference for toxicology | This repository provide the code for the publication "Applying knowledge-driven mechanistic inference to toxicogenomics" (DOI: xxxxxxxxxxxx) and contains the collection of scripts to reproduce the results obtained. Besides the code, this repository provides: | $ git clone git@github.com:ignaciot/MechSpy.git | You can add new mechanisms of your own to MechSpy by editing mechanisms.py. A mock, commented-out "M12" mechanism was added to illustrate where would new mechanisms need to go
MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.
algorithms for analyzing DNA methylation data generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips Epigenome-Wide Association Studies (EWAS)
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs. git clone https://github.com/HKU-BAL/megagta.git.
Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants. Meltos is a novel approach to estimate the variant allele frequency of somatic SVs from whole genome sequencing (WGS) signals and using these VAFs to identify the phylogenetic relationship between SSVs in a multi-sample cell lineage tree using an SNV-only tree as a basis. Our probabilistic framework allows us to assess multiple types of signals taken from the data simultaneously and more accurately calculate the VAF of SV events. Following the maximum parsimony principle, Meltos uses a novel combinatorial algorithm to assign SV clusters on the branches of the given lineage tree, while modestly augmenting the tree topology if needed
A Tool for Robust Computation and Characterization of Curved Membranes | MemSurfer is a software tool to compute bilayer membrane surfaces | Biochemical and Biophysical Systems Group | MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations | Advances in simulation methodologies, code efficiency, and computing power have enabled larger, longer, and more-complicated biological membrane simulations
Analysis tool for protein-protein cross-linking using MS-cleavable cross-lining reagents such as DSBU, DSSO, CDI or PIR linker
Computational tool for metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. The tool (i) is based on machine learning classifiers, (ii) includes automatic model and feature selection steps, (iii) comprises cross-validation and cross-study analysis, and (iv) uses as features quantitative microbiome profiles including species-level relative abundances and presence of strain-specific markers. It provides also species-level taxonomic profiles, marker presence data, and metadata for 3000+ public available metagenomes.
Generation of a Molecular Network from Electron Ionization Mass Spectrometry Data by Combining MZmine2 and MetGem Software | Calculation and visualization of molecular networks based on t-SNE algorithm - metgem/metgem | MetGem is an open-source software for tandem mass-spectrometry data visualization. It's key features are standalone molecular networking and t-SNE based projections
Complex genetic admixture histories reconstructed with Approximate Bayesian Computations | MetHis is a population genetics forward simulation tool designed to simulate arbitrarily complex admixture histories between two populations
Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR.
Computer-Assisted Natural Products Anticipation | a web server for natural products anticipation | Currently running beta version 0.4.2 | "Essence is a function of the relationship." Bachelard 1929 | MetWork used for the identification of bromotryptamine derivatives
Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation.
A Sequence-Based Meta-Predictor for Improving the Prediction of Antiviral Peptides Using Effective Feature Representation. In spite of the large-scale production and widespread distribution of vaccines and antiviral drugs, viruses remain a prominent human disease. Recently, the discovery of antiviral peptides (AVPs) has become an influential antiviral agent due to their extraordinary advantages. With the avalanche of newly-found peptide sequences in the post-genomic era, there is a great demand to develop a sequence-based predictor for timely identifying AVPs as this information is very useful for both basic research and drug development. In this study, we propose a novel sequence-based meta-predictor with an effective feature representation, called Meta-iAVP, for the accurate prediction of AVPs from given peptide sequences. Herein, the effective feature representation was extracted from a set of prediction scores derived from various machine learning algorithms and types of features
an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning
Reference-guided extraction of CRISPR spacers from unassembled metagenomes. MetaCRAST: reference-guided CRISPR detection in metagenomes. MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes. Unlike other tools, it uses expected CRISPR direct repeat (DR) sequences from assembled contigs or bacterial genomes to guide metagenomic CRISPR detection. It uses a fast implementation of the Wu-Manber multipattern search algorithm to rapidly select reads that contain an expected DR sequence. It then proceeds through reads identified in the previous step to find DR sequences within acceptable distances of each other (i.e., with acceptable length spacers between them). Spacers between these DRs are then extracted and clustered into a non-redundant set with CD-HIT
MetaCarvel: A scaffolder for metagenomes | MetaCarvel - Scaffolder for metagenomes | MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2. To run MetaCarvel, you will need Python 2.7.x, Samtools, Bedtools, Networkx(Version < 1.11), NumPy,and OGDF
Analysis of single-cell RNA-seq data using K-nn graph partitions. scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We describe a methodology for partitioning scRNA-seq datasets into metacells: disjoint and homogenous groups of profiles that could have been resampled from the same cell. Unlike clustering analysis, our algorithm specializes at obtaining granular as opposed to maximal groups. We show how to use metacells as building blocks for complex quantitative transcriptional maps while avoiding data smoothing. Our algorithms are implemented in the MetaCell R C++ software package.
Galaxy workflow for differential abundance analysis of 16s metagenomic data. You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. This history is empty. You can load your own data or get data from an external source
Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains.
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. It bundles essential annotation tasks such as feature prediction, functional annotation with Hidden Markov Model (HMM) searches as well as blast and diamond searches. It estimates and visualizes quantitative taxonomic and pathway compositions of multiple metagenomic and proteomics samples using sequencing coverage and proteomics spectral counts, respectively. For visualization, MetaErg provides a HTML interface, bringing all annotation results together in sortable and searchable tables, collapsible trees, and other graphic representations, enabling intuitive navigation of complex data. Analysis statistics: master.stats.txt. Analysis annotation in gff format: master.gff.txt. MetaErg begins biological feature and element prediction by identifying CRISPR elements and non-coding RNA genes (tRNA, rRNA genes)
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.
Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity. Transcriptomics meta-analysis of skeletal muscle response to exercise. Transcriptomics meta-analysis of skeletal muscle response to exercise. The shiny app is available at www.metamex.eu.
Linking Microbiota Functions with Medicine Therapeutics. Metagenomics Medicine mapping system (MetaMed), is a novel and integrative system-wide correlation mapping system to link bacteria functions and medicine therapeutics
A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery.
Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data | Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities | MetaMorpheus: Free, Open-Source PTM Discovery | Download the current version here. For first-time Windows users, choose "MetaMorpheusInstaller.msi" and install MetaMorpheus. Check out our getting started video on YouTube
Analysis pipeline and browser-based software suite for transcriptomic meta-analysis.
Integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data.
Simple, high-level languages for data analysis with the R ecosystem. Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name. MetaR takes advantage of Language Workbench Technology to facilitate data analysis with the R language. It can be used by:. Apache Server at metar.campagnelab.org Port 80. bioinformaticians who wish to package state of the art analysis methods into user friendly metaR analysis language constructs. MetaR can act as a bridge between analysis experts who develop analysis methods in R and wish to distribute these methods to the broadest audience without investing a lot of effort in developing user interfaces.
An integrated, customizable microbial genome evaluation and annotation pipeline. Pipeline for major biological analyses. MetaSanity v1.1.1 - 2020 version. MetaSanity v1.1.1 provides a unified workflow for genome assessment and functional annotation that combines all outputs into a single queryable database – all within an easily distributed Docker image
Spark-based distributed processing tool to recruit metagenomic reads to reference genomes.
A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries | Metagenomic binning based on Hi-C data | pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator | Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamline the processing and binning of metagenomic 3C datasets | Please refer to the tutorial in order to quickly get the pipeline up and running on example data (or your own), and the metaTOR manual for detailed explanations on the parameters
A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis | Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data | Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis
Graphical visualization tool for metabolomics and genomic data within metabolic pathways
Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. The Metabolic Disassembler is a Python package to automatically predict a combination of biosynthetic units in a natural product. This software would help to reveal the starting materials of the target natural product.
FAIR metadata editor for guiding the user through the creation of FAIR Data Point metadata.
metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species. From annotated genomes to metabolic screening in large scale microbiotas. Metage2metabo is a Python3 (Python >= 3.6) tool to perform graph-based metabolic analysis starting from annotated genomes (reference genomes or metagenome-assembled genomes). It uses Pathway Tools in a automatic and parallel way to reconstruct metabolic networks for a large number of genomes. The obtained metabolic networks are then analyzed individually and collectively in order to get the added value of metabolic cooperation in microbiota over individual metabolism and to identify and screen interesting organisms among all. m2m — metage2metabo documentation. Free document hosting provided by Read the Docs
This code implements a pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in the field of metagenomics
Metagenomic read binning using sparse coding
An online software tool for mass spectrometry-based isobaric labeling metabolomics. Metandem - A Data Analysis Tool for Isobaric Labeling-based Metabolomics. Metandem is a free online data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online
Individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes.
Portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists.
A reference methylome database for different organisms that is created from public BS-seq datasets.
Bayesian calibration of methylation levels | This package allows the calibration of methylation levels using MethylCal, a Bayesian calibration tool based on INLA (Rue et al., 2009). The package permits the visualisation of the calibration curve derived from standard controls with known methylation percentages for a selected assay. It also allows the correction of the methylation levels in case and control samples. If cases are provided, MethylCal performs a differential methylation test to detect hyper- and hypo-methylated samples. Besides MethylCal method, the package also includes the calibration and the correction provided by two alternative methods (Warnecke et al., 1997; Moskalev et al., 2011)
Framework for Methyl-Seq genome-wide power calculation and study design issues.
Identifying SNPs in Illumina DNA methylation array data. Detect SNP patterns in Methylation Array data. This is the developer version of Bioconductor package MethylToSNP. Install in R as:
A Metabolomics Support Package for Untargeted Mass Spectrometry. A Metabolomics Support Package for Untargeted Mass Spectrometery. MetumpX is a Ubuntu based software package that facilitate easy download and installation of about 89 tools related to standard Untargeted Metabolomics Mass Spectrometery pipeline. Installation • Authors • License • Revision History
An extended tool for microarray gene expression analysis. Gene expression microarrays capture a complete image of all the transcriptional activity in a biological sample. Microarrays produce a large amount of data, which becomes a challenge when it comes to exploring and interpreting using modern computational and statistical tools. We propose the Microarray Analysis (MiCA) tool that outperforms other similar tools both in terms of ease of use and statistical features requiring minimal input to conduct an analysis. MiCA is an integrated, interactive, and streamlined desktop software for the analysis of microarray gene expression data. MiCA consists of a complete microarray analysis pipeline including but not limited to fetching data directly from GEO, normalization, interactive quality control, batch-effect correction, regression analysis, surrogate variable analysis and functional annotation methods such as GSVA using known existing R packages.
A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors | A high-throughput multiplexed amplicon sequencing workflow to quantify drug resistance mutations (DRMs) against protease, reverse transcriptase and integrase inhibitors. MiDRMpol is computational as well as labor efficient bioinformatics pipeline to detect DRMs from HTS data.The method can be incorporated in large scale surveillance of HIV-1 DRMs
Mapper for full-length T- and B-cell repertoire sequencing.
MicroPeptide identification tool using machine learning. MiPepid is a software specifically for predicting the coding capabilities of sORFs. Given a fasta file containing DNA fasta sequences, for each sequence, MiPepid will find all the sORFs (length <= 303 bp) present in all the 3 translation frames of the sequence, and for each sORF it will return the predicted class label (coding or noncoding) as well as the probability of being in that class. All the results will be written in an output .csv file
Agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response.
Software for extraction of T- and B-cell receptor repertoires from any type of sequencing data.
Software tool for predictive microbiology and microbial risk assessment in foods.
Using metagenomic unmapped reads to provide insights into human microbiota and disease associations | A microbial profiling framework for metagenomic analysis | MicroPro is a software to perform profiling of both known and unknown microbial organisms for metagenomic dataset. A microbe is considered known/unknown if its whole genome is known/unknown according to the NCBI Reference Sequence Database. MicroPro has two pipelines: MicrobialPip and ViralPip. MicrobialPip considers all the microbial organisms including bacteria, archaea and viruses while ViralPip only extracts known and unknown viruses from the provided metagenomics dataset. More details of MicroPro are provided in the following paper:
MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.
Analysing complex metagenomic data with MicroWineBar | MicroWineBar is a graphical tool for analysing metagenomic sequencing samples | MicroWineBar was designed for species abundance tables from shotgun metagenomics data but can also be used for other types of hierarchical data. The tab-delimited files contain absolute and/or relative abundances with taxonomic annotations (or other hierarchical data). As MicroWineBar is not tight to any specific program which generates species abundance tables, one needs to prepare the input:
An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Directory, an inventory that profiles more than 7500 microbes!.
An integrated computational pipeline to infer functional effects of microbiome-host interactions. Abstract Microbiome-host interactions are important to nearly all living organisms, and play important roles in health and disease. Understanding these inter-kingdom cross-talks has a huge potential to advance diverse scientific domains such as the clinical and medical sciences, agriculture, and ecology. Detecting such interactions by experimental techniques remain challenging from a cost and feasibility perspective thus hampering large-scale analyses. Computational approaches not only make the inference of microbiome-host interactions viable but also scalable. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins with host molecular networks.
MicrobiomeR is an R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.
A package for downloading and preprocessing microdata from Brazilian Health Informatics Department (DATASUS)] | Download de dados do DataSUS e pré-processamento no R | O pacote para o R microdatasus apresenta funções para download dos arquivos de microdados do DataSUS (formato DBC), leitura dos arquivos através do pacote read.dbc e pré-processamento para utilização. Nesta última etapa, os rótulos e formato das variáveis são atribuídos e tratados | Plano Diretor de Tecnologia da Informação do Ministério da Saúde, biênio 2017-2018, foi publicada no Diário Oficial da União | Software de gestão hospitalar completo, desenvolvido em tecnologia web que substitui o sistema HOSPUB
R-program supporting a step of workflow of fluxomic analysis of artificial 13C labeling of metabolites. It designed to correct raw mass spectra (MS) of 13C-labeled metabolites of interest for natural isotopes occurrence. The raw mass spectra are supposed to be extracted from MS recording by Ramid.
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology. Workflow and supporting files for Taylor et al: "Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". Companion materials for the manuscript "Taylor et al: Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". This repository contains the primary Nextflow workflow (minion_bacterial.nf) for bacterial nanopore assembly described in the manuscript and accessory scripts for reproducing the results therein. Workflows for the phylogenetic analysis can be run separately from the phylogenetics directory. The time series analysis can be reproduced using the following steps:.
Alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.
De novo Nanopore read quality improvement using deep learning. BACKGROUND:Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS:Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments
R Package for Multiple Isotope Labeling Assisted Metabolomics Data Analysis.
A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome | Ishiya, K., Mizuno, F., Wang, L., & Ueda, S. (2019). MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome. Bioinformatics and biology insights
Snakemake pipeline for imputation of mitochondrial genetic variants using Impute2 Chromosome X protocol.
Learning a mixture of microbial networks using minorization-maximization | "MixMPLN" is a package written in R, which has two features. First feature is generating a proper synthetic sample-taxa count matrix. Second feature is receiving a sample-taxa count matrix and extracting k(number of components) different interaction networks between taxa | Following packages must be installed and loaded in R environment before using "MixMPLN":
Image-processing software developed for counting cells in photographs of blood smears.
Modular Breeding Program Simulator. This repository contains our R-package MoBPS and the associated packages (miraculix/RandomFieldsUtils/MoBPSmaps). A manuscript for the package is finally available in preprint (https://www.biorxiv.org/content/10.1101/829333v1)
CLONAL HEMATOPOIESIS IN A CENTENARIAN COHORT. MOsaic CHromosomal Alterations (MoChA) caller. A bcftools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD). If you use this tool in your publication, please cite the following paper and preprint:. This command will create a list of variants falling within segmental duplications with low divergence (<2%), high levels of missingness (>2%), variants with excess heterozygosity (p<1e-6), and variants that correlate with sex in an unexpected way (p<1e-6).
Modular multi-scale integrated genome graph browser. Long-read sequencing allows for more sensitive and accurate discovery of SVs, which requires to filter and validate thousands of candidates. However, no existing genome browser meets the demand for cancer genomics. Because most visualization tools show an only range of a linear sequence, making them unsuitable for large (over megabase) or nested SVs. Also, no existing genome browsers allow users to simultaneously inspect the read alignments that span the reference allele and an alternative allele caused by a heterozygous SV. Here we present MoMI-G, a graph genome browser to visualize SVs on the variation graph, that provides a graph-based view that displays a genome with branches and alignments on them. Users can filter, visualize with genomic annotations, and inspect SVs with read alignments. A genome graph browser for visualization of structural variants (SVs) as a variation graph:
Identifying Molecular Recognition Features in Intrinsically Disordered Regions of Proteins by Transfer Learning | AVAILABILITY HTML server, please click here. RESTful web server, please click here. (Updated Apr. 10, 2018) Downloadable software, please click here. OVERVIEW A new computational approach for a fast and accurate prediction of MoRFs in protein sequences. MoRFchibi SYSTEM (Malhis et al 2016) includes three different predictors: MoRFCHiBi is most appropriate as a component predictor in other applications. […] | The University of British Columbia
Computational prediction of MoRFs based on protein sequences and minimax probability machine. BACKGROUND:Molecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDRs), and undergo disorder-to-order transitions upon binding to their interaction partners. The functional importance of MoRFs and the limitation of experimental identification make it necessary to predict MoRFs accurately with computational methods. RESULTS:In this study, a new sequence-based method, named as MoRFMPM, is proposed for predicting MoRFs. MoRFMPM uses minimax probability machine (MPM) to predict MoRFs based on 16 features and 3 different windows, which neither relying on other predictors nor calculating the properties of the surrounding regions of MoRFs separately.
Programfor calculation of ion or molecule collision cross sections on parallelized computing architectures.
Strain design framework for modular cell engineering.
TrinhLab - University of Tennessee Knoxville
A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. Deciphering the network of TF-target interactions with information on mode of regulation (activation vs. repression) is an important step toward understanding the regulatory pathways that underlie complex traits. There are many experimental, computational, and manually curated databases of TF-gene interactions. In particular, high-throughput ChIP-seq datasets provide a large-scale map or transcriptional regulatory interactions. ModEx can be installed using the GitHub repository. All of the dependencies will be installed via setup.py script. Saman Farahmand, Todd Riley, Kourosh Zarringhalam, "ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction", BioRxiv, 2019
A data warehouse for the modENCODE project
Software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.
A new and scalable tool for the selection of DNA and protein evolutionary models | ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces
Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX. ModelX: A toolsuite for molecular modeling. ModelX is a toolsuite for biomolecular modeling inspired on the assumption that Molecular Biology conformational landscape is huge but limited, and also on the fact that interactions between biological entities can be decomposed into small structural motifs that are recycled and reused by nature while shaping new relationships.
MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool.
MolMeDB is an open chemistry database about interactions of molecules with membranes.
An integrative data and analytic platform connecting phenotypes to genotypes across species. Combine genotype and phenotype data across species for patient variant prioritization, functional annotation and pathogenicity determination. Securely share & discuss patients with colleagues all around the world.
Software tool for behavioral control and data acquisition.
Monoallelic Gene Inference from Chromatin (MaGIC) - tool to classify genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.
Machine learning tool set and web application for monoallelic gene inference from chromatin. Classifies genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data.
Monoallelic gene inference from chromatin (MaGIC)
MoonDB is a database containing predicted Extreme Multifunctional (EMF) proteins (i.e. proteins with several unrelated functions), as well as a set of manually curated moonlighting proteins. Moonlighting proteins are a subclass of multifunctional proteins.
Multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method.
A computational program to investigate the evolution of PDZ-binding target specificity. PDZ domains bind the extreme C-terminus of target proteins and are critical components of signaling and trafficking pathways. MotifAnalyzer-PDZ identifies enrichment trends for specific amino acids in a PDZ-binding motif-satisfying sequence across multiple organisms
Open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment. Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-data. This code is associated with the paper from Beraldo et al., "MouseBytes, an open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment". eLife, 2019. http://dx.doi.org/10.7554/eLife.49630. Quality control (QC) procedure in MouseBytes checks the content of xml files against the potential errors and flag the files that do not meet the criteria (refer to "QC Documents" folder). Such xml files belong to a cognitive task experimented using Bussey-Saksida Mouse Touchscreen System and exported via ABET II software. Note that each xml file must contain the machine-generated (ABET II) features like "Analysis Name", "Schedule Name", "Max_Number_Trials", and "Max_Schedule_Time"
A data repository and analysis suite for curated primary mouse phenotype data. Available genotype resources and tools. RESTful API for getting data and metadata. Already have an account? Sign In. ...an integrated resource to explore physiology
Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection. Data analysis pipeline used for the assembly and differential abundance analysis of M. rosenbergii transcriptome in response to MrNV infection. Transcriptomic analysis (RNAseq) of Macrobrachium rosenbergii post-larvae in response to Macrobrachium rosenbergii nodavirus (MrNV) infection. Phongthana Pasookhush, Charles Hindmarch, Siwaporn Longyant, Paisarn Sithigorngul, William G. Bendena, Parin Chaivisuthangkura. Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) postlarvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation. BMC Genomics volume 20, Article number: 762 (2019), DOI: 10.1186/s12864-019-6102-6 Article URL
Tool for haplotype-phased structural variant detection.
Quantifying Functional Impact of Noncoding Variants with Multi-task Bayesian Neural Network. The python script for MtBNN. The help information can be obtain by
Multiple transformer-based language models for accurate DNA methylation prediction
A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic. …methods and tools for Chem-Bio-Med-Informatic Studies. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic forms
Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. This is the repository for "Mutation effect estimation on protein-protein interactions using deep contextualized representation learning" (MuPIPR). This repository contains the source code and links to some datasets used in our paper. (to be updated)
MuSiC2 ( Mutational Significance in Cancer) is a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events.
Tool for finding connected clusters in multi-parametric networks.
A plug-in to the Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using a multi-omic proteogenomic approach.
Multi-processing tool for designing CRISPR guide RNA libraries.
Models discrete and continuous gene flow to reconstruct complex population admixtures.
Set of tools to perform integrative gene mapping studies.
Community Extraction in Multilayer Networks with Heterogeneous Community Structure. An R package to identify strongly connected vertex-layer communities in multilayer networks. An R package that implements the multilayer extraction algorithm to identify densely connected vertex-layer sets in multilayer networks. multilayer.extraction(): identify densely connected vertex-layer communities within multilayer networks. This is a significance based approach that seeks to optimize a score derived from the strength of connection within multilayer communities. See the above reference for more details.
Deep learning with multimodal representation for pancancer prognosis prediction | Our model estimates the time-til-death for patients across 20 different cancer types using the vast amount of multimodal data that is available for cancer patients | git clone https://github.com/gevaertlab/MultimodalPrognosis | For more details, see our paper
This is the dockerized environment for the winning algorithm in the 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3.
CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber type-specific histology. Because manual immunohistochemical analysis of features such as skeletal muscle fiber typing, capillaries, myonuclei, and fiber size-related parameters is time consuming and prone to user subjectivity, automatic computational methods could allow for faster and more objective evaluation. Here, we developed Muscle2View, a free CellProfiler-based pipeline that integrates all key fiber-morphological variables, including the novel quantification of the capillary-to-fiber interface, in one single tool. Provided that the images are of sufficient quality and the settings are configured for the specific study, the pipeline allows for automatic and unsupervised analysis of fiber borders, myonuclei, capillaries, and morphometric parameters in a fiber type-specific manner from large batches of images in <10 min tissue sample.
Versatile methodological aid to functional genomics in the neuromuscular field.
A multifaceted gateway for exploring integrative pan-cancer genomic data. Somatic mutation and gene expression dysregulation are considered two major tumorigenesis factors. While independent investigations of either factor pervade, studies of associations between somatic mutations and gene expression changes have been sporadic and nonsystematic. Utilizing genomic data collected from 11 315 subjects of 33 distinct cancer types, we constructed MutEx, a pan-cancer integrative genomic database. This database records the relationships among gene expression, somatic mutation and survival data for cancer patients. MutEx can be used to swiftly explore the relationship between these genomic clinic features within and across cancer types and, more importantly, search for corroborating evidence for hypothesis inception.
MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
Detection of non-coding mutation hotspots in cancer genomes | Non-coding MUTation hotSPOT dectection in cancer genomes | The MutSpot R package systematically and unbiasedly scans cancer whole genomes to detect mutation hotspots. MutSpot first builds a background mutation model that corrects for covariates of mutation probability, such as local nucleotide context, replication timing and epigenomic features. Then MutSpot evaluates the mutation recurrence of focal DNA regions using a Poisson binomial model to account for varying mutation rates across different tumors. Mutation hotspots identified have significantly higher mutation recurrence compared to the background genomic mutation rate, suggesting positive selection in cancer and involvement in tumorigenesis
Variant effect prediction with interpretation at the protein structure level
Tool for automated analysis of genomic mutations in gene regulatory networks.
an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles. scripts and facilities for in-silico mutagenesis with FoldX. Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark. MutateX: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles Matteo Tiberti, Thilde Terkelsen, Tycho Canter Cremers, Miriam Di Marco, Isabelle da Piedade, Emiliano Maiani, Elena Papaleo, submitted to biorxiv
Tool for plotting complex mutation data with flexibility.
Privacy-protecting browser-based personal Genome analysis for genomics education and exploration. MySeq is a web-application for privacy-protecting interactive analysis of personal genomes (distributed as compressed-and-indexed VCF files) inspired by GENOtation (previously the Interpretome) and DNA.LAND Compass. MySeq is intended for use as a genomics educational platform. Analyzing the PTC Tasting Phenotype with MySeq. This page is an example analysis of the "bitter tasting" trait using the MySeq application in an embedded context. Here MySeq is used to both query a whole genome VCF for NA12878 (from Genome in a Bottle) by genomic coordinates and predict the bitter tasting phenotype directly. All of the queries demonstrated here are performed "live" in the browser, that is these are not pre-generated results. Try MySeq as a "standalone" application. MySeq is a single-page web application for privacy-protecting personal genome analysis
ImageJ macro for high throughput analysis of myelinating cultures.
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Antibiotic resistance prediction in minutes. Table of Contents generated with DocToc. AMR prediction (Mykrobe predictor). Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed
A Portal for Signaling Interactions in Muscle Regeneration. myogenesis and regeneration portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. Myogenesis & REGeneration Portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. The information is organized in two layers: the first concerns cell-cell interactions, while the second layer describes the most relevant signaling pathways underlying the crosstalk between the cell types participating in muscle regeneration. A user-friendly interface allows users to explore, via an interactive model, cell and pathway crosstalk
A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping | Not a member? Reigist in www.biomarkercenter.org/nglycositeatlas | Database UniProtKB AC/ID Gene Protein Site Peptide Motif Source Year Reference
Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes.
An R package for quality control of NanoString nCounter data | NACHO: NAnostring quality Control dasHbOard | NACHO does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application
An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence. This is for predicting NAGbinding sites in a protein. A web server for predicting N-Acetylglucosamine (NAG) interacting residues in a protein. Home page of NAGbinder, which is a web based tool developed for predicting of NAG binding residues in a protein. NAGbinder is a Python-based tool for predicting NAG interacting residues in an uncharacterized protein chain. Prediction of NAG interacting residues. Reference: Patiyal et. al. (2019) NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence
Noncoding Assessment of long RNAs in Magnoliophyta Species.
Comprehensive repository for semantic data in life sciences.
Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods | Library bias correction for multiplex RNAseq | Library bias correction for multiplex RNAseq. GitHub Gist: instantly share code, notes, and snippets | Instantly share code, notes, and snippets |
Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics.
A novel method for human lncRNA-disease association prediction based on network consistency projection. Copyright (C) 2019 Zecheng Huang(2111705162@mail2.gdut.edu.cn),Guobo Xie(xiegb@gdut.edu.cn). This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Type: Package Title: NCPHLDA:A Novel Method for Human LncRNA-Disease Association Prediction Based on Network Consistency Projection. To analyze these data on NCPHLDA to further infer potential associations between lncRNAs and diseases, you should input the appropriate code in the matlab Command Window:
A package for clustering analysis of multilayer omics data. Clustering of Omics Data of Multiple Types with a Multilayer Network Representation. Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>)
Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity | Link of paper: https://www.nature.com/articles/s41598-019-50121-3 A Novel Method For Predicting Drug-Drug Interaction By Neural Network Due to the great importance of this issue in the economy, industry, and health, proposing appropriate computational methods for predicting unknown DDI with high precision is challenging. We propose a novel machine learning method for predicting unknown DDIs called "NDD", using a two-layer fully connected neural network. NDD uses various characteristics of drugs to have comprehensive information. Multiple drug similarities are calculated. NDD integrat various drug similarities with a non-linear similarity fusion method called "SNF" to achieve high-level features. Dependency: python version 3.5.3 deep learning lib keras: https://github.com/fchollet/keras/ machine learning lib scikit-learn: https://github.com/scikit-learn/scikit-learn Contact: nasim.rohani74@gmail.com
A non-equilibrium simulator for multibody self-assembly at the cellular scale. NonEquilibrium Reaction-Diffusion Self-assembly Simulator. Additional documentation through doxygen can be found within docs/ by opening index.html
A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs | Gephi plugin for network exposure models | NET-EXPO is a Gelphi plugin that computes various types of network exposure metrics for the purpose of visualization exposure within a network for analysis. Currently network exposure model (Marsden, et al. 1993, Burt, 1987, Valente, 1996, 2005), affiliation exposure model (Fujimoto, et al., 2011, 2012), and limited support for decomposition exposure model (Fujimoto, 2012, Fujimoto, et al., 2013) are supported
Standard and network-based gene enrichment analysis in human and model organisms | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms | NETGE-PLUS is optimized to be used on a Google Chrome browser | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms, including S. scrofa, S. cerevisiae, E. coli and A. thaliana
Network propagation of rare mutations in Alzheimer’s disease reveals tissue-specific hub genes and communities | Source code for network propagation | NETPAGE (NETwork Propagation-based Assessment of Genetic Events) is a novel computational framework for gene-based association testing of rare variants that integrates prior knowledge about tissue-specific gene interaction networks (Scelsi et al., in preparation)
Bayesian simultaneous network estimation across unequal sample sizes | --> 'Data_generate.m' generates the precision matrices and dataset corresponding to that as described in the simulation study | --> 'NExUS.m' computes the estimated partial correlation matrices corresponding to the dataset.Variable 'Partial_corr_mean' (which is a 3D array) gives the all estimated partial correlation matrices. Variable 'lambda_2_square_mean' provides the similarity index for each pair of categories | --> In case of real data, note that it is recommended to normalize the sample corresponding to each variable in the data to have mean 0 and variance 1
Next Generation-Targeted Amplicon Sequencing (NG-TAS) - an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.
CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation. NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations.
Structured Reviews for Data and Knowledge Driven Research | The NGLY1 Deficiency Knowledge Graph | This is the repository for the NGLY1 Deficiency Knowledge Graph, the reasoning context to support hypothesis discovery for NGLY1 Deficiency-CDDG (DOID:0060728) research. The user can navigate the knowledge in the graph in the Neo4j Browser website. This knowledge graph is a structured review around the research question what is the mechanism underpinning the NGLY1-AQP1 regulation association and explaining the reduced transcriptomic expression of multiple Aquaporins in NGLY1 deficient cells?. The graph v3.2 is the first deployed in the Wikibase application for community contribution and curation
NGLess is a domain-specific language for NGS (next-generation sequencing data) processing with a focus on metagenomics
Network-augmented Gene Set Enrichment Analysis.
NGSEP (Next Generation Sequencing Experience Platform) - accurate variant calling across species and sequencing protocols.
Guide Subspace Learning for Unsupervised Domain Adaptation. Guided Subspace Learning(GSL demo). In the file, there are multiple .m files. NGSL.m : Core codes of NGSL algorithm. GSL.m : Core codes of GSL algorithm.
A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data | NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed
Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data. VCF file of our variant call set: https://drive.google.com/file/d/1iyeuaz5w6uSVP9UyV6DjSc-GvMrYYMyr/view?usp=sharing. The analysis pipeline can be run following instructions in the Python script pipeline.py.
R package for fast and accurate trisomy prediction in non-invasive prenatal testing.
NITPicker (Next Iteration Time-point Picker) selects optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making, while maximising information about the shape of the underlying curves.
Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution. R package for our Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID), joint work with Seyoung Park (https://sites.google.com/view/seyoungpark/home). Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID)
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge | A tool for divide-and-conquer tree estimation via a shared distance matrix | NJMerge is a tool for scaling phylogengy estimation methods to large datasets. NJMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). NJMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2018)
Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories | This project is to convert user query to SPARQL in the Physiome Model Repository. The information looking by users usually is model entities | Natural Language Interface for Model Entity Discovery (NLIMED) is an interface to search model entities (i.e. flux of sodium across the basolateral plasma membrane, the concentration of potassium in the portion of tissue fluid) in the biosimulation models in repositories. The interface utilises the RDF inside biosimulation models and metadata from BioPortal. Currently, the interface can retrieve model entities from the Physiome Model Repository (PMR, https://models.physiomeproject.org) and the BioModels (https://www.ebi.ac.uk/biomodels/)
Labelling chest x-ray reports using an open-source NLP and ML tool for text data binary classification. Natural language processing and machine learning of a comma separated value (CSV) file with text data and labels. nlp_ml is a command line script that performs natural language processing and machine learning of a CSV (comma separated value) file with text data and labels. The CSV file must have the columns 'text' and 'class'. The code randomly generates classification pipelines, performs 10-fold cross validation for assessing model performance on the training dataset, and saves the results to a SQLite database. The code uses the SMOTE oversampler to avoid issues with imbalanced datasets. nlp_ml solves supervised binary classification problems using text data. When generating your CSV file, replace commas with spaces in the elements of the text column prior to saving the file.
Normal Mode Analysis as a Routine Part of a Structural Investigation | Webtool for Normal Mode Analysis | Web-server for Normal Mode Analysis of proteins | Are you submitting large files to WEBnma? Provide your email address in the submission box above and we will send you a link that you can visit to inspect your results when they are ready. Alternatively, you can bookmark the URL appearing in your web browser once you have submitted your job. The results can be accessed at this URL within two weeks of your submission date
Blind spectral unmixing of highly mixed multispectral flow and image cytometry data. Matlab code to spectrally unmix highly mixed multispectral flow and image cytometry data. To use NMF-RI on new data (tissue or flow cytometry) we recommend to use the ´main.m´ code distributed and load new cytometry data to the existing folder hierarchy.
Single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis | In Vitro Transcription NMR. Protocol, code and examples for the co-transcriptional RNA folding network reconstruction | The protocol describes how to setup and analyse observation of a co-transcriptional RNA folding network by Systems NMR approach. While most experimental approaches can monitor only a single molecule class or reaction type at a time, Systems NMR permits single-sample dynamic quantification of entire “heterotypic” networks – involving different reaction and molecule types. It thus provides a deeper systems-level understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of “omics”
Bayesian semi-nonnegative matrix tri-factorization to identify pathways associated with cancer phenotypes | Bayesian Semi-Nonnegative Matrix Tri-Factorization | BSNMTF is a semi-nonnegative matrix tri-factorization method in the framework of Bayesian learning to identify pathways associated with cancer phenotypes (e.g., cancer sub-types or treatment outcome) from a real-valued input matrix (e.g., copy number alterations or normalized log transformed gene expression data)
Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease. Deep learning enables accurate prediction of interplay between lncRNA and disaeas. ###########################################################################################. NNLDA is implemented in Python 3.5 and use Tensorflow 1.12.0. Package numpy and pandas are also required. The experimental data are downloaded from LncRNADiseas2.0 database
Network-based Observability and Controllability Analysis of Dynamical Systems. NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox for MATLAB and Octave. Daniel Leitold, Anges Vathy-Fogarassy, and Janos abonyi, NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox (MATLAB version), 2017.
NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis.
An R package for computing network perturbation amplitudes using gene expression data and two-layer networks | NPA - Network Perturbation Amplitude | R package and data for NPA models | The NPA (Network Perturbation Amplitude) and BIF (Biological Impact Factor) methods allow to understand the mechanisms behind and predict the effect of exposure based on transcriptomics datasets.This approach enables to translate the gene expression fold-changes into differential values for each network node, and to summarize this at the network level to provide aquantitative assessment of the degree of perturbation of the network model, the Network Perturbation Amplitude (NPA).Combining multiple relevant network models, the overall biological impact of a perturbing agent, the Biological Impact Factor (BIF),can be calculated by aggregating individual NPA scores | After package installation, networks are installed with no precomputed data
The Neyman Pearson detection of microsaccades with maximum likelihood estimation of parameters. Neyman–Pearson Detector (NPD) for saccadic eye movements. By default, our algorithm reads in files X.csv and Y.csv, where the X and Y coordinates of the tracked eye-gaze positions are stored in each of the csv files. Data in the X.csv and Y.csv must be square matrices of same dimensions, and each trail of the tracked eye-gaze positions forms the rows of the input file. Our algorithm can perform the NPD on each row of the dataset independently
Quantitative Structural Interpretation of Protein Crosslinks. NRGXL: a tool to compute protein crosslinker conformations and energies
CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. NRLcalc: calculation of the Nucleosome Repeat Length. The NRLcalc app provides a visual interface for the bulk calculation of the Nucleosome Repeat Length (NRL) based on multiple phasograms computed with NucTools (https://github.com/homeveg/nuctools).
software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
DNA comparison tool with increased speed, sensitivity and accuracy.
Massively Parallel Simulator for Individual-based Modelling of Microbial Communities.
Archaic mitochondrial DNA inserts in modern day nuclear genomes. Scripts used to detect archaic NUMTs in NGS data. A pipeline including a collection of scripts used to analyse NUMTs discovered in whole genome paired read data. flanking_region_analysis.py is a script used to calculate match ratios with archaic genomes of a specific genomic region. numt_stats.py is a script to calculate various statistics for discovered NUMTs. mito_variance.py is a script to calculate pariwise differences between all sequences of an alignment.
Estimating cancer spatial and temporal heterogeneity and evolution through alignment-free methods | NGS tool for Unsupervised analysis of fastQ files using Alignment-free | A software to support an alignment-free sequence comparison of large-scale fastq files using a k-mer counting methods paired with distance metrics, Jensen-Shannon divergence and Hellinger Distance | git clone https://github.com/ARoddy/NUQA.git | NUQA reads in a set of raw fastq files - ideally, these are DNA-seq files produced from multiple samples taken from the same patient. Based on these it will identify differences between the files and produce a distance matrix and a newick tree file | Eigen (where /Eigen file containing the headers is located at /usr/local/include for an example run check file 'Eigen_help.txt')
A natural products likeness scorer-web application and database | NaPLeS - Natural Product Likeness Score calculator | NaPLeS is an open source web application based fully on open data. Source and installation instructions are available at GitHub. Please submit bug reports, feature requests and general issues through the issues tracker at GitHub. NaPLeS is developed and maintained by the Steinbeck group at the University Friedrich-Schiller in Jena, Germany
NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions.
NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks. Abstract Background Variant detection from high-throughput sequencing data remains an important, unresolved yet often overlooked problem. Long-read sequencing technologies, such as Oxford Nanopore and PacBio sequencing, present unique advantages to detect SNPs and small indels in genomic regions that short-read sequencing cannot reliably examine (for example, only ∼80% of genomic regions are marked as “high-confidence region” to have SNP indel calls in the Genome In A Bottle project). However, existing software tools for short-read data perform poorly on long-read data; instead, several recent studies showed promising results in variant detection on long-read data by deep learning.
Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly.
An Implemented Decision Support Framework for Nanomaterial Identification. Official repository of the NanoDefiner e-tool for nanomaterial classification. This is the official repository for the NanoDefiner e-tool, a decision support framework for the characterisation of potential nanomaterials. It is one of the products delivered by the NanoDefine project.
Computational tool to detect DNA modifications using Nanopore long-read sequencing data.
Web server for nanopore MinION sequencing data analysis.
R package to analyze and compare nanopore sequencing data.
Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats. Several tools exist to analyze tandem repeats (e.g. tandem-genotypes and RepeatHMM)
RNA modifications detection by comparative Nanopore direct RNA sequencing. RNA modifications detection from Nanopore dRNA-Seq data. Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples. Analyses performed for the nanocompore paper. Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro
An Open Access Knowledge Base for Microbial Natural Products Discovery. The Natural Products Atlas Network views of chemical space. The Natural Products Atlas provides a unique tools for exploring natural products chemical space, offering perspective on the position that any molecule occupies
NaviKey is a tool for querying descriptive data and has been implemented as (a) a Java applet providing the contents of DELTA files (see example with the DELTA sample data files), (b) a stand-alone Java application for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively (c) a module ("plug-in") of the Java-based Diversity Navigator database client for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively.
NeOGen (genetic Ne for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (Ne) and demographic modelling software.
Tool for the identification of approximate DNA sequence symmetries.
Predicting fusion neoantigens from RNA sequencing data. The Section for Bioinformatrics at the Biocenter of Innsbruck Medical University is commited to the generation, management, integration, and leveraging data from genomics studies. Quantification of the tumor immune contexture. Zlatko Trajanoski awarded with ERC Advanced Grant.
An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunological resources
High-throughput neoantigen prediction and recognition potential pipeline.
Web server that is able to improve improve large-scale protein function prediction with massive network information.
Network-based multi-task learning models for biomarker selection and cancer outcome prediction. Network-based transfer learning models for biomarker selection and cancer outcome prediction. Download eight .pk files(sample_breast_expression.pk, sample_breast_label.pk, sample_ov_expression.pk, sample_ov_label.pk, sample_PRAD.pkl, sample_PRAD_label.pkl, sample_ppi.pkl, sample_gene_names.pkl) and two .py files(NetTL_three_domains.py, NetSTL_three_domains.py) into the same fold. Run python command and execute: python3 NetTL(NetSTL)_three_domains.py The results will be exported as txt files in the same fold. sample_OV.pkl: : Ovarian Cancer gene expression data set. The size of the data is 100 x 500, 100 samples and 500 genes.
An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo.
Exploring Network Structure, Dynamics, and Function using NetworkX. Software for Complex Networks — NetworkX 3.5.1rc0.dev0 documentation. NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. It provides:. With NetworkX you can load and store networks in standard and nonstandard data formats, generate many types of random and classic networks, analyze network structure, build network models, design new network algorithms, draw networks, and much more.
Neural network identification of RiPP precursor peptides | NeuRiPP (Neural Network Identification of RiPP Precursor Peptides) | NeuRiPP is a neural network framework designed for classifying peptide sequences as putative precursor peptide sequences for RiPP biosynthetic gene clusters. It consists of two modules:
A Unified Approach to MEG Source Analysis under the Continuous Stimuli Paradigm | The magnetoencephalography (MEG) response to continuous auditory stimuli, such as speech, is commonly described using a linear filter, the auditory temporal response function (TRF) | This repository contains the implementation of our direct TRF estimation algorithm in python (version 3.6 and above)
A Tool to Predict Cleavage Sites of Neuropeptide Precursors. BACKGROUND:Neuropeptides are a class of bioactive peptides produced from neuropeptide precursors through a series of extremely complex processes, mediating neuronal regulations in many aspects. Accurate identification of cleavage sites of neuropeptide precursors is of great significance for the development of neuroscience and brain science. OBJECTIVE:With the explosive growth of neuropeptide precursor data, it is pretty much needed to develop bioinformatics methods for predicting neuropeptide precursors' cleavage sites quickly and efficiently. METHOD:We started with processing the neuropeptide precursor data from SwissProt and NueoPedia into two sets of data, training dataset and testing dataset. Subsequently, six feature extraction schemes were applied to generate different feature sets and then feature selection methods were used to find the optimal feature set of each
A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo. NeuroChaT is an open-source neuron characterisation toolbox. MNI: Original conception and design of the software architecture, primary development of algorithms and subsequent implementation in Python, primary user’s manual development, iterative development of software based on user feedback, originator of NeuroChaT acronym
Software Package for Quantification of Cortical Motor Maps Using Frameless Stereotaxic Transcranial Magnetic Stimulation.
Tool for the prediction of neuropeptide precursors based on optimal sequence composition.
The Effect of Medication and Deep Brain Stimulation on Posture in Parkinson's Disease. NeuroPostureApp©, Klinik f&uumlr Neurologie, UKSH Campus Kiel. WebApp to measure bending angle in camptocormia patients. Based on the article **to be published** from Nils Margraf and Günther Deuschl et al.
A free Python toolbox for fast multi-modal and reproducible brain connectivity pipelines. Neuropycon package of functions for electrophysiology analysis, can be used from graphpype and nipype. Neuropycon — ephypype 0.1dev0 documentation. Neuropycon — graphpype 0.1dev0 documentation. Neuropycon is an open-source multi-modal brain data analysis kit which provides Python-based pipelines for advanced multi-thread processing of fMRI, MEG and EEG data, with a focus on connectivity and graph analyses. Neuropycon is based on Nipype, a tool developed in fMRI field, which facilitates data analyses by wrapping many commonly-used neuro-imaging software into a common python framework.
Standard Electroencephalography (EEG) server that mediates between the raw EEG devices and all the various EEG applications that the user may wish to run to analyse the incoming EEG data.
Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes. Transcriptomics of cortical excitatory and inhibitory neurons
Implementation of Neutrosophic Recommender System
Neutrosophic Recommender System for Medical Diagnosis Based on Algebraic Neutrosophic Measures
An Open, Up-to-Date Resource for the Molecular Sciences Community. A repository for quantum chemistry basis sets. The new Basis Set Exchange (BSE) for Quantum Chemistry. If you are looking for the Basis Set Exchange website (which can be used to browse and download this data in a more user-friendly way), visit https://www.basissetexchange.org. This project is a library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data. This library is used to form the backend of the new Basis Set Exchange website. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community Benjamin P. Pritchard, Doaa Altarawy, Brett Didier, Tara D. Gibson, and Theresa L. Windus J. Chem. Inf. Model. 2019, 59(11), 4814-4820 doi:10.1021/acs.jcim.9b00725. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community
Gene Expression platform to investigate gene expression and functionalities in the tomato genome. It includes expression data from cultivated specie/variety Heinz 1706, Ailsa Craig e Solanum pimpinellifolium.
A fast and efficient genome polishing tool for long read assembly. Fast and accurately polish the genome generated by noisy long reads. NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo
A random forest method for prediction of N-Glycosylation sites in eukaryotic protein sequence. N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. It plays a vital role in various biological processes such as protein folding, stability, immunogenicity of different proteins, cell signaling and protein targeting. N-glycosylation predominantly occurs in N-X-[S T] sequon where X is any amino acid other than proline. However, not all N-X-[S T] sequons in proteins are glycosylated. Therefore, accurate prediction of N-glycosylation sites is essential to understand N-glycosylation mechanism. We developed a random forest method, Nglyc, to predict N-glycosylation sites in eukaryotic protein sequences. The method used 315 features derived from a protein sequence and its sequence homologs. Training and testing was performed using a dataset containing 895 N-glycosylation sites and 853 non-glycosylated sites obtained from 846 PDB structures
Inferring Continuous Subjective Ratings With Deep Regression. Data and code of the BrainLinks-BrainTools NiceBot project, manuscript "Human-Compliant Robot Behavior: Combining Continuous Subjective Evaluation with Multimodal Deep Regression Analysis".
A computational method to study intercellular communication. It uses human or mouse gene expression data of interacting cells in order to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.
An Open-Source Nursing-Sensitive Natural Language Processing System Based on Word Embedding | This study develops and evaluates an open-source software (called NimbleMiner) that allows clinicians to interact with word embedding models with a goal of creating lexicons of similar terms. As a case study, the system was used to identify similar terms for patient fall history from homecare visit notes (N = 1 149 586) extracted from a large US homecare agency. Several experiments with parameters of word embedding models were conducted to identify the most time-effective and high-quality model. Models with larger word window width sizes (n = 10) that present users with about 50 top potentially similar terms for each (true) term validated by the user were most effective. NimbleMiner can assist in building a thorough vocabulary of fall history terms in about 2 hours
Predicting and Designing therapeutics against the Nipah virus.
Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Release Notes for NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis with Multi-State Equilibrium Binding Models. Please download, install, and start NmrLineGuru according to the repo page:. Before you use NmrLineGuru for your own data or project, please repeat the example simulations/fittings in the tutorials and make sure you can reproduce the example results. Feng C, Kovrigin EL, Post CB (2019) NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Scientific Reports 9:16023. [DOI]
Online tool to predict the survival rate in non-small cell lung cancer patients.
Interactive tool for presenting cervical cancer screening indicators in the Nordic countries.
Framework for researchers to select the best method for the normalization of their gene expression data based on the evaluation of different methods in the principle of the consistency of metrics and the consistency of datasets.
Genetic diversity and epidemiology of Genogroup II noroviruses in children with acute sporadic gastroenteritis in Shanghai, China, 2012-2017 | BACKGROUND:Noroviruses (NoVs) are considered an important cause of acute gastroenteritis (AGE) across all age groups, especially in children under 5 years of age. We investigated the epidemiology of noroviruses in outpatient children from the Children's Hospital of Fudan University in Shanghai, China. METHODS:Stool specimens were collected between January 2012 and December 2017 from 1433 children under 5 years of age with acute gastroenteritis. All samples were analysed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II NoVs amplifying both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes
Modelling cell surface dynamics and cell-cell interactions using Cell Studio. A Notch-Delta receptor binding process agent-based model using Unity 3D. The simulation was built and tested on Unity version 4.6.1, which is freely available for download at https://unity3d.com/get-unity/download/archive. To use the simulation, download the repository from GitHub, save it to a new folder (e.g. notch-delta-model), and create a project in Unity by clicking “create a new project” and select that folder (it should contain only the Assets folder and the readme file). Do not import any package. Then, load one of the scenes in the Assets folder by double clicking it.
Web-based Resources to Simulate and Analyze the Three-Dimensional Genome. A web platform to simulate and browse the three-dimensional architecture of genomes. In NDB user can find data for 3D genome structures and also computational tools for simulating the genome. The server is also made for visualization the structures and dynamics of the genome, allowing users to explore the 3D organization of chromosomes from their computer. This platform enables users to visualize and annotate the 3D chromosome structures with experimental tracks from ENCODE or with their own data, allowing for an integrative experience for all genome scientists.
A new tool for the dynamic analysis of nucleosome positioning | R package for nucleosome architecture comparison | Nucleosome Dynamics - Singularity | Nucleosome Dynamics Singularity image is a containerized implementation of 'Nucleosome Dynamics suite' | Nucleosome Dynamics Docker Container | Nucleosome Dynamics - docker implementation | This repository includes the set of R programs implementing 'Nucleosome Dynamics' analyses | Nucleosome positioning plays a major role in transcriptional regulation and most DNA-related processes | Nucleosome positioning plays a major role in transcriptional regulation DNA replication and DNA repair | R package aimed at comparing the reads of two MNase-seq experiments for nucleosome positioning and detecting significant inclusions, evictions and shifts
a nutrigenomics exploratory and analytical platform. Nutrigenomics data mining platform. Nutrigenomics is defined as the science studying the role of nutrients and bioactive food compounds on gene expression. Whereas the idea of modulating human health by food intake is a millenial concept, the increasing number of research efforts on this field is pointing out that nutrition may exert its impact on health outcomes by directly affecting the expression of genes involved in critical metabolic pathways. Nowadays its widely accepted that cellular processes spanning from gene expression to protein synthesis can be regulated by dietary compounds. However there is a limited understanding of the underlying molecular mechanisms which are involved. NutriGenomeDB makes use of publicly available gene expression data obtained from nutrigenomics experiments in order to bring a the first platform for nutrigenomics data exploration
Development and Validation of a Machine Learning Algorithm for Predicting Response to Anticholinergic Medications for Overactive Bladder Syndrome. Prediction of Response to Anti-Cholinergic Medication for Overactive Bladder. Number of Previously Failed Medications 0 ≥1.
Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. Detect prescription of oral anticoagulants (OAC) in clinical text using regular expressions. Developed and used in Bean et al. (2019 submitted) "Semantic Computational Analysis of Anticoagulation Use in Atrial Fibrillation from Real World Data".
Building Open Access to Research (OAR) Data Infrastructure at NIST. The NIST Open Access to Research (OAR) Public Data Repository (PDR) system software. Publishing Data Repository (oar-pdr). The oar-metadata package is a prerequisite which is configured as git sub-module of this package. This means after you clone the oar-pdr git repository, you should use git submodule to pull in the oar-metadata package into it:
Out-of-Core Matrices Analyzer (OCMA) uses state-of-the-art computational techniques that can nimbly perform eigen and Singular Value Decomposition (SVD) analyses.
A novel one-class classification approach to accurately predict disease-gene association in acute myeloid leukemia cancer. Disease causing gene identification is considered as an important step towards drug design and drug discovery. In disease gene identification and classification, the main aim is to identify disease genes while identifying non-disease genes are of less or no significant. Hence, this task can be defined as a one-class classification problem. Existing machine learning methods typically take into consideration known disease genes as positive training set and unknown genes as negative samples to build a binary-class classification model. Here we propose a new One-class Classification Support Vector Machines (OCSVM) method to precisely classify candidate disease genes.
An open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. All files can be found on the Chen Lab RNA-Seq server: /home/ubuntu/chenlab_v2/proj/PatrickN/desktop_pipeline_v0.1/. OCTAD:Open Cancer Therapeutic Discovery. Bin Chen, PhD. MSU. contact: Bin.Chen@hc.msu.edu. This version includes some new data files, so be sure to download those from the above directory. The pipeline is configured to run within the folder structure as found in the above directory. William Zeng. MD Candidate. UCSF. contact: billy.zeng@ucsf.edu. Please contact Patrick: patrick.newbury@hc.msu.edu with any issues. https://s3-us-west-2.amazonaws.com/chenlab-data-public/octad In the parent folder for this pipeline, create a folder named "data". Place all files from this download into this data folder. Consolidated many data files into new files: CCLE_OCTAD.RData, metadata.RData
A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data. Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS is a set of graphical tools for high-throughput preprocessing and analysis of vibrational spectroscopy data. Currently, the preprocessing is primarily geared towards images from infrared absorption spectroscopy with focal plane array detectors
Open-source add-on kit for automation of zone elution in planar chromatography. Follow this link to download an image of raspbian with the OC_manager set-up, last update: 20180605. Shiny app to operate apparatus of office chromatography.
Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions.
ODAM (Open Data for Access and Mining) is an Experiment Data Table Management System (EDTMS) that makes research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.
A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China
Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree reconciliation.
A reference database of inferred immune receptor genes | Welcome to OGRDB - the curated Open Germline Receptor Database! | OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly
A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vertebrate Genomes. OHNOLOGS version 2.0 is now live with more genomes and more genome duplications!. Singh P.P. and Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Singh PP & Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Full text.
Estimating Natural Selection to Predict Functional Overlapping Genes. Program for estimating dN/dS in overlapping genes (OLGs). OLGenie is a Perl program for estimating dN/dS to detect selection and function in overlapping genes (OLGs). It relies on no external dependencies, facilitating maximum portability. Just download and run
Determining significance of total overlap length between genomic regions sets. MOTIVATION:Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive p-value. RESULTS:Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported.
Alignment tool for optical mapping using a seed-and-extend approach.
Locality-sensitive hashing for the edit distance | We have provided the resources necceasary to generate the figures from ``Locality sensitive hashing for the edit distance'' by Guillaume Marçais, Dan DeBlasio, Prashant Pandey, and Carl Kingsford. Which is to appear inthe proceedings of ISMB/ECCB 2019 | The two main directories contain the necceasry code to produce the phylogeny figures (is_trees) and the random sequences figure (random_sequences). All of the figure generation is performed in a combination of perl and python. The omh_compute directory contains the code neccesary for the figure generation and is written in c++. This directory needs to be compiled before anything can be run in the other two
Method for the statistical analysis of RNA-Seq paired design data.
The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. It is developed at the National Center for Biotechnology Information.
Ontology-based, data-driven metadata tracking system.
516 unique variants and 831 patients registered in an updated centralized Variome database | OPA1 (optic atrophy 1 (autosomal dominant)) | Autosomal dominant optic atrophy (DOA, Kjer type, MIM#165500) is characterized by moderate to severe loss of visual acuity with insidious onset in early childhood, blue-yellow dyschromatopsia and central scotoma
Open Source Solution for Real-time Peri-event Time Histogram Based on Open Ephys | Online Peri-Event Time Histogram for open ephys | Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them | conda create --name opeth --file requirements.txt python
OPRA (Optimal Protein-RNA Area) is useful for identifying potential RNA-binding sites on proteins and can help to model protein-RNA interactions of biological and therapeutic interest.
High nodal FDG uptake increases risk of distant metastasis in patients with oropharyngeal squamous cell carcinoma. BACKGROUND:The purpose of this study was to investigate if FDG uptake metrics in primary tumor and lymph node metastases in patients with oropharyngeal squamous cell carcinoma (OPSCC) has a prognostic value beyond UICC8 staging in a multiple endpoint model. METHODS:Patients with OPSCC treated with primary radiotherapy at Rigshospitalet in the period 2010-2017 were included. All patients had a pretreatment FDG PET CT scan performed. Four cause-specific Cox regression models were built for the hazard ratios (HR) of recurrence in T-, N-, M-site, and death with no evidence of disease (NED), respectively. The following variables were included: T-, N-stage, p16 status, metabolic tumor volume, and FDG uptake in both primary tumor and lymph nodes.
Algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.
Accurate and Robust Monocular SLAM with Omnidirectional Cameras. A real-time robust monocular visual SLAM system based on ORB-SLAM for fisheye cameras, without rectifying or cropping the input images. We develop an improved monocular visual SLAM system by using omnidirectional cameras. Our method extends the ORB-SLAM2 framework with the enhanced unified camera model (EUCM) as a projection function, which can be applied to catadioptric systems and wide-angle fisheye cameras. Without rectifying or cropping the input images, the proposed system can use the full area of the images even with strong distortion.
Automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa.
OSCA (OmicS-data-based Complex trait Analysis) is a software tool for the analysis of complex traits using multi-omics data.
Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer.
Gene Expression-Based Survival Analysis Web Tool For Adrenocortical Carcinoma. Gene expression profiling data with long-term clinical follow-up information are great resources to screen, develop, evaluate and validate prognostic biomarkers in translational cancer research. However, an easy-to-use interactive online tool is needed to analyze these profiling and clinical data. In the current work, we developed OSacc (Online consensus Survival analysis of ACC), a web tool that provides rapid and user-friendly survival analysis based on seven independent transcriptomic profiles with long-term clinical follow-up information of 259 ACC patients gathered from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. OSacc allows researchers and clinicians to evaluate the prognostic value of genes of interest by Kaplan-Meier (KM) survival plot with hazard ratio (HR) and log-rank test in ACC.
An online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer | Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http: bioinfo.henu.edu.cn CESC CESCList.jsp. The Kaplan-Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer
An interactive online consensus survival tool for uveal melanoma prognosis analysis. Uveal melanoma (UM) is a rare, aggressive, but the most frequent primary intraocular malignancy in adults, and up to 50% of patients develop a tendency of liver metastases. Great efforts have been made to develop biomarkers that facilitate diagnosis, prediction of the risk, and response to treatment of UM. However, a biologically informative and highly accurate gold standard system for prognostic evaluation of UM remains to be established. To facilitate assessment of the prognosis of UM patients, we established a user-friendly Online consensus Survival tool for uveal melanoma, named OSuvm, by which users can easily estimate the prognostic values of genes of interest by the Kaplan-Meier survival plot with hazard ratio and log-rank test.
An overlapping DNA fragments generator for molecular cloning and synthetic biology | Reference: Ferreira-Junior, J.R.S. ; Digiampietri, L.A. . OVERFRAG: an Overlapping Fragments Generator for Molecular Cloning and Synthetic Biology. Proceedings of the XLII Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (SBBq), pp. 2, 2013
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.
An online database for the dragonflies and damselflies of Bangladesh. Welcome to the Odonata of Bangladesh, database of the dragonflies and damselflies of Bangladesh. Situated in the South-east Asia, Bangladesh is gifted with the rich network of water resources like ponds, lakes, marshes, rivers, streams and mangrove swamps. This diverse range of water bodies along with many tropical forest patches has generated suitable habitat for many Odonata species. Till date, nearly hundred species of Odonates have been recorded from Bangladesh. The current project, supported by Rufford Small Grant, is designed to assemble and disseminate information of diversity, ecology and behavior of the Bangladeshi dragonflies and damselflies.
New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical information collected from various sources. Complete Database Variable Definitions
ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques.
Oligogenic resource for variant analysis (ORVAL)
Interuniversity Institute of Bioinformatics in Brussels
High Biodiversity Arises from the Analyses of Morphometric, Biochemical and Genetic Data in Ancient Olive Trees of South of Italy | Multivariate analysis of data and geographic display of results | OliveR is an R package containing a shiny application that provides a vast series of statistical tools for exploring and analyzing both quantitative (such as morphometric or biochemical) and genetic data that can be associated to geographical coordinates. Through the use of shapefiles, the application allows visualizing both data and results of a statistical analysis directly on a geographical basis
Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions | Protein phosphorylation is one of the most prevalent post-translational modifications where kinases phosphorylate their selected substrates to maintain proper signal transduction in order to regulate cellular processes. Omic-Sig is developed to stratify phospho-substrates and their associated kinases by computing and ranking the differential abundances between paired samples (e.g., Tumor and its adjacent normal tissue). The differential abundances are calculated using mass spectrometry-based phosphoproteomics and global proteomics data as well as transcriptome data from RNA-Seq. Omic-Sig also provides visualization of the computational results
Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma. OmicShare Tools为完全免费开放生物信息云工具网站。OmicShare Tools云平台所涵盖的生物信息基础工具全面，云平台中所有工具皆为基迪奥开发，操作简单方便，工具输出结果可直接用于SCI文章发表。. 如果您在数据处理过程中，使用了OmicShare Tools完成了分析或在OmicShare Forum得到了有价值的帮助，我们期望您在论文发表时，在方法学部分或致谢部分引用或提及OmicShare平台。例如：XXXX analysis was performed using the OmicShare tools,a free online platform for data analysis (http://www.omicshare.com/tools)。这样便于更多的同行了解和分享OmicShare平台。.
A R package for integration of multi-omics datasets via association rules mining. tool for the analysis of multimodal high-throughput data. OmicsARules is a tool for the analysis of multi-omics high-throughput data based on the use of association rules mining. OmicsARules supports to identify recurrent and associated patterns, and provides a new dimension for exploring single or multiple omics data across sequencing platforms or across samples. Besides, a new rule-interestingness measure Lamda3 is embeded in OmicsARules, it can be used to evaluate the association rules and identify biologically significant patterns. Association rule mining and visualizing were implemented in R environment using package arules and ggplot2
Associate Omics Data with Phenotypes in One-Click | a tool kit for visualization and analysis of omics data | click here or paste the repo URL:https://github.com/huizhanglab-jhu/OmicsOne.git to https://gke.mybinder.org/ as below: | Try without installation via mybinder.org
OmicsQ is a Shiny-based web application designed for preprocessing and quantitative analysis of Omics data. It streamlines the preparation of data for subsequent analysis using specialized tools such as PolySTest for statistical testing and VSClust for clustering analysis.
A web server for integrated OMICS analysis | OmicsX is a user-friendly web server for integration and comparison of different omic datasets with optional sample annotation information. The tool includes four modules for gene-wise correlation, sample-wise correlation, subtype clustering, and differential expression. OmicsX provides researchers the analysis results including inter-omics correlations, conservative clusters, differential expressions, enriched biological pathways and associated phenotypes with visualization, searching, and data downloading, thus help to suggest the biological indications from the comparison of different omic data
A comprehensive integrated resource of signaling pathways in activity flow representation, enzyme-substrate interactions in protein post-translational modifications, protein complexes, protein annotations and protein roles in inter-cellular signaling.
Unifying single-cell annotations based on the Cell Ontology. Single cell typing based on cell ontology. please see the document of OnClass at https://onclass.readthedocs.io/en/latest/
Hierarchical domain structure reveals the divergence of activity among TADs and boundaries. An Optimized Nested TAD caller for Hi-C data. OnTAD is an Optimized Nested TAD caller for Hi-C data. OnTAD <Hi-C matrix> [-penalty <float>] [-maxsz <int>] [-minsz <int>] [-ldiff <float>] [-lsize <int>] [-bedout <chrnum int> <chrlength int> <int>] [-log2] [-o output_file]
Bioinformatics Analysis Identified Key Molecular Changes in Bladder Cancer Development and Recurrence. Here you can link TCGA survival data to mRNA, miRNA, or lncRNA expression levels. To get started simply input either a Tier 3 TCGA mRNA, miRNA, or MiTranscriptome beta lncRNA. More information can be found at this publication, youtube, or Omnes Res. News. A pan-cancer analysis using data in OncoLnc: OncoRank.
Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of new mechanisms to control tumorigenesis through the integration of genomic, pharmacological, clinical, and structural data with the network of cancer-associated protein-protein interactions experimentally detected in cancer cells.
An authentic learning approach to teaching cancer genomics. On this site you can both (a) make and upload, and (b) download and analyse simulated patient case studies.
A sequence-based clustering method to identify cancer drivers
An Ontology for Chemical Kinetic Reaction Mechanisms. A knowledge-graph built with the integration of semantic technologies and software agents for enhancing the experience of chemists in querying chemical kinetic reaction mechanisms. This User Interface (UI) demonstrates the query capability of OntoKin
Musculoskeletal optimal control. OpenSim Moco solves optimal control problems with musculoskeletal models defined in OpenSim, using direct collocation. OpenSim Moco is a software toolkit to solve optimal control problems with musculoskeletal models defined in OpenSim, including those with kinematic constraints. Using the direct collocation method, Moco can solve a wide range of problems, including motion tracking, motion prediction, and parameter optimization. The design of Moco focuses on ease-of-use, customizability, and extensibility. Just like OpenSim itself, Moco has interfaces in XML/command-line, Matlab, Python, Java, and C++.
Tool for assessing taxonomic metagenome profilers. Implements commonly used performance metrics together with convenient visualizations.
Open-community Profiling Assessment tooL (OPAL)
Open-source and scalable computer-assisted sperm analysis (CASA) tool. Allows users to study three classical sperm quality parameters: motility, morphometry and membrane integrity (viability) and offers the possibility of analyzing the guided movement response of spermatozoa to different stimuli or different motile cells.
Open source collaborative platform for the annotation of human genetic variation. A modular annotation tool for genomic variants. Open-CRAVAT is a python package that performs genomic variant interpretation including variant impact, annotation, and scoring. It has a modular architecture with a wide variety of analysis modules that are developed both by the CRAVAT team and the broader variant analysis community. Open-CRAVAT is a product of the Karchin Lab at Johns Hopkins University in collaboration with In Silico Solutions with funding provided by the National Cancer Institute's ITCR program. Open Custom Ranked Analysis of Variants Toolkit. CRAVAT 5 is in GRCh38/hg38. If you need to annotate GRCh37/hg19 variants, check the hg19 box under Input section or use CRAVAT 4 which is in GRCh37/hg19. Documentation and Getting Started. Get started with OpenCRAVAT here or with `pip install open-cravat`.
Robotic microscopy for everyone. The OpenFlexure project, which aims to make high precision mechanical positioning available to anyone with a 3D printer - for use in microscopes, micromanipulators, and more. http://openflexure.org.
Improved cortical boundary registration for locally distorted fMRI scans. An MRI analysis toolbox, primarily for laminar analysis. In order to protect your privacy, we only use cookies that are essential for the functioning of this website. Many of the functions for general fMRI preprocessing are wrappers for existing well-established neuroimaging tools. The wrappers should be seen as a consistent MATLAB command line interface to these functions, not as a reimplementation. A large part of these functions are written for my own convenience. A substantial part is new method development, mainly regarding laminar analysis. From this project root, run tvm_installLaminarAnalysisToolbox.m in MATLAB.
A PyTorch framework for tertiary protein structure prediction.
OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS.
3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data.
Unit testing, model validation, and biological simulation. Unified, simple data access python library for data & facts about C. elegans anatomy. A data access layer in Python which integrates disparate structures and representations for C. elegans anatomy and physiology. Enables a simple Python API for asking various questions about the cells of the C. elegans and enabling data sharing for the purpose of building a data-to-model pipeline for the OpenWorm project. OpenWorm is an open source project dedicated to creating a virtual C. elegans nematode in a computer. The web client of a Geppetto application. We're exploring the development of the worm via DevoWorm, an interdisciplinary project under the OpenWorm umbrella, focused on developmental processes in Nematodes and other forms of life through data analysis, visualization, and simulation.
Open Source Registry System for Rare Diseases (OSSE) - software for the creation of patient registries. Necessary interoperability between different registries is supported from the start and allows to federate those registries on a national and international level.
Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritise drug targets. Through large-scale genomic experiments and the development of innovative computational techniques, the partnership aims to help researchers select the best targets for the development of new therapies. At the heart of Open Targets is a consortium of complementary partner institutions that bring their respective expertise and capabilities to collaborative experimental and informatics projects. Bridging the gap between academic research and pharmaceutical drug development, Open Targets has made significant contributions to understanding the relationships between targets and diseases, established leading informatics tools in the Open Targets Platform and Open Targets Genetics, and contributed to global initiatives such as the Cancer Dependency Map.
The Open Targets Platform is a comprehensive tool that supports systematic identification and prioritisation of potential therapeutic drug targets. By integrating publicly available datasets including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships. The Platform is a freely available resource that is actively maintained with bi-monthly updates. The data can be accessed through an intuitive web user interface, an API, Google BigQuery, and a comprehensive set of datasets available for download in JSON and Parquet formats. The pipeline and infrastructure codebases that support the Platform are open-source and can be used to create a self-hosted private instance of the Platform with custom data.
Open-source optical projection tomography of large organ samples. The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice.
An open-source whole slide image analysis tool | Orbit has many build-in image analysis algorithms. Tissue quantification using machine learning techniques, object / cell segmentation, and object classification are the basic ones. Region of interest (ROI) can be defined by manual annotations or via a trainable exclusion map. Everything can be combined | Sophisticated Image Analysis Algorithms
Visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.
OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.
Orthologs are homologs seperated by speciation events. Paralogs are homologs separated by duplication events. Detection of orthologs is becoming much more important with the rapid progress in genome sequencing.
Web server for whole-genome comparison and annotation of orthologous clusters across multiple species.
Human osteoporosis-related gene database.
A novel tool for predicting unconventional protein secretion. OutCyte, as a versatile tool, can predict input proteins as signal-peptide containing, transmembrane-domain containing, intracellular or unconventionally secreted
A visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling | With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial
Parallel processing pipeline software for automatic analysis of bisulfite sequencing data.
Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation. Predicting Protein Folding Routes.
Prediction of N4-acetylcytidine (ac4C) modification sites in mRNA | prediction of acetylation sites in mRNA | PACESPrediction of ac4C(N4-acetylcytidine) sites in mRNA | Citation:Zhao W., Zhou Y., Cui Q. & Zhou Y. PACES: prediction of N4-acetylcytidine (ac4C) modification sites in mRNA. Sci Rep 9, 11112, doi:10.1038/s41598-019-47594-7 (2019)
Characterizing and Predicting Protein Hinges for Mechanistic Insight. PACKMAN: PACKing and Motion ANalysis
Generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools.
Portable Database for Metabolism. It is a format to centralizes, in a new graph-based PADMet, all information about a metabolic network. It also provides methods to import, to update, to analyse and to export data, in a library.
A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.
PAFScaff (Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding) is designed for mapping genome assembly scaffolds to a closely-related chromosome-level reference genome assembly. It uses (or runs) Minimap2 to perform an efficient (if rough) all- against-all mapping, then parses the output to assign assembly scaffolds to reference chromosomes.
Interpretable and Integrative Deep Learning for Survival Analysis Using Histopathological Images and Genomic Data. A biologically interpretable integrative deep learning model that integrates PAthological images and GEnomic data. PAGE_net_pretrain : code for pretraining and saving the pretrained model. Integration of aggregated pathological images and genomic data
A Pathway Graph Kernel based Multi-Omics Clustering Approach for Discovering Cancer Patient Subgroups. Install dependencies: if using virtual env omit --user parts. pip install -r requirements.txt --user. For mosek set environment variable MOSEKLM_LICENSE_FILE to your license file install mosek package with
Tool for statistical analysis and visualization of quantitative proteomics data
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis-a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance
Ultrafast and accurate clustering of phenotypic data of millions of single cells | PARC, “phenotyping by accelerated refined community-partitioning” - is a fast, automated, combinatorial graph-based clustering approach that integrates hierarchical graph construction (HNSW) and data-driven graph-pruning with the new Leiden community-detection algorithm
Program to Assemble Spliced Alignment. PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
R package for analyses of alternative polyadenylation (APA) related gene expression, including the characterization of poly(A) sites, quantification of association between genes with/without repeated measurements, clustering of APA-related genes to infer significant APA specific gene modules, and the evaluation of clustering performance with a variety of indexes.
PASER for automated analysis of neural signals recorded in pulsating magnetic fields | PASER: Processing and Analysis Schemes for Extracellular Recordings | Currently, PASER can only be used with data saved by Open Ephys GUI [Ref. 4], specifically .continuous files. See https://github.com/open-ephys/plugin-GUI or http://www.open-ephys.org/ for more information
Pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.
The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features. It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system. It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence.
Mapping functional elements at single amino acid resolution in human cells. Identification of functional elements for a protein of interest is important for achieving a mechanistic understanding. However, it remains cumbersome to assess each and every amino acid of a given protein in relevance to its functional significance. Here, we report a strategy, PArsing fragmented DNA Sequences from CRISPR Tiling MUtagenesis Screening (PASTMUS), which provides a streamlined workflow and a bioinformatics pipeline to identify critical amino acids of proteins in their native biological contexts. Using this approach, we map six proteins-three bacterial toxin receptors and three cancer drug targets, and acquire their corresponding functional maps at amino acid resolution
A10 Presence and frequency of M184V mutation in the MOBIDIP trial | AbstractThe MOBIDIP trial evaluated the simplification by protease (PI r) monotherapy for HIV infection versus dual therapy and boosted protease inhibitor plus lamivudine (PI r + 3TC) in controlled patients under second-line regimens. MOBIDIP was interrupted because of a significant number of patients with virological failure (VF) at week 48 (W48) in PI r (33 133, ∼25%) versus in PI r + 3TC (4 132, ∼3%). At the time of first-line VF, 96 per cent of patients harbored the M184V mutation. The presence of the M184V mutation was related to a protective effect against VF in the PI r + 3TC arm. We developed a methodology that allows to determine the frequency of M184V I mutations in the HIV reverse transcriptase (RT) gene in peripheral blood mononuclear cells (PBMC) obtained before MOBIDIP simplification
R package for crosstalk correction in Pathway Deregulation Score (PDS) inferred by Pathifier algorithm.
A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. “rectal_table”: All the nonsynonymous mutations in TCGA rectal cancer dataset and its coresponding Polyphen-2 scores. The first column is the sample names, the second column is the mutated genes and the third column is the functional impact score corresponding to each mutations. “CoreGroup2Gene.txt”: contains the mapping of pathways to genes (genes entrez id). The first column is the name of pathways, the second column is genes included in the pathways. The file "example1.R” is an example of R codes which read the data file “rectal_table” and “CoreGroup2Gene.txt” and analyze the 9 pathways in “CoreGroup2Gene.txt” together. The file returns “pairprob.txt” which contains the probabilities of A>B, A<B and A=B for all pairs of pathways.
Fusion detection in assembled transcriptomes. Post-Assembly Variant Finder (PAVFinder). PAVFinder is a Python package that detects structural variants from de novo assemblies (e.g. ABySS, Trans-ABySS). As such, it is able to analyse both genome and transcriptome assemblies:.
Efficient haplotype matching between a query and a panel for genealogical search | Efficient haplotype matching between a query and panel using PBWT-Query | Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang
Principle Component Analysis-based iterative PAM50 subtyping (PCA-PAM50) improves consistency between breast cancer intrinsic and clinical subtyping reclassifying a subset of luminal A tumors as luminal B.
An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing molecular dynamics trajectories via a web browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables 'plug-and-play' trajectory visualization. Jacob Durrant software July 29, 2019September 30, 2019
Topological structure analysis of chromatin interaction networks. Analysis and visualisation tools for PCHi-C interaction networks
A database of Plant Chloroplast Inverted Repeats. Plant Chloroplast Inverted Repeats. Welcome to PCIR! Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching, and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21,433 IRs, 113 plants chloroplast genomes, 16,948 functional genes and 21,659 visual maps. This database offers an online prediction tool for detecting IRs based on Chloroplast DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features
Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. An R-package for specification, simulation and likelihood calculation of phylogenetic comparative models. PCMBase : Simulation and likelihood calculation of phylogenetic comparative methods. Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree.
A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Database, Volume 2017, 2017, bax098
Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment.
Parameter fitting toolbox for partial differential equations in Python.
Populating Chemical Space with Peptides using a Genetic Algorithm. In drug discovery one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in chemical space marked by a molecule of interest. Herein we report the peptide design genetic algorithm (PDGA, code available at https: github.com reymondgroup PeptideDesignGA), a computational tool capable of producing peptide sequences of various chain topologies (linear, cyclic polycyclic or dendritic) in proximity of any molecule of interest in a chemical space defined by MXFP, an atom-pair fingerprint describing molecular shape and pharmacophores. We show that PDGA generates high similarity analogs of bioactive peptides, including in selected cases known active analogs, as well as of non-peptide targets.
A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling the comparison of the expression profiles of several genes simultaneously, as well as to visualize co-expression information. One section describes how to download the expression data in a format that is easy to export to spreadsheet software and to generate figures that are ready for presentations or publications.
PSI Extended Fasta Format (PEFF) is a proposed unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools.
PELE-MSM is a Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies. IIt is a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for the estimation of absolute protein-ligand binding free energies, one of the most significant challenges in computer-aided drug design. Based on a ligand pathway approach, an initial short enhanced sampling simulation is performed to identify reasonable starting positions for more extended sampling. This stepwise approach allows for a significantly faster convergence of the free energy estimation using the Markov State Model (MSM) technique. PELE-MSM was applied on four diverse protein and ligand systems, successfully ranking compounds for two systems. Based on the results, current limitations and challenges with physics-based methods in computational structural biology are discussed.
a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
Identification of pathogenic variant enriched regions across genes and gene families.
PERs is a tool for Identification of pathogenic variant enriched regions across genes and gene families.
Portal for Families Overcoming Neurodevelopmental Disorders (PFOND) provides a structured web interface for the information sharing with individuals struggling with the consequences of rare developmental disorders.
This library is primarily to offer a command-line tool to convert between the following formats for proteogenomics related data. It is also possible to convert regular non-proteogenomics mzIdentML or PRIDE XML files to mzTab. A secondary function of this library is to gather metadata and statistics about mzIdentML, mzTab, and PRIDE XML files for validation purposes. Primarily this tool is powered by the ms-data-core-api library to read/write files. Primarily this tool is powered by the ms-data-core-api library to read/write files.
The Han Chinese Genomes Database (PGG.Han) serves as the central repository of the genomic data of the Han Chinese Genomes Project (Phase I). As is its current version, PGG.Han archives genomic data of 114,783 Han Chinese individuals (a.k.a. Han100K), including high coverage WGS data (n = 319), low coverage WGS data (n = 11878), and high-density SNV data with 8,056,973 variants genotyped or partially imputed (n = 102,586. PGG.Han aims to facilitate: 1) population structure analysis; 2) ancestry inference; 3) imputation; 4) GWAS. Computational tools are implemented into the PGG.Han, and an online user interface is provided for data analysis and results visualization.
PGG SNV is a database for understanding evolutionary and medical implications of human single nucleotide variations in diverse populations. The tool provides useful web tools for figure illustration. Users can upload their local files with specific format (see readme and example at the top-right corner of each tool) generated by their own analysis to draw their figures as well as download them. The current version includes tools on (a) heatmap plot of population differentiation; (b) word map plot of allele frequency distributions; (c) manhattan plot of natural selection signals; and (d) heatmap plot for linkage disequilibrium analysis.
PGP-UK is an open access resource of human multi-omics data.
PGxLOD is intended to host pharmacogenomic knowledge that the PractiKPharma project will extract from various sources such as the literature and Electronic Health Records.
This is the codebase for the PGxMine project to using text-mining to identify papers for curation into PharmGKB. It is a Python3 project that makes use of the Kindred relation classifier along with the PubRunner project to run tools across PubMed and accessible PubMed Central.
Pathogen–Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts.
PHENO aims to provide access to plant phenotypic datasets, with a major focus on the woody plant domain. Plant phenotyping is central to plant research and breeding and is becoming increasingly throughput, with large amounts of data being generated from diverse experimental settings. Access to phenotypic datasets annotated according to widely accepted standards contributes for data interoperability, enabling powerful genotype-phenotype association studies.
PHENOtypic STAte MaP (PHENOSTAMP) is an algorithm that combines the Clustering Classification and sorting Tree(CCAST) algorithm (Anchang et al. 2014) with an optimal 2D visualization of projected single-cell data using a neural network. It is mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.
Practical Haplotype Graph (PHG) facilitates genome-wide imputation and cost-effective genomic prediction. Successful management and utilization of increasingly large genomic datasets are essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, a sorghum Practical Haplotype Graph (PHG) pangenome database stores all identified haplotypes and variant information for a given set of individuals.
PHI-Nets is a network resource for Ascomycete fungal pathogens to annotate and identify putative virulence interacting proteins and siRNAs.
PHOSforUS is a fully biophysical parameter-based protein phosphorylation site predictor.
Scalable data integration and visualization for multiple phylogenetic inference methods.
PICEAdatabase is a web database for Picea omics and phenotypic information.
Pipeline for Integrated Microarray Expression Normalization Tool kit (PIMENTo) for tumor microarray profiling experiments.
PINOT is a Protein Interaction Network Online Tool.
Tool for tumor subtype discovery in integrated genomic data.
PIPE-T is a Galaxy Workflow for processing and analyzing miR expression profiles by RTqPCR. It is a tool that offers several state-of-the-art options for parsing, filtering, normalizing, imputing and analyzing RT-qPCR expression data. Integration of PIPE-T into Galaxy allows experimentalists with strong bioinformatic background, as well as those without any programming or development expertise, to perform complex analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment
PSB Interface for plant phenotype analysis
PIPR is a multifaceted protein-protein interaction prediction based on Siamese residual RCNN.
PIRATE is a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.
This tool contains scripts for PIRCh-seq. It provides a pipeline for functional classification of non-coding RNAs associated with distinct histone modifications
Pan immune repertoire database (PIRD) collects raw and processed sequences of immunoglobulins (IGs) and T cell receptors (TCRs) of human and other vertebrate species with different phenotypes. You can check the detailed information of each sample in the database, choose samples to analyze according to your need, and upload data to analyze. Your analysis results will be auto-saved, so you can return to check them at any time.
PK-DB is a database and web interface for pharmacokinetics data and information from clinical trials as well as pre-clinical research. PK-DB allows to curate pharmacokinetics data integrated with the corresponding meta-information
Web-based tool for plasmid reconstruction from bacterial genomes.
Promoting transparency and reproducibility in enhanced molecular simulations | The public repository of the PLUMED consortium | PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual | The community-developed PLUgin for MolEcular Dynamics | PLUMED is an open-source, community-developed library that provides a wide range of different methods, which include: | Home News People Download Doc Forum Cite NEST Funding
PMBD is a Comprehensive Plastics Microbial Biodegradation Database.
PMD-FDR is a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits.
High-dimensional Bayesian phenotype classification and model selection using genomic predictors.
Patient Navigation Barriers and Outcomes Tool™ (PN-BOT™), a new information management and reporting tool for oncology PN programs.
The PNC package is to identify personalized driver genes of an individual patient by using network control principle .
PNV is an assessment of Machine Learning algorithms for estimating land potential.
Interactive visual environment for rule-based modelling of biochemical systems.
PPCheck is a bioinformatics tool to identify protein-protein interactions, predict hotspots, perform compuational alanine scanning, predict native-like docking pose and calculate residue conservation for a protein.
Genome-wide prediction and prioritization of human aging genes by data fusion.
Tool for extracting comprehensive protein-protein interaction information.
PPNID: a manually curated reference database and identification tool for plant-parasitic nematode.
A Software Platform for Facilitating Population Genomic Analyses. Installation — PPP 0.1.1 documentation. Free document hosting provided by Read the Docs
personalized PageRank and semantic similarity measures for entity linking. BACKGROUND:Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain. RESULTS:We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies
Boosting phosphorylation site prediction with sequence feature-based machine learning | Index of /~pralay/resources/PPSBoost | Shyantani Maiti, Atif Hassan, Pralay Mitra (In press). Boosting phosphorylation site prediction with sequence feature-based Machine learning. PROTEINS: Structure, Function, and Bioinformatics
Novel method for interrogating receiver operating characteristic curves for assessing prognostic tests.
PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species
PQStat is an application which enables users to carry out a statistical data analysis in a simple and accurate way.
PRALINE 2 is a framework for tailor-made sequence alignments. It allows almost all aspects of a sequence alignment algorithm to be customised, such as the alphabets used (AA, DNA, secondary structure, disorder, motif matches, etc.). Includes a command-line tool for common use cases without writing any custom code.
Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit
Pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments.
> HOMEPAGE BROKEN! | Predicting functional targets of RNA binding proteins based on CLIP-seq peaks | RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle
PRECOG (Predicting coupling probabilities of G-protein coupled receptors) lets you predict coupling probabilities of Class A GPCRs to 11 G-proteins based on input sequence information (either WT or mutated). It is built by training logistic-regression algorithm on sequence- and structure-based features, derived from a set of Class A GPCRs.
PRECOG: Predicting coupling probabilities of G-protein coupled receptors
Improved version of Protein Repeat Identification by Graph Spectral Analysis. Protein Repeat Identification by Graph Spectral Analysis. PRIGSA2 is a graph based algorithm which implements knowledge-based and de novo approach for the identification of structural repeats in proteins. The tool takes PDB file as input and gives the periodicity and coordinates as output
PRIMEval is a tool for optimization and screening of multiplex oligonucleotide assays.
Privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents.
> NAME EQUAL TO (PUB. DIFFERENT) bio.tools/prism-ppi | > NAME (PRISM) SIMILAR TO (PUB. DIFFERENT) bio.tools/prism_3 (PRISM 3), bio.tools/prism-primer (PriSM), bio.tools/prism (PrISM) | methylation pattern-based, reference-free inference of subclonal makeup | Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. (v1.0.1) | PRISM requires the mapping result of Bismark, a bisulfite read mapping tool. Also note that PRISM only applies to RRBS data, and unfortunately, the feasibility of PRISM to the data from other methylation profiling techniques such as whole genome bisulfite sequencing (WGBS), methylated DNA immunoprecipitation sequencing (MeDIP-Seq), or methyl-CpG binding domain-based capture sequencing (MBDCap-Seq) has not been verified | BAM file of RRBS reads, aligned by Bismark
Large-scale prediction of binding affinity in protein-small ligand complexes.
European H2020 e-Infrastructure grant, BioExcel, grant no. 675728
European H2020 e-Infrastructure grant, BioExcel, grant no. 823830
European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536
PRODIGY-CRYSTAL (PROtein binDIng enerGY prediction to classify CRYSTALlographic interfaces) is an automatic web server for distinguish crystallographic from biological interfaces in protein complexes.
PROMO (Profiler of Multi-Omics data) - interactive tool for analyzing clinically-labeled multi-omic cancer datasets.
PRP is a comprehensive integrated regulatory information and analysis portal for plant genomes. Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a 'cell system'. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time.
A Hybrid Model for Predicting Pattern Recognition Receptors using Evolutionary Information. Prediction of pattern recognition receptors. PRRpred is a web server designed for predicting pattern Recognition Receptors (PRRs) and Non-PRRs
Atlas of polygenic burden associations across the human phenome.
PReMiS analyzes mass spectrometric data collected from the 6×5 LC-MS/MS Peptide Reference Mix and calculates quality control metrics for instrument performance. Thermo raw files and AB Sciex wiff files can be analyzed directly. Data in other vendor formats must be converted to mzML prior to analysis. In addition to its general reporting features, PReMiSallows you to track performance over time and compare parameters across instruments.
Photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.
Splicing-detection method for short-read and long-read RNA-seq analysis.
Fully-sensitive seed finding in sequence graphs using a hybrid index | Graph REad Mapper (C++ implementation) | Google protocol buffer >= v3.0.0
An extensive database for pan-species microsatellite investigation and marker development. A Django app for Pan-Species Microsatellite Database. Pan-Species Microsatellite Database. Microsatellites (simple repeat sequences, SSRs or short tandem repeats, STRs), are tandem repeats of short DNA motifs with length of 1-6 bp which have extensively been exploited as powerful genetic markers for diversity applications, and are involved in gene regulation as well as implicated in numerous genetic diseases even in cancers. PSMD was developed as a web-based comprehensive database comprising 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms covered almost all species with available genomic data. PSMD enables scientists to easily browse, filter, compare, download SSRs with relevant information
Prediction of FUS-like phase separation proteins
Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.
Systems Biology Lab, National Chung Hsing University
PSSRdt is a novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data.
Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper. R scripts to create crosstalk maps that visualize multi-layered proteoform data. PTM-CrossTalkMapper is a flexible toolkit to visualize multi-layered quantitative post-transcriptional modification (PTM) data. The preprint manuscript can be found on bioRxiv
R package for PTM site localization and motif extraction from proteomic datasets.
PTR is an approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics.
PTRBC is a tool for predicting the required pre-surgery blood volume in surgical patients based on machine learning. This clinical data analysis tool can be used to do data cleaning and predict the required transfusion volume of red blood cells in surgical patients based on machine learning methods. Meanwhile, this tool can process the similar classification or regression problems. In other words, a general prediction model can be established for the input data specified.
Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis. Probabilistic Transcriptome-wide Association Analysis (PTWAS). This repository contains the software implementations and necessary annotation resources for a suite of statistical methods to perform transcriptome-wide association analysis (TWAS). These methods are designed to perform rigorous causal inference connecting genes to complex traits. The statistical models and the key algorithms are described in the manuscript [1]
programmatic access to chemical annotations integrated in PubChem | PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies
parallel variation calling tools. PVCTools is Parallel Variation Calling Tools, which tries to call variation using multiple threads. Basically, the reference genome will be splited into small pieces, and corresponding alignment BAM files will be extracted. Under this way, it will speed up the process of variation calling a lot
Poly-Exposure and Poly-Genomic Scores Implicate Prominent Roles of Non-Genetic and Demographic Factors in Four Common Diseases in the UK. ABSTRACT While polygenic risk scores (PRSs) have been shown to identify a small number of individuals with increased clinical risk for several common diseases, non-genetic factors that change during a lifetime, such as lifestyle, employment, diet, and pollution, have a larger role in clinical prediction. We analyzed data from 459,613 participants of the UK Biobank to investigate the independent and combined roles of demographics (e.g., sex and age), 96 environmental exposures, and common genetic variants in atrial fibrillation, coronary artery disease, inflammatory bowel disease, and type 2 diabetes. We develop an additive modelling approach to estimate and validate a poly-exposure score (PXS) that goes beyond consideration of a handful of factors such as smoking and pollution
Python implementation of likelihood-free inference by ratio estimation. Likelihood-Free Inference by Ratio Estimation (LFIRE). PYLFIRE is a Python package that uses ELFI (Engine for Likelihood-Free Inference) and glmnet for performing Likelihood-Free Inference. PYLFIRE requires Python 3.6 or greater and a Fortran compiler, for Mac users brew install gcc will take care of this requirement or conda install gcc if you are using anaconda. You can install PYLFIRE by typing in your terminal:
Python reconstruction operators in neural networks | Python Reconstruction Operators in Neural Networks. High level python API for PYRO-NN-Layers | Implementation of reconstruction operators in CUDA for Tensorflow for the PYRO-NN Framework | Python Reconstruction Operators in Machine Learning (PYRO-NN-Layers) brings state-of-the-art reconstruction algorithms to neural networks integrated into Tensorflow. This repository contains the actual Layer implementation as CUDA kernels and the necessary C++ information control classes according to the Tensorflow API | At this point the geometry is fully setup and can be used to create projections and reconstructions
Fast and scalable processing of whole exome and targeted sequencing data. PaCBAM_Performance_analysis – Google Drev
PaSGAL (Parallel Sequence to Graph Aligner) is designed to accelerate local sequence alignment of sequences to directed acyclic sequence graphs (DAGs), e.g., variation graphs, splicing graphs.
Fast Signal Feature Extraction Using Parallel Time Windows | Motivation: Hand amputations can dramatically affect the quality of life of a person. Researchers are developing surface electromyography and machine learning solutions to control dexterous and robotic prosthetic hands, however long computational times can slow down this process. Objective: This paper aims at creating a fast signal feature extraction algorithm that can extract widely used features and allow researchers to easily add new ones. Methods: PaWFE (Parallel Window Feature Extractor) extracts the signal features from several time windows in parallel. The MATLAB code is publicly available and supports several time domain and frequency features
Sequencing simulator for PacBio sequencing with a high fidelity.
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly.
PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands.
Agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. Create beautiful and semantically meaningful articles with pandoc. science pandoc publishing scientific-writing pandoc-scholar. Plain pandoc is already excellent at document conversion, but it lacks in metadata handling. Pandoc scholar offers simple ways to include metadata on authors, affiliations, contact details, and citations. The data is included into the final output as document headers. Additionally all entries can be exported as JSON-LD, a standardized format for the semantic web. Pandoc a universal document converter. Create beautiful, semantically enriched articles with pandoc. If you need to convert files from one markup format into another, pandoc is your swiss-army knife. (← = conversion from; → = conversion to; ↔︎ = conversion from and to).
An iterative clustering method for single-cell RNA sequencing data | Single-cell Panoramic View Clustering (PanoView) | PanoView is an iterative PCA-based method that integrates with a novel density-based clustering, ordering local maximum by convex hull (OLMC) algorithm, to identify cell subpopulations for single-cell RNA-sequencing. For details of the method, please see our paper at PLOS Computational Biology (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007040)
Time-course network medicine platform integrating molecular assays and pathophenotypic data.
Open-source web-based search and metadata organization of scientific literature.
Tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.
A hybrid and scalable error correction algorithm for indel and substitution errors of long reads. BACKGROUND:Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads. METHODS:In this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes the k-mer coverage information of high throughput Illumina short-read sequences to rectify the PacBio long-read sequences.
Graph realignment tools for structural variants.
Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed.
Fast inference and visualization of ancestral scenarios. PastML infers ancestral characters on a rooted phylogenetic tree with annotated tips, using maximum likelihood or parsimony. The result is then visualised as a zoomable html map.
User-friendly interface to explore evolutionary scenarios.
Catalogue of public databases for molecular typing and microbial genome diversity.
Identify structurally conserved regions at the protein surfaces.
The workflow involves a computational technique that employs propagation of drug-protein and protein-protein interactions to predict the biological pathways that are affected by a drug or compound. Reliable, openly available repositories (CHEMBL, TTD, DrugBank, PharmGKB, IUPHAR, Intact, MINT) were used for connecting pharmaceutically relevant compounds to their target proteins in human and the target proteins to their first-degree interactors. Since these databases differ in their architecture and accessibility, diverse sub-workflows with filtering steps were created ensuring the quality of the retrieved data.
A comprehensive pathway database for model organisms. Quantitative metabolomics services for biomarker discovery and validation. Specializing in ready to use metabolomics kits. Your source for quantitative metabolomics technologies and bioinformatics. PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. A Pathway for Every Protein
Efficient pan-cancer whole-slide image classification and outlier detection using convolutional neural networks.
De Novo Pathway-Based Classification of Breast Cancer Subtypes. Breast cancer is a heterogeneous disease for which various subtypes have been identified. If you find this web application useful please cite:. Alcaraz et al., De novo pathway-based classification of breast cancer subtypes (manuscript in preparation).
Interaction-network tool to search for the most relevant protein-protein interactions around a drug's target(s), and then analyzes for which phenotypes the network is enriched relative to the entire interaction network.
A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology | A Convenient High-Throughput Workflow for Preprocessing, Deep Learning Analytics and Interpretation in Digital Pathology | MedRxiv Manuscript: https://www.medrxiv.org/content/10.1101/19003897v1 | Fig. 1. PathFlowAI Framework: a) Annotations and whole slide images are preprocessed in parallel using Dask; b) Deep learning prediction model is trained on the model; c) Results are visualized; d) UMAP embeddings provide diagnostics; e) SHAP framework is used to find important regions for the prediction
Python package that transforms pathway knowledge from three major pathway databases into a unified abstraction using Biological Expression Language as the pivotal, integrative schema.
Open source software for analyzing spatial navigation search strategies | Search Strategy analysis and more for spatial navigation data in rodents | Morris Water Maze search strategy and entropy analysis | For a more detailed overview of Pathfinder please visit our Wiki | Created by Matthew Cooke at The University of British Columbia, Jason Snyder Lab | The Pathfinder package is a search strategy analysis tool for the Morris Water Maze, and can be expanded for other spatial navigation tasks. The program analyses X-Y coordinate data exported from commercially available tracking software. Pathfinder currently supports outputs from: Ethovision, Anymazy, WaterMaze, and ezTrack. We then calculate the best-fit search strategy for the trial. Trials are fit into one of: Direct Swim, Directed Search, Focal Search, Spatial indirect, Chaining, Scanning, Thigmotaxis, and Random Search
Pathway Commons aims to collect and disseminate biological pathway and interaction data. Data is collected from partner databases and is represented in the BioPAX standard. By representing data in BioPAX, Pathway Commons is able to provide a detailed representation of a variety of biological concepts including: Biochemical reactions; gene regulatory networks; and genetic interactions; transport and catalysis events; and physical interactions involving proteins, DNA, RNA and small molecules and complexes.
Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model, which can be queried using our web API (documented below). This API can be used by computational biologists to download custom subsets of pathway data for analysis, or can be used to incorporate powerful biological pathway and network information retrieval and query functionality into websites and software.
Proteoform-centric network construction enables fine-granularity multiomics pathway mapping | PathwayMatcher is a free, open-source software to search for pathways related to a list of genes, proteins or proteoforms in Reactome | PathwayMatcher was benchmarked against different reference datasets covering multiple types of omics data | We present next the Cypher language queries to find the numbers shown in the summary statistics. These can also be used to get the protein-pathway mapping used in PathwayMatcher | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | 7448 valid tools on Nov 10, 2019
Tool for the transformation of metabolic pathways and the development of pathfinding algorithms that establish relevant links between compounds that are essential to the biofuel production process.
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) | St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal | Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore
Combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. A toolkit for predicting non-classical secreted proteins by combining the gradient boosting machine in an ensemble learning framework . A combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins | In this work, we first constructed a high-quality dataset of experimentally verified “non-classical” secreted proteins, which we then used to create benchmark datasets. Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection
The Software Tool for Peptide Specificity Analysis (PeSA) is an open-source software designed as a tool to use in the analysis of peptide arrays, permutation arrays and OPALs. The analysis can be used to generate motifs to share the results as a position-specific scoring matrix (PSSM).
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data | Tool for identifying/classifying solvent molecules in macromolecular x-ray crystal structures | -- Paul Smith, PhD. Assistant Prof. of Chemistry, FordhamUniversity (psmith66@fordham.edu) -- Laurel Jones, PhD Candidate,Northwestern University -- Michael Tynes, Data Sciences GraduateProgram, Fordham University | -- PeakProbe must be run under the "phenix.python" environment or be made aware of the locations of all necessary CCTBX imports -- A PDB file and structure factor data are required and can be specified in any order or suitable format as per PHENIX norms -- The program has several modes of operation and many configurable parameters, but the essentials are covered below
A mine with peanut data from Legume Information Systems (LIS) PeanutBase
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. Program to simulate pedigree structures. The method can use sex-specific genetic maps and randomly assigns the sex of each parent (or uses user-specified sexes) when using such maps. ./ped-sim -d <in.def> -m -o <out_prefix> --intf <filename>. The above both produce three output files: [out_prefix].seg containing IBD segments, [out_prefix].fam, a PLINK format fam file with all simulated relatives, and [out_prefix].log, a log of what Ped-sim printed to stdout. Sample ids for simulated individuals
A pediatric diseases map generated from clinical big data from Hangzhou, China. Freelyavailable pediatric critical care data for researchers. Haomin Li#*,Gang Yu#, Cong Dong, Zheng Jia, Jiye An, Huilong Duan, Qiang Shu*. PedMap: a pediatric diseases map generated from clinical big data from Hangzhou, China. Scientfic Report 2019. DOI : 10.1038/s41598-019-54439-w. A pediatric disease map shows the relationships among the most common pediatric diseases, incidence rates, ages of onset and seasonal patterns in children based on more than 5 million outpatient visits at The Children's Hospital Zhejiang University School of Medicine (ZUCH)
Software package for semi-automated processing of protein footprinting data.
PepPro is a Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking.
Peptide-centric search engine for novel peptide identification and validation.
PepVis tool is a python based GUI pipeline which can be used to model and prepare large-scale peptide structure from the sequence and also to perform large-scale peptide virtual screening. PepVis integrates ModPep and Gromacs for modelling and structure optimization of the peptides, while it integrates AutoDock Vina,ZDOCK, AutoDock CrankPep(ADCP) for performing peptide virtual screening. The protein-peptide complexes can be rescored using ZRANK2 and the flexible refinement of the large protein-peptide complexes can also be performed using FlexPepDock. The parallel job execution has been implemented using GNU parallel and the user can provide inputs using GUI which will produce the bash script based on the customized input provided by the user and can be run in terminal.
Proteogenomics workflow for the expert annotation of eukaryotic genomes.
A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via non-covalent interactions and are of outmost importance, due to numerous cellular functions in which they participate. In an effort to collect data regarding this heterogeneous group of proteins we designed and constructed a database, called PerMemDB. PerMemDB is currently the most complete and comprehensive repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred - a computational method that specializes in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains. The first version of the database contains 231,770 peripheral membrane proteins from 1009 organisms.
Web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.
PertInInt is a tool using an integrative approach uncovers genes with perturbed interactions in cancers. The tool enables rapid uncovering of significantly somatically mutated protein functional regions. The goal of the analytical PertInInt method is to rapidly uncover proteins with significant enrichments of somatic Perturbations In Interaction and other functional sites.
PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. If bulk sequencing data is used, we expect that mutations originate from diploid regions of the genome. Due to variance in VAF values, we recommend the use of bulk data in cases when sequencing depth is at least 1000x (haploid coverage). As output, PhISCS reports tree of tumor evolution together with a set of eliminated mutations, where eliminated mutations represent mutations violating Infinite Sites Assumption (due to deletion of variant allele or due to recurrent mutation) or mutations affected by copy number aberrations that were missed during the tumor copy number profiling (e.g. gain of non-variant allele).
PhaSePro is the comprehensive database of proteins driving liquid-liquid phase separation (LLPS) in living cells. LLPS is a molecular process employed by all living organisms to form membraneless organelles, mediating crucial cellular functions. PhaSePro is manually curated, it is solely based on experimentally verified cases of LLPS, integrating a wide range of information on the biophysical driving forces, biological function and regulation of these molecular systems.
PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures that may facilitate phase separation related proteins identification for all human proteins.
PhagePromoter is a python tool that predicts promoter sequences in phage genomes, using machine learning models.
PhageXress us a Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing.
PharmOmics is a A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing. It is a Web server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Integration. PharmOmics apps were implemented with Rshiny and depend on javascript. In case of failed loading, please check your antivirus setting and whitelist/temporary disable to solve the issue.
Pharmacophore is a tool for modeling and hit identification based on druggability simulations.
PheGWAS is a three-dimensional approach to dynamically visualize GWAS across multiple phenotypes. It does interactive 3D visualization on many variants many phenotypes
PheValuator is a phenotype algorithm evaluator.
Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders.
Phen2Gene is a phenotype-driven gene prioritization tool, that takes HPO (Human Phenotype Ontology) IDs as inputs, searches and prioritizes candidate causal disease genes. It is distributed under the MIT License by Wang Genomics Lab. Additionally, we have provided a web server and an associated RESTful API service for running Phen2Gene. Finally, a mobile app for Phen2Gene and several other genetic diagnostic tools from our lab is being tested and will be available soon.
Web catalog of high-priority measures for consideration and inclusion in biomedical and epidemiologic research.
PheonoCam is tracking vegetation phenology across diverse biomes using Version 2.0 of the PhenoCam Dataset. This tool facilitates the retrieval and post-processing of PhenoCam time series. The post-processing of PhenoCam data includes outlier removal and the generation of data products such as phenological transition dates.
Database for phenotypic characterization of rare cardiac diseases.
Software package for the prediction of flowering phenology.
Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity.
Gene/disease prioritization tool that utilizes heterogeneous gene disease network.
PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications.
PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation.
Database of human genotype-phenotype associations.
PhenomeXcan is a tool for mapping the genome to the phenome through the transcriptome.
Open platform for harmonization and analysis of genetic and phenotypic data.
Phenoscape is a Logical Model of Homology for Comparative Biology.
PhiMRF is an R package for Poisson Hierarchical Markov Random Field model for analysis of spatial dependency on count data.
PhilDB is capable of storing data at any frequency supported by Pandas. At this time only daily data has been extensively tested with some limited sub-daily usage. Timeseries database project is for storing potentially changing timeseries data. For example, hydrological data, like streamflow data, where the timeseries may be revised as quality control processes improve the recorded dataset over time.
Phobos is a software for the automated analysis of freezing behavior in rodents. Unlike other programs, it uses manual quantification of a short video to calibrate parameters for optimal freezing detection. Phobos works with 3 user interfaces (UIs) for this purpose. The main user UI is where the user loads videos for quantification, defines an output folder and creates the .xls file with the results. The Video Parameters UI is where the user defines the beginning and end times for freezing detection in the videos and crops the image to restrict the analysis to a specific area. Finally, the Manual Quantification UI is used to manually quantify freezing in a video, which will then be used as a reference for the calibration process.
Phoenix Enhancer is an online service/tool for proteomics data mining using clustered spectra.
Phosphoproteome prediction is a tool for predicting phosphorylation levels of the proteome across cancer patients. It integrates four components into itsalgorithm, including (i) baseline correlations between protein and phosphoprotein abundances, (ii) universal protein–protein interactions, (iii) shareable regulatory information across cancer tissues and (iv) associations among multi-phosphorylation sites of the same protein.
PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances.
PhyDL (Phylogenetics by Deep Learning) is a deep learning predictor for phylogenetic reconstruction.
Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.
PhySigs uses the input of a phylogeny with nodes representing clones in a patient tumor, a signature matrix containing the set of mutational signatures to use in the analysis, and a feature matrix for the set of mutations introduced in each clone. In particular, the mutational categories in the feature matrix should correspond to the mutational categories used in the signature matrix. PhySigs automatically computes the count matrix, as it is simply a diagonal matrix containing the sum of columns in the feature matrix. PhySigs then solves the Tree-constrained Exposure (TE) problem for all possible clusterings of the clones that correspond to a partition of the phylogeny. The output of the TE problem is a relative exposure matrix composed of groups of identical columns corresponding to clusters of clones with identical exposures (denoted by blue and yellow). Edges between these clusters in the phylogeny are interpreted to be where exposure shifts occurred (denoted by a lightning bolt).
PhySpeTree is an automated pipeline for reconstructing phylogenetic species trees.
Phydelity, a redesign of PhyCLIP, is a statistically-principled and phylogeny-informed tool capable of identifying putative transmission clusters in pathogen phylogenies without the introduction of arbitrary distance thresholds
This tool is a gene database for Phyllosticta citricarpa and sister species.
PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies). One of PhyloCSF’s main current applications is to help distinguish protein-coding and non-coding RNAs represented among novel transcript models obtained from high-throughput transcriptome sequencing.
PhyloMagnet provides fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. The tool has a pipeline for screening metagenomes, looking for arbitrary lineages, using gene-centric assembly methods and phylogenetics
PhyloNet is a tool that applies a divide-and-conquer method for scalable phylogenetic network inference from multilocus data.
A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.
Dynamic web application that enables the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes.
PhysMPrePro is an energy model for recognizing the prokaryotic promoters based on molecular structure.
PhysiCell is a physics-based cell simulator.
An InterMine interface to data from Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, which hosts 81 assembled and annotation genomes, from 78 viridiplantae species.
Database of plant protein inter-cultivar variability and function.
PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data.
Deep-learning method for prediction of π-helices in protein sequences.
PiVR is a closed-loop platform to study unrestrained sensorimotor behavior. PiVR has been developed to track a variety of animals in real time and present them with light stimuli.
Application for designing molecular beacons for live cell imaging of endogenous mRNAs.
Tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data.
PipeMEM is a Framework to Speed Up BWA-MEM in Spark with Low Overhead.
R package for inferring ethnicity from placental DNA methylation microarray data.
PlaSMo stands for Plant Systems-biology Modelling and the mission of the project was ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.
PlaScope is a targeted approach to assess the plasmidome of bacteria.
PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.
An integrated web resource of data & tools to mine Planarian biology
Plant is a website and database provides systematic annotations of all types of endogenous plant small RNA loci.
PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including Oryza sativa L. (japonica and indica), Arabidopsis thaliana, Chlamydomonas reinhardtii, Medicago truncatula, Trifolium pratense, Populus trichocarpa and Phyllostachys edulis.
Web-based platform of nucleotide sequence alignments of plants.
PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables users to retrieve regulatory interactions of interest by circRNAs, miRNAs and mRNAs across eight model species. Sequences search is also available. And an enrichment analysis tool has been provided for Gene Ontology categories of miRNA targets.
PlantRegMap is a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.
PlantSimLab is a modeling and simulation web tool for plant biologists.
The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world. The web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.
Plant Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of plant pathway knowledge.
Plant Regulomics is a data-driven interface for retrieving upstream regulators from plant multi-omics data, which integrates 20,737 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58,112 functional terms and 695,414 protein-protein interactions) from six plant species, namely Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Solanum lycopersicum and Triticum aestivum, along with the orthologous genes from 56 whole-genome sequenced plant species. These data were well-organized to gene modules and further implemented into the same statistical framework.
PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly.
PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).
Automatised pharmacophoric deconvolution of plant extracts.
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Software package for rapid, accurate, and flexible batch annotation of plastomes.
Identification and characterization of bacterial plasmid contigs from short-read draft assemblies.
Web-based visualization tool for exploring pleiotropy across complex traits.
PlotTwist (Plotting data from Time-lapse experiments With Indicators of conditions at Set Times) is an app for visualizing the data and statistics of continuous data, with a focus on time-dependent measurements. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To facilitate the visualization of individual measurements, the data can be shown as 'small mutliples' or in 'heatmap-style'. To further facilitate the comparison, the mean and 95% CI can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha). Several color blind friendly palettes are available to label the data. The comparison of multiple conditions is enabled by multiple file upload (csv or xls format), where each file represents a condition.
MHC-I epitope presentation prediction based on transfer learning.
PmiREN is a comprehensive encyclopedia of plant miRNAs.
PnGT stand for 'Physicochemical n-Grams Tool'. It is a tool for protein physicochemical descriptor generation . Physicochemical n-Grams Tool (PnGT) is an open source standalone software for calculating physicochemical descriptors of protein developed using the Python scripting language.
Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens.
PointFinder is an Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites.
PointSite is a point cloud segmentation tool for identification of protein ligand binding atoms.
PolyASite is a consolidated atlas of polyadenylation sites from 3' end sequencing. A portal to the curated set of poly(A) sites that we inferred in the human, mouse and worm genomes, based on all 3’ end sequencing datasets that we could identify in the SRA nucleotide database as of June 2019.
PolyPharmacology Browser (PPB) - Web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data
Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.
A tool for population level deletion calling from short paired-end sequence reads.
An approach for reproducibly visualizing and assigning population affiliation in genomic samples of uncertain origin. Quick inference of population history. PopInf is a method to infer the major population (or populations) ancestry of a sample or set of samples. Below are steps for running PopInf. PopInf is incorporated into the workflow system snakemake. All necessary files and scripts are in this directory. There are instructions on preparing the reference panel in a folder called "Reference_Panel". There are also instructions on preparing the unknown samples in a folder called "Unknown_Samples"
Tool for linkage disequilibrium decay analysis based on variant call format files.
Network-Based Web Resource for Exploring Population Structure.
PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar databases with different species, it may need to be adjusted to fit your file names.
The Parkinson's Disease Mendelian Randomization Research Portal. iPDGC PD MR Research Portal
Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. Potpourri provides a MATLAB interface for ease of use. These instructions will guide you to build and run Potpourri on MATLAB.
Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis | Scripting languages such as Python and Bash are appreciated for solving simple, everyday tasks in bioinformatics
A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits | Gait analysis is used to quantify changes in motor function in many rodent models of disease. Despite the importance of assessing gait and motor function in many areas of research, the available commercial options have several limitations such as high cost and lack of accessible, open code. To address these issues, we developed PrAnCER, Paw-Print Analysis of Contrast-Enhanced Recordings, for automated quantification of gait. The contrast-enhanced recordings are produced by using a translucent floor that obscures objects not in contact with the surface, effectively isolating the rat's paw prints as it walks. Using these videos, our simple software program reliably measures a variety of spatiotemporal gait parameters. To demonstrate that PrAnCER can accurately detect changes in motor function, we employed a haloperidol model of Parkinson's disease (PD)
Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.
Prediction of S-nitrosylation sites by integrating support vector machines and random forest. PreSNO is only available to academic users
The PreciseDose system represents the first integrated computational environment combining classical pharmacokinetic–pharmacodynamic modeling with quantum-biological digital twin simulation. It enables organ-level prediction of drug absorption and distribution through AI-assisted algorithms and real-time numerical solvers. The system has been validated using external pharmacokinetic datasets and benchmarked against established models (Teoreler data). Outputs include physiologically accurate dose simulations and interactive 3D distribution maps. This record introduces a novel multidisciplinary advancement in precision pharmacology and computational medicine.
Fast prediction of bacteriophage Virion proteins using un-biased multi-perspective properties with recursive feature elimination | Bacteriophage virion proteins (BVPs) are bacterial viruses that have a great impact on different biological functions of bacteria. They are significantly used in genetic engineering and phage therapy applications. Correct identification of BVP through conventional pathogen methods are slow and expensive. Thus, designing a Bioinformatics predictor is urgently desirable to accelerate correct identification of BVPs within a huge volume of proteins. However, available prediction tools performance is inadequate due to the lack of useful feature representation and severe imbalance issue. In the present study, we propose an intelligent model, called Pred-BVP-Unb for discrimination of BVPs that employed three nominal sequences-driven descriptors, i.e
Prediction of disease-causing and neutral mutations in human transmembrane proteins. Transmembrane proteins (TMPs) act as a gate to the interior of the cells. A tool to discriminate the disease-causing and neutral mutations of membrane proteins. We have used 4 different type of datasets for developing the classification models and these datasets are available in the follwoing link
Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees | Prediction of protein-RNA binding affinity | PredPRBA, a computational method that can effectively predict Protein-RNA Binding Affinity using Machine Learning Algorithm
Predicting the change of percent spliced in (delta-PSI or ) caused by genetic variants.
PrimerMiner is an R package for the development and validation of DNA metabarcoding COI primers for aquatic invertebrates.
Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities | Prioritizing Cancer Drugs for Interested Cancer | Prioritize candidate cancer drugs for drug repositioning based on the random walk with restart algorithm in a drug-drug functional similarity network. 1) We firstly constructed a drug-drug functional similarity network by integrating pathway activity and drug activity derived from the NCI-60 cancer cell lines. 2) Secondly, we calculated drug repurposing score according to a set of approved therapeutic drugs of interested cancer based on the random walk with restart algorithm in the drug-drug functional similarity network. 3) Finally, the permutation test was used to calculate the statistical significance level for the drug repurposing score
Sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. This server predicts protein-protein binding affinity change upon mutation using sequence-based features and functional class. ProAffiMuSeq shows a correlation of 0.73 and a mean absolute error (MAE) of 0.86 kcal/mol in cross-validation. In the test dataset, the performance remains consistent with a correlation of 0.75 with MAE of 0.94 kcal/mol. In a blind dataset of 473 mutations (Geng et al. 2019, Proteins 87, 110-119) it showed a correlation and MAE of 0.27 and 1.06 kcal/mol, respectively, comparable to structure-based methods. Further, our method showed a MAE of 1.21 kcal/mol, when tested with a set of 552 additional non-redundant interface mutations in 80 complexes deposited in SKEMPI 2.0 (Jankauskaitė et al. 2019, Bioinformatics 35, 462-469)
a database of carbohydrate-binding proteins. An open access database ready to answer your sweetest queries. Carbohydrate-binding proteins play crucial roles across all viruses and organisms
a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection | ProGeo-neo requires a Linux operation system (centos6) with Python (V2.7) , Perl and Java installed
An online dataset for accelerating the complete characterization of the human protein-phenotype landscape in biomedical literature. Identifying protein-phenotype relations is of paramount importance for applications such as uncovering rare and complex diseases. One of the best resources that captures the protein-phenotype relationships is the biomedical literature. In this work, we introduce ProPheno, a comprehensive online dataset composed of human protein phenotype mentions extracted from the complete corpora of Medline and PubMed Central Open Access. Moreover, it includes co-occurrences of protein-phenotype pairs within different spans of text such as sentences and paragraphs. We use ProPheno for completely characterizing the human protein-phenotype landscape in biomedical literature
Web-based application for exploration and analysis of protein structures using network formalism.
Ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.
ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery. Automated online software for anticancer drug target/mechanism deconvolution. . ProTargetMiner is also available directly through this web page: http://protargetminer.genexplain.com. The ProTargetMiner R Shiny package is an automated online software for anticancer drug target mechanism deconvolution
predictor for cellular protein stability. Tool for classification of protein variations predictor. A benchmark database for variations. Datasets for training and testing cellular protein stability predictor ProTstab:. Stability of biomolecules, especially of proteins, is of great interest and significance. Protein stability has been the major target for protein engineering, mainly to increase the stability, but sometimes also to destabilize proteins . Effects on stability are among the most common consequences for disease-related variations , thus this phenomenon is of interest for variation interpretation to explain the effects of harmful variants. We trained a novel machine learning tool for prediction of protein stability, especially melting temperature Tm. The tool is based on amino acid sequence information and using GBRT (Gradient boosting of regression trees) algorithm.
Assessing the shared variation among high-dimensional data matrices. Réflexions autour de l'analyse de la variance basée sur une analyse type procuste pour estimé la part de la variance d'un tableau expliquée par un ou plusieurs autres tableaux
web-based tool for the prediction, deciphering and design of promiscuous peptides that bind to HLA class I molecules. PromPDD :HLA peptide-binding fingerprints : HLAsupE : Publication : Download: tutorial. PromPDD were developed based on the prediction models generated using the average relative binding (ARB) matrix method.PromPDD enables the prediction and deciphering of promiscuous peptides that bind to multiple HLA molecules within or cross HLA supertypes in a simpler and more direct way. We expanded the application of PromPDD to HLA class I alleles with limited experimentally verified data by generating pan-specific matrices using a derived modular method, and more than 2500 HLA molecules encoded by HLA-A and -B genes are available in PromPDD
sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence. Machine Learning using Multivariate Linear Regression to Predict the Strength of a Promoter.
Integrative tool that employs similarity matching within our customized phage parts library and machine learning of prophage genetic features, to score the probability of a prophage being active.
Proteome-wide prediction of peptide tandem mass spectra by deep learning.
Alignment-free phylogeny reconstruction based on whole-proteome sequences.
A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins | A RESOURCE FOR FUSION PROTEINS AND THEIR INTERACTIONS | Milana Frenkel-Morgenstern's Cancer Genomics and BioComputing Lab at Bar-Ilan University, Israel | Result for the search by Unspecified: | Lars Juhl Jensen's Cellular Network Biology Group at The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark | ProtFus is a resource that has information about fusion proteins and their interactions, based on a text mining approach. "Tagging" is a process of registering the mention of given entities in a particular document | Text mining has been an active research topic for decades; however, it is only fairly recently that biomedical text-mining tools have been developed that make it practically applicable to a wide range of problems
Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining. Map amino acid sites of post-translational modifications from models or data to reference positions. Code to generate results and figures relevant to the ProtMapper manuscript. The Protmapper maps references to protein sites to the human reference sequence based on UniProt, PhosphoSitePlus, and manual curation.
a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing catalytic promiscuity. ProtMiscuity contains information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 different organisms. It can be searched or browsed by protein names, organisms and descriptions of canonical and promiscuous reactions. Entries provide information on reaction substrates, products and kinetic parameters, mapping of active sites to sequence and structure and links to external resources with biological and functional annotations.
bypassing the imputation of missing values in differential expression analysis of proteomic data. Python package for differential abundance analysis of proteomics data
Solubility from protein sequence prediction.
protein quality control in E. coli | Publicly available database regarding protein quality control in E. coli | You are using an unsupported browser. Please switch to recent version of either Chrome, Firefox, Edge, Opera or Safari
Integration of structural information with interactomics data.
a taxonomic toolkit for multi-species and metaproteomic analysis. ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. What is ProteoClade? — ProteoClade 0.0.1 documentation. Free document hosting provided by Read the Docs
ProteoRE (Proteomics Research Environment) is a Galaxy-based instance for the functional analysis and the exploration of proteomics and transcriptomics data in biomedical research; ProteoRE comprises 18 tools organized into five subsections for: i) data manipulation; ii) human and iii ) mouse species database annotation; iv) functional analysis; and v) pathway analysis along with graphical representations.
Fully managed proteomics data analysis. Cloud-based proteomic data analysis that helps users go from raw MS data to results efficiently. Modern app + open source algorithms + powerful analysis tools
ProteomeHD is an R script for creating a co-regulation map of the human proteome enables identification of protein functions.
Web portal dedicated to the diatom Pseudo-nitzschia multistriata. A genome browser, a BLAST service and a download section are available.
Pseudo-nitzschia multistriata genome portal
Obtaining psychological embeddings through joint kernel and metric learning | A python package for inferring psychological embeddings | PsiZ: A Psychological Embedding Package | Experiments using the PsiZ package published in Behavior Research Methods | PsiZ provides the computational tools to infer a continuous, multivariate stimulus representation using ordinal similarity relations. It integrates well-established cognitive theory with contemporary computational methods. The companion Open Access article is available at https://link.springer.com/article/10.3758/s13428-019-01285-3 | You will need a Python interpretter (>= 3.6) along with the an installation of the psiz package (version 0.1.0) in your preferred environment. You can install the correct version of the psiz package using pip: pip install psiz==0.1.0. You can also find version 0.1.0 on GitHub: https://github.com/roads/psiz/archive/v0.1.0.tar.gz
An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translational annotations to de novo variants, which are found in subjects but not in their parents, in developmental and neuropsychiatric disorders. Large-scale genomic and proteomic data are integrated into PsyMuKB, including developmental brain expressions, neuronal single-cell transcriptome, regulatory elements, and transcript annotations, protein-protein interactions (PPI) and protein isoform expressions. It aims to provide users with a comprehensive data exploration of de novo variants, such as their genomic locations on alternatively spliced isoforms, expression patterns of the mutation-disrupted genes and/or isoforms, and interaction network of impacted proteins
Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles.
Web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.
a curated lung disease gene expression database | An accessible R package to download PulmonDB data | PulmonDB is a transcriptomic database of IPF and COPD with curated annotation | PulmonDB is a gene expression database with Chronic Obstructive Pulmonary Diseases (COPD) and Idiopathic Pulmonary Disease (IPF) experiments. It has homogenized values using individual contrast and manual curated annotation that can be download or accessed by http://pulmondb.liigh.unam.mx
Punchline is a tool for identifying and comparing significant Pfam protein domain differences across draft whole genome sequences.
Efficient and accurate prediction of transmembrane topology from amino acid sequence only.
Software tools for automated transmission electron microscopy.
A Global Optimizer for Nanoclusters. Python program for aggregation and reaction. PyAR stands for "Python program for aggregation and reaction"
A command-line tool for analysis of big biological data sets for distributed HPC clusters.
A general-purpose program for parameterizing biological models specified using the BioNetGen rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML).
Python package for easy retrieval of biological data from heterogeneous sources.
Discontinuous Boundary Elements for Fluid Flow Problems in Discrete Fracture Networks. Modeling fluid flow in three-dimensional (3D) Discrete Fracture Networks (DFNs) is of relevance in many engineering applications, such as hydraulic fracturing, oil gas production, geothermal energy extraction, nuclear waste disposal and CO2 sequestration. A new Boundary Element Method (BEM) technique with discontinuous quadratic elements and a parallel Domain Decomposition Method (DDM) is presented herein for the simulation of the steady-state fluid flow in 3D DFN systems with wellbores, consisting of planar fractures having arbitrary properties and wellbore trajectories. Numerical examples characterized by DFNs of increasing complexity are investigated to evaluate the accuracy and efficiency of the presented technique.
Python-based effective feature generation tool for DNA, RNA and protein sequences.
scalable data extraction and analysis for heterogeneous genomic datasets. Python Library for data analysis based on GMQL. The doucumentation can be found at the following link: http://pygmql.readthedocs.io. API for calling interactively the GMQL Engine from Python
An open-source Pythonic library to compute landscape metrics. Open-source Python library to compute landscape metrics. Example notebooks of the PyLandStats library. Test and Deploy Your Code with Confidence. Test Coverage History & Statistics. PyLandStats documentation! — PyLandStats 2.0.0a1 documentation. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". PLOS ONE, 14(12), 1-19. doi.org/10.1371/journal.pone.0225734. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". Preprint available at bioRxiv. https://doi.org/10.1101/715052. Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you'll be testing your code in minutes. Test code coverage history for martibosch/pylandstats. Open-source Pythonic library to compute landscape metrics within the PyData stack (NumPy, pandas, matplotlib...)
Python Library to Build Screens in a Declarative Way | Python library to develope paradigms for psychological experiments | PyParadigm is a small library to build paradigms for psychological experiments. It utilizes pygame, and is installable via pip | Welcome to PyParadigm — PyParadigm 0.1 documentation | PyParadigm is a small set of classes and functions designed to make it easy to write psychological paradigms in Python | PyParadigm takes another approach
An improbability drive for rare events. pyretis - Rare Event Simulations with python. PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling .
PyRadiomics is an ontology-guided radiomics analysis workflow (O-RAW).
> CORRECT NAME OF TOOL COULD ALSO BE 'AVAILABILITY:PyRanges' | efficient comparison of genomic intervals in Python | (beta) Performant Pythonic GenomicRanges | PyRanges are collections of intervals that support comparison operations (like overlap and intersect) and other methods that are useful for genomic analyses. The ranges can have an arbitrary number of meta-data fields, i.e. columns associated with them | PyRanges is in a beta state. We are extremely responsive to bug-reports, so if you have problems or come across unexpected behavior, please create an issue | GenomicRanges and genomic Rle-objects for Python | Feel free to ask questions of the type "how do I do X with pyranges?" on public forums like Stack Overflow, Bioinformatics Stack Exchange or Biostars. You can use endrebak85#gmail.com to point me to the question(s) | "Finally ... This was what Python badly needed for years." - Heng Li
Python framework for rate-based neural simulations. PyRates is a framework for neural modeling and simulations, developed by Richard Gast and Daniel Rose at the Max Planck Institute of Human Cognitive and Brain Sciences, Leipzig, Germany. Max Planck Institute for Human Cognitive and Brain Sciences. Welcome to the PyRates documentation! — PyRates 0.7.1 documentation. Welcome to the PyRates documentation!¶. PyRates is a Python 3 tool for building rate-based neural models and performing numerical simulations of their dynamic behavior. Efficient software solutions for building and analyzing neural models are of tremendous value to the field of computational neuroscience. Open-source Python toolbox for rate-based neural modeling. PyRates requires an installation of Python >=3.6.1
Software developed to generate dynamic molecular interaction fields (dMIFs) and pharmacophore features based on analyzing the protein environment of water molecules in molecular dynamcis simulations.
PySpacell is a Python Package for Spatial Analysis of Cell Images. Technologies such as microscopy, sequential hybridization, and mass spectrometry enable quantitative single-cell phenotypic and molecular measurements in situ. Deciphering spatial phenotypic and molecular effects on the single-cell level is one of the grand challenges and a key to understanding the effects of cell-cell interactions and microenvironment. However, spatial information is usually overlooked by downstream data analyses, which usually consider single-cell read-out values as independent measurements for further averaging or clustering, thus disregarding spatial locations. With this work, we attempt to fill this gap. We developed a toolbox that allows one to test for the presence of a spatial effect in microscopy images of adherent cells and estimate the spatial scale of this effect.
a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites. volume calculation and segmentation. PyVOL: Protein Pocket Visualization, Segmentation, and Characterization. PyVOL is a python library packaged into a PyMOL GUI for identifying protein binding pockets, partitioning them into sub-pockets, and calculating their volumes
A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model Organisms | Pyntheon; A post translational modifications (PTMs) mapping tool for 87 different species, these PTMs are taken from a large array of popular lab specimens | we are presenting, Universal Functional PTMs Mapping Tool (Pyntheon) which maps post translational modifications (PTMs) present in the functional regions of proteins of almost all lab specimens that are popular among research community. From viruses to human, this tool includes 87 species (see species_id.txt) can help mapping the mutations to PTMs sites or give information about the PTMs present for a list of proteins (UniProt ID) of interest
a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica | Pipeline to automate the processing of amplicon data | PypeAmplicon v1.0: Python pipeline for analysis of amplicon data | Wijeratne S & Pavinato VAC. (2018, November 17). PypeAmplicon: Python pipeline for analysis of amplicon data (Version v1.0). Zenodo. doi: http://doi.org/10.5281/zenodo.1490421
An automatic pipeline for macaque functional MRI preprocessing. Non-human primate functional MRI (fMRI) is a growing field in neuroscience. However, there is no standardized method for monkey fMRI data analysis, specifically for data preprocessing. The preprocessing of monkey fMRI data is challenged by several technical and experimental specificities of the monkey research such as artifacts related to body movements or to intracranial leads. Here we propose to address these challenges by developing a new versatile pipeline for macaque fMRI preprocessing. We developed a Python module, Pypreclin, to process raw images using state of the art algorithms embedded in a fully automatic pipeline. To evaluate its robustness, we applied Pypreclin to fMRI data acquired at 3T in both awake and anesthetized macaques, with or without iron oxide contrast agent, using single loop or multichannel phased-array coils, combined or not with intracranial implanted electrodes.
PythonVideoAnnotator is a graphical application written in Python, to analyze and create notes for events in videos. It was developed with the aim of helping neuroscience and ethology researchers to identify animals’ behaviors based on the information extracted from the video.
Quantitative hyperspectral image unmixing (Q-HIU) method is intended for quantitative data analysis of multi-set and individual Raman micro-spectroscopy images, allowing to efficiently retrieve non-negative spatial concentration maps and non-negative spectral profiles of the images’ chemical constituents (components) with no a priori information, minimum input parameters, and great operation speed.
Can We Use Satellite-Based FAPAR to Detect Drought? | Quality Assurance for Essential Climate Variables | The FP7 QA4ECV project was initiated in 2014 to demonstrate how reliable and traceable quality information can be provided for satellite and ground-based measurements of climate and air quality parameters. The project developed and applied a Quality Assurance framework on new and improved multi-decadal data records of the Land ECVs Albedo, Leaf Area Index (LAI), and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), and of the Atmosphere ECVs nitrogen dioxide (NO2), formaldehyde (HCHO), and carbon monoxide (CO) | We encourage you to browse through the website and survey the scope of QA4ECV activities
Quantitative predictions of transcription factor binding changes due to sequence variants.
A tool for real-time quality control assessment of mass spectrometry-based proteomics data.
Web-Tool for Performance Diagnosis and Prediction of liquid chromatography-mass spectrometry (LC-MS) Systems.
QGIS is a free and open source Geographic Information System.
Statistical procedure for genome-wide detection of QTL hotspots using public databases.
Distance Constraints Applied on Model Quality Estimation. QMEAN, the Qualitative Model Energy ANalysis, is a composite scoring function assessing the major geometrical aspects of protein structures. Estimates of structure quality are provided for full structures as well as on a local per residue scale. QMEAN Qualitative Model Energy ANalysis. QMEAN - Qualitative Model Energy ANalysis. Reference for the QMEANDisCo scoring function:. For optimum performance, please add the SEQRES of your model here. Merge branch 'release-3.1.0' · 3c2b6012. Local quality is either estimated using the raw QMEAN scoring function or one of the two specialized functions QMEANBrane and QMEANDisCo. They all provide scores in range [0,1] with one being good. Reference for the QMEAN scoring function:
The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure.
A Researcher-Patient Matching Platform and Multimodal Biorepository. WELCOME TO QUEBEC PARKINSON NETWORK. Quebec Parkinson Network now allows researchers, clinicians and patients to regroup. Promoting collaboration of different actors in the fight against Parkinson's disease, the Network wants to be the new leader of the research on the disease. Support, act and help researchers and clinicians in the fight against Parkinson's disease by participating in research projects. For more information, visit the Participants section. Congress of the “Société Francophone Posture, Équilibre et Locomotion” (SOFPEL) – December 4 & 5, 2019
an unofficial research purposed implementation of ClinRisk’s QRISK3 algorithm into R. 10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017). This function aims to calculate risk of developing cardiovascular disease of individual patients in next 10 years. The package was based on published risk prediction algorithm <https://qrisk.org/three/src.php>. A QRISK3 R package implements QRISK3 algorithm into R. Validation of CRAN R package "QRISK3". This respiratory provides the validation programs including QRISK3 SAS macro and original C function for CRAN package "QRISK3" for transparency and replication. Welcome to the QRISK ® 3-2018 risk calculator https://qrisk.org/three. This calculator is only valid if you do not already have a diagnosis of coronary heart disease (including angina or heart attack) or stroke/transient ischaemic attack
Reconstructing Phylogenetic Networks Based on Quartet and Sextet | User Manual for QS-Net Introduction The QS-Net is a phylogenetic network reconstruction method taking advantage of information on the relationship among six taxa
Comprehensive ensemble in QSAR prediction for drug discovery. There exist a new type of QSAR individual classifier that is an end-to-end neural network model based on 1D-CNN and RNN. It extracts sequential features automatically from the SMILES.
Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models.
Clinical Integration of Automated Processing for Brain Quantitative Susceptibility Mapping | Cornell MRI Research Lab Research Interests | Quantitative Susceptibility Mapping | Quantitative Susceptibility Mapping (QSM) provides a map of local tissue magnetic susceptibility
A Bulked Segregant Analysis and Visualization Pipeline for QTL-seq | In recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic trait values, has gained increasing popularities in research community. However, there is no publicly available user friendly software for the identification and visualization. Hence, we developed a tool named QTL-BSA (QTL-bulked segregant analysis and visualization pipeline), which could facilitate the rapid identification and visualization of candidate QTLs from QTL-seq. As a proof-of-concept study, we have applied the tool for the rapid discovery and the identification of genes related with the partial blast resistance in rice
an integrative resource for quantitative trait loci across multiple human molecular phenotypes. QTLbase curates and compiles genome-wide QTL summary statistics for many human molecular traits across over 70 tissue/cell types. The database comprises tens of millions significant genotype-molecular trait associations under different conditions. Users can visualize QTL results in phenome-wide and tissue-wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides a one-stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation
R package for random-effect multiple quantitative trait loci (QTL) mapping in autopolyploids.
Automating the Derivation of Force Field Parameters from Quantum Mechanics. Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites.
A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data | A novel biclustering algorithm for analyses of transcriptomic data | QUBIC2 is a novel biclustering algorithm for analyses of gene expression data from bulk and single-cell RNA-Sequencing. This introductory vignette provides an overview of installation and usage
> HOMEPAGE MISSING! | An Automated Protocol for Free Energy Calculations of Protein Mutations in Q | Predicting the effect of single-point mutations on protein stability or protein-ligand binding is a major challenge in computational biology. Free energy calculations constitute the most rigorous approach to this problem, though the estimation of converged values for amino acid mutations remains challenging. To overcome this limitation, we developed tailored protocols to calculate free energy shifts associated with single-point mutations. We herein describe the QresFEP protocol, which includes an extension of our recent protocols to cover all amino acids mutations, based on the latest versions of the OPLS-AA force field. QresFEP is implemented in an application programming interface framework and the graphic interface QGui, for the molecular dynamics software Q
Overcoming computational bottlenecks in sequence quality control. Abstract With the recent torrent of high throughput sequencing (HTS) data the necessity for highly efficient algorithms for common tasks is paramount. One task for which the basis for all further analysis of HTS data is initial data quality control, that is, the removal or trimming of poor quality reads from the dataset. Here we present QuAdTrim, a quality control and adapter trimming algorithm for HTS data that is up to 57 times faster and uses less than 0.06% of the memory of other commonly used HTS quality control programs. QuAdTrim will reduce the time and memory required for quality control of HTS data, and in doing, will reduce the computational demands of a fundamental step in HTS data analysis. Additionally, QuAdTrim impliments the removal of homopolymer Gs from the 3’ end of sequence reads, a common error generated on the NovaSeq, NextSeq and iSeq100 platforms
A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology. QuantiMus is a machine-learning based program used for histological analysis of skeletal muscle. Developed as a plugin for the image analysis tool flika, QuantiMus is a versatile, fast, and precise to complete histological analysis. QuantiMus is written in Python and is open-source
Decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery.
Modern general-purpose multi-threaded quantum computing library.
an integrated platform of electronic and atomic-scale modelling tools | QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals
Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence | Code for computing various support scores for internodes | See http://www.biorxiv.org/content/early/2017/07/27/168526 for the preprint | If you cannot find our supplementary text, please download it from here: https://github.com/lutteropp/QuartetScores/issues/4
Query Tabular is a Galaxy-based tool which manipulates tabular files. Query Tabular automatically creates a SQLite database directly from a tabular file within a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting.
Collection of C++ code snippets, that can be picked and combined to build complex, spatially explicit population genetics simulators and inference frameworks.
QuiC generates quality control metrics for liquid chromatography and mass spectrometry in near real-time from raw files from various vendors and bottom-up proteomics workflows using a commercially available standard. Requires Biognosys iRT Kit to enable automated, fast and accurate QC monitoring of your data sets.
Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.
Tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. R-BIND: The RNA-Targeted BIoactive ligaNd Database. The dataset includes only bioactive ligands with demonstrated activity in cell culture and/or animal models. This database is expected to expedite the discovery of RNA chemical probes. R-BIND was created by the Hargrove Lab at Duke University
R2 is a biologist friendly web based genomics analysis and visualization application
a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. Recently, the success of AlphaFold on creating 3D protein models demonstrates sequence-dependent inference plays a crucial role in computational proteomics. A web server of reduced amino acid alphabet for sequence-dependent inference
RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting Therapeutics | Pipeline for the downstream analysis of 5-RACE Next Generation Sequencing experiments | This is a custom R script for the downstream analysis of RACE-seq data | To run the RACE-SEQ-lite script you will need to have an R version ( >=3.4) installed on your system. All the necessary R packages will get installed and loaded automatically
rapid analysis of ChIP-Seq data for contig based genomes. RACS: Rapid Analysis of ChIP-Seq data for contig based genomes -- repository
Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices | BACKGROUND:With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field
Computationally efficient de novo locus assembler for population studies using RADseq data.
Database of enhancers identified by high-throughput reporter assays.
Webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach.
A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae.
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Alu', 'III-transcribed', 'Pol III-transcribed', 'III-transcribed Alu' | Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function | Pipeline to identify expressed Alu elements using RAMPAGE | A schematic flow shows the pipeline
Tool for node label ranking and classification in biological networks.
RAPPAS stands for Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences. It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment.
RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms. The purpose of this web portal is to facilitate the discoverability of these data. RARe search is an implementation of DataDiscovery.
An RNA-Seq Analysis Workflow with Snakemake. RASflow: RNA-Seq Analysis Snakemake Workflow
R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework.
Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
Enables robust generation of splicing regulatory maps and rapid query of regulatory patterns of RNA binding protein (RBP) of interest.
RBP atlas is an interactive online data mining tool.
tool for prioritising copy number variations in germline conditions. Validating copy number variants from using allele balance from NGS data. RBV: Read Balance Validator is a corroborates copy number variants (CNV) from whole exome and whole genome sequence data. It uses the relative reads for the reference and alternative allele at a given position (the read balance) to determine the probability that a putative CNV is real
RCMF is a robust collaborative matrix factorization method to predict miRNA-disease associations.
RCSM(Recommended Connectivity-map Scoring Methods) is a comprehensive evaluation of connectivity methods for L1000 data.
Extends the RDF import and export functionality in Semantic MediaWiki (SMW) to enable using SMW as a collaborative platform for editing semantic data.
RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel.
> TOOL (matuskalas) | Comprehensively benchmarking applications for detecting copy number variation | The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group Note: (matuskalas): Lumpy (or lumpy-sv) is a completely different tool, atm missing in bio.tools (https://github.com/arq5x/lumpy-sv)
A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs. The goal of the Retinal Fundus Glaucoma Challenge (REFUGE) is to evaluate and compare automated algorithms for glaucoma detection and optic disc/cup segmentation on a common dataset of retinal fundus images.
A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Currently, The database includes about 700 samples of 50 public studies that were reprocessed by our refined pipeline. The database also contains ENCODE histone ChIP-seq and DNase-seq data to correlate m6A modifications. It provided multi-dimensional information (e.g. cell or tissue specificity) to query m6A modification relevance in cellular processes. In addition, a built-in modern genome browser presented a comprehensive atlas of m6A modifications which is helpful to visualize m6A modification sites between different samples and conditions.
R package for associating evolutionary rates with convergent traits.
Robust intEnSiTy nORmalization mEthod for Multiplexed Imaging.
Random Forest Quality Assessment to identify a predicted protein structure in the correct fold.
a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression | RF model and functions to estimate tumor purity using methylation data | Install minfi and RF_purify package from GitHub | R-package to predict ABSOLUTE and ESTIMATE tumor purity using a Random Forest regression model trained on TCGA Illumina 450k DNA-methylation array data. Purity prediction functions can be applied to 450k and 850k array data preprocessed with the Bioconductor package minfi
Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
RGADE is a tool with genomic features and differential expression of the innate immune system from a smut-resistant genotype.
RGRPT is a New Algorithm for Identifying Genome Rearrangements in the Mammalian Evolution. Genome rearrangements are the evolutionary events on level of genomes. It is a global view on evolution research of species to analyze the genome rearrangements. We introduce a new method called RGRPT (recovering the genome rearrangements based on phylogenetic tree) used to identify the genome rearrangements. We test the RGRPT using simulated data. The results of experiments show that RGRPT have high sensitivity and specificity compared with other tools when to predict rearrangement events. We use RGRPT to predict the rearrangement events of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog). RGRPT has recognized a total of 1,157 rearrangement events for them at 10 kb resolution, including 858 reversals, 16 translocations, 249 transpositions, and 34 fusions fissions.
a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progression of cancer, such as breast cancer, lung cancer and so on. RHPCG serves as a valuable resource for understanding the roles of Hippo signaling pathway in carcinogenesis. The features of RHPCG contain: (i) the landscape of Hippo gene alterations at multiple omics level; (ii) quick search Hippo regulatory motifs by mRNA, lncRNA, circRNA or miRNA; and (iii) all the Hippo related motifs can be visualized as network and be downloaded freely
The RICE-GUARD project will develop a wireless sensor network comprised of low-cost measurement nodes that will be capable of transmitting readings of the relevant in-field site-specific environmental variables in real-time to a central server. Rice blast is the most serious disease of cultivated rice. It is caused by the fungus Magnaporthe grisea (Pyricularia oryzae Cav.), which in favourable conditions can produce yield losses of up to 100 %. Although rice blast is present wherever rice is cultivated, its intensity (incidence and severity of disease) is highly variable and depends on cropping system and climate.
Rapid Imputation for COnsortias PIpeLIne | Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies | RICOPILI: Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies by Stephan Ripke is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Based on a work at https://sites.google.com/a/broadinstitute.org/ricopili/download
Medical Imaging Dataset Annotation Tool for and with Deep Learning.
Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions.
Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment.
web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations | The RIPper is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in genome sequences of Ascomycota | The RIPper was built using Asp.Net Core with an AngularJs based front-end and uses session storage to keep a users files for a defined amount of time. The RIPper has no account or database requirements
drawing SVG graphics to visualize and map genome-wide data on the idiograms | Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms | For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species | RIdeogram is a R package to draw SVG graphics to visualize and map genome-wide data on idiograms (Scalable Vector Graphics http://tutorials.jenkov.com/svg/index.html)
Tool for RNA–RNA interaction extraction from the literature.
Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).
Multiple-kernel learning for genomic data mining and prediction | Multiple Kernel Learning for Classification or Regression Problems | Provides R and C++ function that enable the user to conduct multiple kernel learning (MKL) and cross validation for support vector machine (SVM) models. Cross validation can be used to identify kernel shapes and hyperparameter combinations that can be used as candidate kernels for MKL. There are three implementations provided in this package, namely SimpleMKL Alain Rakotomamonjy et. al (2008), Simple and Efficient MKL Xu et. al (2010), and Dual augmented Lagrangian MKL Suzuki and Tomioka (2011) <doi:10.1007/s10994-011-5252-9>. These methods identify the convex combination of candidate kernels to construct an optimal hyperplane
R package for a Boolean sensitivity analysis against various types of mutations.
A transcriptional toolbox for exploring peripheral neuro-immune interactions. Abstract Correct communication between immune cells and peripheral neurons is crucial for the protection of our bodies. Its breakdown is observed in many common, often painful conditions, including arthritis, neuropathies and inflammatory bowel or bladder disease. Here, we have characterised the immune response in a mouse model of neuropathic pain using flow cytometry and cell-type specific RNA sequencing (RNA-seq). We found few striking sex differences, but a very persistent inflammatory response, with increased numbers of monocytes and macrophages up to 3½ months after the initial injury. This raises the question of whether the commonly used categorisation of pain into “inflammatory” and “neuropathic” is one that is mechanistically appropriate. Finally, we collated our data with other published RNA-seq datasets on neurons, macrophages and Schwann cells in naïve and nerve injury states
discovering somatic coding indels from tumor RNA-Seq data. Somatic indel discovery tool for tumor RNA-Seq data. RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. You can also use RNAIndel as a postprocessor to classify indels called by your own caller. RNAIndel supports GRCh38 and 37
Fixed-parameter tractable sampling for RNA design with multiple target structures.
visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix. A pipeline to detect sample mix-ups in RNASeq data. Generate a sample similarity matrices from RNASeq data. Sample confusion is a common laboratory problem. In RNASeq this is frequently tested for by checking whether sex-specific genes (e.g. those located on the Y chromosome or the X inactivation gene) are congruent with the sex listed for that sample in the metadata. However, this method cannot be used to detect sample confusion between patients of the same sex, and is less sensitive when the phenotype skews the sex ratio of samples away from 1:1. Here we present a tool that leverages RNASeq reads to call genomic SNPs, and use that to generate a similarity matrix between all samples to detect sample confusion. git clone https://github.com/nicokist/RNASeq_similarity_matrix
Prediction of mRNA subcellular localization using deep recurrent neural networks | RNATracker is a deep learning approach to learn mRNA subcellular localization patterns and to infer its outcome. It operates on the cDNA of the longest isoformic protein-coding transcript of a gene with or without its corresponding secondary structure annnotations. The learning targets are fractions/percentage of the transcripts being localized to a fixed set of subcellular compartments of interest
a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associations between drug sensitivity and RNA molecules including mRNAs, lncRNAs and miRNAs at four molecular levels (expression, copy number variation, mutation and methylation) from integrated analysis of three large-scale pharmacogenomic databases (GDSC, CellMiner and CCLE). Currently, RNAactDrug contains more than 4924200 RNA molecules-drug sensitivity associations at multidimensional molecular levels covering more than 19770 mRNAs, 11119 lncRNAs, 438 miRNAs and 4155 drugs. RNAactDrug aims to help make use of the full breadth and depth of existing large-scale pharmacogenomic data by making this knowledge accessible to both basic researchers
Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise interactions, reflecting nearly 120 years of computation time on the CRG's high-performance computing cluster. It combines experimentally identified interactions (e.g. from ENCODE) with ab initio predictions, enabling full coverage of the RNA-binding proteome.
RNAdemocracy is an ensemble method for RNA secondary structure prediction using consensus scoring.
An online tutorial and data portal for the RNA structurome era. This is an animated dialog which is useful for displaying. Timeline of HTS-associated RNA structure probing methods
RNAfamProb Program, Program for Estimations of Posterior Probabilities on RNA Structural alignment. NeoFold Program, Program for Maximum-expected-accuracy Estimations of RNA Secondary Structures with Incorporating Homologous-RNA sequences. This project provides the RNAfamProb program, a program for estimations of posterior probabilities on RNA structural alignment. This project provides the NeoFold Program, a program for the maximum-expected-accuracy estimations of RNA secondary structures with incorporating homologous-RNA sequences. This project has been written in mainly Rust, a systems programming language.
Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition. RNAm5CPred: A webserver for RNA 5-methylcytosine sites prediction. A webserver for RNA 5-methylcytosine sites prediction. RNAm5CPred was developed by using support vector machine based on three different kinds of nucleotide composition features including KNF (K-nucleotide frequencies), KSNPF (K-spaced nucleotide pair frequencies) and pseDNC (pseudo dinucleotide composition). The input for the server is the RNA sequence. More details can be found in the tutorial
RNAsamba is a tool for computing the coding potential of RNA sequences using a neural network classification model. It can be used to identify mRNAs and lncRNAs without relying on database searches.
Efficient utilization on PSSM combining with recurrent neural network for membrane protein types prediction | RNN-for-membrane-protein-types-prediction | This repo includes the implementation of preprocessing for proteins and network architecture for training
RNSCLC-PRSP software to predict the prognostic risk and survival in patients with resected T1-3N0-2 M0 non-small cell lung cancer | Background:The clinical outcomes of patients with resected T1-3N0-2M0 non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic prediction tools have been reported in many published studies, a convenient, accurate and specific prognostic prediction software for clinicians has not been developed. The purpose of our research was to develop this type of software that can analyze subdivided T and N staging and additional factors to predict prognostic risk and the corresponding mean and median survival time and 1-5-year survival rates of patients with resected T1-3N0-2M0 NSCLC. Results:Using a Cox proportional hazard regression model, we determined the independent prognostic factors and obtained a prognostic index (PI) eq
Data repository of NIH Roadmap Epigenomics Mapping Consortium containing genome-wide maps of histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues.
An Abstraction Layer and User Interface for Knowledge Graphs to Support Question Answering | ROBOKOP is a tool for reasoning over structured biomedical knowledge databases as part of the NCATS translator and reasoner programs. The ROBOKOP system consists of a web based user interface, an API server, and several worker servers. The code is separated into three separate repositories
ROBOKOP KG is an Integrated Knowledge Graphs from Federated Sources.
A Tool for Automating Ontology Workflows | ROBOT is a tool for working with Open Biomedical Ontologies | R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019 | ROBOT is a tool for working with Open Biomedical Ontologies. It can be used as a command-line tool or as a library for any language on the Java Virtual Machine | If no --reasoner is provided, ROBOT will default to ELK. The following other reasoner options are supported: | ROBOT will always perform a logical validation check prior to automatic classification | Equivalent Classes (--equivalent-classes-allowed) | Generated Axioms(--axiom-generators)
Joint inference of Runs of Homozygosity and rates of heterozygosity
Powerful analysis strategy for LC-MS metabolomic datasets.
a light-weight R package for interfacing with OMOP-formatted electronic health record data. R package to easily interface with OMOP-formatted EHR data. ROMOP, please wait... This may take a minute or two. Launching ROMOP, please wait... This may take a minute or two. ... ROMOP is a flexible R package to interface with the Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model. Briefly, OMOP is a standardized relational database schema for Electronic Health Record (EHR) or Electronic Medical Record (EMR) data (i.e., patient data collected during clinical visits to a health system). The main benefit of a standardized schema is that it allows for interoperability between institutions, even if the underlying EHR vendors are disparate. Benjamin S. Glicksberg 9/14/2018
RPAND is an R package for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade–clade competitive effects or the effect of species richness on phenotypic divergence.
RPGeNet v2.0 - Retinitis Pigmentosa Gene Network: interacting with the network of genes related to retinitis pigmentosa genes.
Hierarchical deep learning model for predicting ncRNA-protein interaction.
Heart rate variability analysis software. BACKGROUND AND OBJECTIVES:Heart rate variability (HRV) has increasingly been linked to medical phenomena and several HRV metrics have been found to be good indicators of patient health. This has enabled generalised treatment plans to be developed in order to respond to subtle personal differences that are reflected in HRV metrics. There are several established HRV analysis platforms and methods available within the literature; some of which provide command line operation across databases but do not offer extensive graphical user interface (GUI) and editing functionality, while others offer extensive ECG editing but are not feasible over large datasets without considerable manual effort
Reduced representation bisulfite sequencing simulator for next-generation sequencing.
UCSF Chimera tool for viewing and comparing protein distance maps.
Evolutionary-oriented database of RNA recognition motif sequences.
A new, fast method to search for morphological convergence with shape data. The goal of RRphylo is to compute phenotypic evolutionary rates, estimate ancestral states, locate rate shifts on the tree, and compare vectors of phenotypes and evolutionary rates among species. RRphylo is not based on any evolutionary model, and is best suited to work with phylogenies of fossil species.
Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.
Starting from a list of genes, returns upstream or downstream sequences.
Accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.
Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences.
Regulostat Inferelator (RSI) - network biology platform to uncover molecular devices that predetermine cellular response phenotypes.
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy.
Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma | Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The source for the 'SQLite' engine is included
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'RT', 'TRNs', 'TRNs RT', 'provocative' | Replication timing networks reveal a link between transcription regulatory circuits and replication timing control | Create community RT network For RT Networks visualization. It will return None, but creates txt file for the input for the SAFE algorithm | > pip install -r requirements.txt | Before running below do_something.py, please edit parameters in each file
RUFUS is a Pedigree-based estimation of human mobile element retrotransposition rates.
Removing Unwanted Variation-III (RUV-III) - normalization for Nanostring nCounter gene expression data.
RXN is a unique tool for digital chemistry, based on the Molecular Transformer, using a simple Ketcher drawing interface and made it available on IBM Cloud to perform a variety of tasks: converting Experimental Protocols into Action Sequences, predicting Chemical Reactions, Retrosynthesis Pathways, Experimental Procedures and automating the compilation and execution of Chemical Syntheses.
Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet.
Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations.
fast and accurate reference-guided scaffolding of draft genomes. Fast Reference-Guided Scaffolding of Genome Assembly Contigs. Index of /shares/schatzlab/www-data/ragoo. A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome. Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17. Contigs and reference fasta files may now be gzipped. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:
RaNA-Seq is an open bioinformatics tool for the quick analysis of RNA-Seq data. It performs a full analysis in minutes quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the interpretation of results with functional analyses. Our analysis pipeline integrates cutting edge bioinformatics tools and simplify its application with a friendly Web interface designed for non-experienced users in these analyses. Each analysis can be customized setting up input parameters and applies generally accepted and reproducible protocols. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication.
Consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
Identification of radical amino acid changes in multiple sequence alignments.
Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R | Filter plant hydroxyproline rich glycoproteins | ragp - hydroxyproline aware filtering of hydroxyproline rich glycoprotein sequences | ragp is an R package primarily designed for mining and analysis of plant hydroxyproline rich glycoproteins. It incorporates a novel concept with an additional analysis layer where the probability of proline hydroxylation is estimated by a machine learning model. Only proteins predicted to contain hydroxyprolines are further analysed for HRGP characteristic motifs and features. ragp can also be used for protein annotation by obtaining predictions for several protein features based on sequence (secretory signals, transmembrane regions, domains, glycosylphosphatidylinositol attachment sites and disordered regions). Additionally ragp provides tools for visualization of the mentioned attributes
RainBio is a visual tool for comparing gene sets or protein sets, in a proportional way. RainBio is an alternative to the classical Venn diagrams and Euler diagrams. In particular, RainBio can compare up to 15 sets, while Venn diagrams are limited to 6, and proportional Venn diagram are approximated above 4 sets. RainBio can perform the exact proportional visualization of up to 6 sets, and support intersection clustering, allowing to visualize up to 15 sets. RainBio uses the same file format that InteractiVenn. Several demo datasets are available on the website.
Rare Metabolic Diseases Database: platform independent, web-based information system for rare metabolic diseases based on filed case reports.
Spectral characteristics of urine specimens from healthy human volunteers analyzed using Raman chemometric urinalysis (Rametrix) | Raman chemometric urinalysis (Rametrix™) was used to analyze 235 urine specimens from healthy individuals. The purpose of this study was to establish the "range of normal" for Raman spectra of urine specimens from healthy individuals. Ultimately, spectra falling outside of this range will be correlated with kidney and urinary tract disease. Rametrix™ analysis includes direct comparisons of Raman spectra but also principal component analysis (PCA), discriminant analysis of principal components (DAPC) models, multivariate statistics, and it is available through GitHub as the Rametrix™ LITE Toolbox for MATLAB®. Results showed consistently overlapping Raman spectra of urine specimens with significantly larger variances in Raman shifts, found by PCA, corresponding to urea, creatinine, and glucose concentrations
An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi. A package for arbuscular mycorrhyzal fungi colonization. Marco Chiapello , Debatosh Das, Caroline Gutjahr. Ramf: An open-source R package for statistical analysis and display of quantitative root colonization by arbuscular mycorrhiza fungi. _Frontiers Plant Science_. **In press**. If you use the package, please cite it:
R-program supporting the initial step of the workflow of 13C assisted fluxomic analysis: extraction of mass spectra (MS) of 13C-labeled metabolites of interest from raw mass spectrometer recordings saved in NetCDF files.
A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics. RankerGUI platform for the comparison of differential expression profiles using a rank-based statistical approach. RankerGUI automates the analysis of complex gene expression signatures. The Pipeline is easy to use and freely available to the scientific community. Users can upload data via a web page and can be notified of the analysis completion by email. The output includes detailed data analysis reports and diagrams. Documentation provides full information on used methods
Measuring Rapid A-Ci Curves in Boreal Conifers. R scripts for automatic correction of Rapid A-Ci curves. An R package for the batch treatment of Rapid carbon dioxide response curves (A-Ci) generated by the LI-COR® portable photosynthesis systems. The Rapid A-Ci measurement method (RACiR™) can save a lot of time characterising photosynthetic capacity of multiple plants. devtools::install_github("ManuelLamothe/RapidACi"). If, later on, you need to adjust leaf area values, you need to provide a dataframe containing at least one column for the unique sample identifier (named: “sample_ID”), and one column with the leaf area in mm2 (named: “LeafArea_mm2”)
A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning.
a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present in the humans. Deficiency or malfunctioning of any enzyme leads to accumulation of toxic metabolites and thus, various storage defects. One major application of this database is, all the necessary information about these enzymes can be found in this portal
RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data. The Rat Genome Database (RGD) was established in 1999 and is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. In addition, it provides easy access to corresponding human and mouse data for cross-species comparisons. RGD's comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.
3D graphics python package for cognitive psychology experiments.
Rare variant association testing for multicategory phenotype.
raxmlGUI1,2 is a graphical user interface to RAxML3, one of the most popular and widely used software for phylogenetic inference using maximum likelihood.
Rbbt stands for “Ruby Bioinformatics Toolkit”. It is a framework for software development in bioinformatics. It covers three aspects:. Workflow wrapping the TF text-mining results from https://github.com/fnl plus other databases. High Throughput Sequencing related functionalities. Rbbt wrapper for the Variant Effect Predictor. Auto-downloads and installs the software.
An R Package for Automated Chimerism Data Analysis.
Prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays.
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data | User interface to reanalyze and explore all public data in Metabolomics Public Data | Reanalysis of Data User Interface for MS2 (ReDU) | Compare Your Data to Public Data via Multivariate Analysis | ReDU is a community- and data-driven approach to find and reuse public data containing tandem MS data at the repository scale. ReDU is a launchpad for co- or re-analysis of public data via the Global Natural Product Social Molecular Networking Platform (GNPS). Our aim is to empower researchers to put their data in the context of public data as well as explore questions using public data at the repository scale | Reanalysis of Data User Interface | Projection of your data onto a precalculated principal components analysis score plot of public data
A Repository of Functional Dashboards providing comprehensive functional insights inferred from 16S microbiome data sets | Motivation: 16S rRNA gene amplicon based sequencing has significantly expanded the scope of metagenomics research by enabling microbial community analyses in a cost-effective manner. The possibility to infer functional potential of a microbiome through amplicon sequencing derived taxonomic abundance profiles has further strengthened the utility of 16S sequencing. In fact, a surge in 'inferred function metagenomic analysis' has recently taken place, wherein most 16S microbiome studies include inferred functional insights in addition to taxonomic characterization. Tools like PICRUSt, Tax4Fun, Vikodak and iVikodak have significantly eased the process of inferring function potential of a microbiome using the taxonomic abundance profile
R package for annotating RNA editing in plastid genomes.
Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database
THIS PAGE IS DEPRECATED, GO TO : https://bio.tools/inserm-remap
> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'jats:list-item' | A quantitative method for proteome reallocation using minimal regulatory interventions | Regulation based Proteome Minimization (ReProMin) | Three files are needed for the analysis:
Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. This toolkit contains the required scripts to transform sequencing files into ReQTL input files and run the MatrixEQTL R package to identify significant variation-expression relationships
Drug response similarity prediction using Siamese neural networks.
a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. BACKGROUND:Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach. Filtering approaches may eliminate potential antigens based on limitations in the accuracy of prediction tools used. Machine learning approaches are heavily dependent on the selection of training datasets with experimentally validated antigens (positive control) and non-protective-antigens (negative control). The use of one or few bacterial proteomes does not assess PVC conservation among strains, an important feature of vaccine antigens
Reaction Diffusion Dynamics (ReaDDy) - software framework for interacting-particle reaction dynamics.
Tool to predict and analyze biochemical reactions.
assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage. Read-SpaM. Test runs on simulated reads from bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary
Real-time is a health monitoring through urine metabolomics.
Tool for preparing 3D models of biochemical structures for augmented and virtual reality.
Robust comparative analysis and contamination removal for metagenomics.
Reciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for the sequence comparisons necessary to finding RBHs.
Reciprocal Best Hits - Best Bidirectional Hits
Rapid determination of appropriate reference genomes.
Tool for users to reconstruct imputation reference panels of 1000G, and to investigate the imputation accuracy changes pattern for a particular population of interest.
Refgenie manages storage, access, and transfer of reference genome resources. It provides command-line and Python interfaces to download pre-built reference genome "assets", like indexes used by bioinformatics tools. It can also build assets for custom genome assemblies. Refgenie provides programmatic access to a standard genome folder structure, so software can swap from one genome to another.
Reconstructing signaling pathways using regular language constrained paths | Connect the dots in protein interaction networks ... using regular expressions! | RegLinker is an algorithm for the automated curation of signaling pathways. Given a signaling pathway and a background interactome, RegLinker will automatically rank the interactions in the background interactome as candidates for inclusion into the signaling pathway | Connect the dots in protein interaction networks... using regular expressions!
a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Predict disease-causing probability of human intronic SNVs. regSNP-intron is a tool which predicts disease-causing probability of human intronic single nucleotide variants (iSNVs). regsnp-intron predicts the disease-causing probability of intronic single nucleotide variants (iSNVs) based on both genomic and protein structural features. ANNOVAR (>= 2016Feb01): Follow the instructions at http://annovar.openbioinformatics.org/en/latest to install, and prepare Ensembl gene annotation. Or paste input here (use example). Or upload a file size limit: 10K rows
Performance of fast association analysis between allele frequencies and continuous traits. Uses linear regression to estimate marker effects on continuous traits.
RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Phenotypic data can be used to focus on likely disease genes.
a high resolution transposable element insertion site mapping tool for population resequencing. This tool is for mapping TEs from resequencing data: Stajich lab. RelocaTE2: a high resolution transposable element insertion sites mapping tool for population resequencing. RelocaTE2 is an improved version of RelocaTE (Robb et al., 2013). RelocaTE2 is highly sensitive and accurate in mapping transposable elements (TE) polymorphisms at single base pair resolution. RelocaTE2 uses the reads associated with TEs as seeds to cluster the read pairs on chromosomes. It automatically detects the target site duplication (TSD) of a TE insertion from alignments in each cluster, which enable high resolution mapping of TE polymorphisms. Unlike parallel searching of multi-TE elements in RelocaTE, RelocaTE2 searches all TEs in one cycle, which enables us find polymorphisms of thousands of TEs in an individual genome or large population in a reasonable timeframe without losing sensitivity and specificity
Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets. Venue - Responsive HTML5 Template. Tool to identify Bioremediation enzymes from. RemeDB aims at identifying Pollutant Degrading Enzymes (PDE) from metagenomic sequences. A hassle-free tool to predict bioremediation enzymes from metagenomic datasets
reference-free orientation of nanopore cDNA reads with deep learning. Transcriptome long-read orientation with Deep Learning. ReorientExpress is a program to create, test and apply models to predict the 5'-to-3' orientation of long-reads from cDNA sequencing with Nanopore or PacBio using deep neural networks for samples without a genome or a transcriptome reference. For details on the benchmarkings and analyses performed with this program, please see our publication: https://www.ncbi.nlm.nih.gov/pubmed/31783882
Web server to extract sequence repeats from protein and DNA sequences.
RepeatFiller incorporates newly-detected repeat-overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in the chains, which makes it feasible to consider all seeds including those that overlap repetitive regions.
RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
RepeatScout is a tool to discover repetitive substrings in DNA.
A New Multi-scale Backbone Architecture | A New Multi-scale Backbone Architecture – 程明明教授主页 | Figure 1. We propose a novel building block for CNNs, namely Res2Net, by constructing hierarchical residual-like connections within one single residual block. The Res2Net represents multi-scale features at a granular level and increases the range of receptive fields for each network layer. The proposed Res2Net block can be plugged into the state-of-the-art backbone CNN models, e.g., ResNet, ResNeXt, BigLittleNet, and DLA. We evaluate the Res2Net block on all these models and demonstrate consistent performance gains over baseline models
An R package for fine-scale mapping of resistance to dispersal. Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an R package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals
Algorithm for protein residue-residue contact-map prediction.
Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder | Many proteins contain regions of intrinsic disorder, not folding into unique, stable conformations. Numerous experimental methods have been developed to measure the disorder of all or select residues. In the absence of experimental data, computational methods are often utilized to identify these disordered regions and thus gain a better understanding of both structure and function. Many freely available computational methods have been developed to predict regions of intrinsic disorder from the primary sequence of a protein, including our recently developed Rosetta ResidueDisorder. While these methods are very useful, they are only designed to predict intrinsic disorder from the sequence
Programs can use RestraintLib's API to calculate restraints programmatically without interacting with this web page. To see the format of the requests, check the API documentation.
determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms | The overaching goal of RetSynth is to streamline the arduous and complex step of selecting enzyme/reactions pairs to produce a target compound for bioengineering microbial organisms
Pathogenicity prediction of human missense variants based on protein sequence, structure and dynamics | computationally predicting effects of saturation mutagenesis | In silico saturation mutagenesis | perform a complete scan of all possible 19 amino acid substitutions at each site on a human sequence. See example: H-Ras
RiboFlow is an ecosystem for analyzing ribosome profiling data at read length resolution.
RiboPy is an ecosystem for analyzing ribosome profiling data at read length resolution.
Ribo Ecosystem is a set of software tools, built around the ribo file format, to facilitate analyzing ribosome profiling data at ribosome protected footprint length resolution. It consists of a pipeline, RiboFlow, and two interfaces RiboR and RiboPy.
a computational framework for visualization, quality control and statistical analysis of ribosome profiling data. Visualization, Quality and Statistics for Ribosome Profiling. This is package RiboVIEW for Visualization, Quality and Statistics for Ribosome Profiling
Web tool for bacterial classification through m/z data from ribosomal proteins.
a genomic database of rice relatives for rice research | Welcome to RiceRelativesGD, a genomic database of rice relatives for rice research! | The cultivated rice (Oryza sativa) is one of the most important crops in the world
An open source database(s) for genetics, genomics and functional research in rice species
> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'PQN', 'Windham', 'eGTEx' | Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform | Abstract Motivation In the analysis of proteomics data from mass spectrometry (MS), normalization is an important preprocessing step to correct sample-level variation and make abundance measurements for each specific protein comparable across different samples. Under heterogeneous samples such as in the Phase I study of the Enhancing Genotype-Tissue Expression (eGTEx) project (Jiang, et al., 2019), the samples coming from 32 different tissues, and without prior housekeeping protein information or spike-ins, how to robustly correct the bias but keep tissue internal variations becomes a challenging question. Majority of previous normalization methods cannot guarantee a robust and tissue adaptive correction
A standalone GUI-based package for robust co-evolutionary analysis of proteins. RocaSec is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the multiple sequence alignment data of a protein for inferring the underlying co-evolutionary sectors. In addition, when information on the protein biochemical domains is provided, RocaSec returns the corresponding statistical association between inferred sectors and biochemical domains
RBM ( Restricted Boltzmann Machine ) is an unsupervised Rotation Factorization in Restricted Boltzmann Machines.
Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish.
correlation of expressed SNVs with splicing using RNA-sequencing data. RsQTL: correlation of expressed SNVs with splicing patterns using RNA-sequencing data. This toolkit contains the required scripts to transform sequencing files into RsQTL input files and run the MatrixEQTL R package to identify significant variation-splicing relationships
tool for drawing graphs that can be represented by the BioNetGen language, which is used to formulate mathematical, rule-based models of biochemical systems.
Tool computes reaction similarity based on the molecular signatures of participating molecules.
Alignment-free gapped mapping of noisy long reads. Spaced context based Locality Sensitive Hashing. Spaced context based Locality Sensitive Hashing (S-conLSH) is a new mapper that facilitates gapped mapping of noisy long reads to the corresponding target locations of a reference genome, with multiple spaced patterns. Spaced-context based Locality Sensitive Hashing
Searching algorithm for Type IV effector proteins (S4TE) - software package developed for the prediction of Type IV effector proteins and the analysis of their genomic context.
Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. SAAVpedia is a platform for identification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data. Home Y.-M. Kang 2019-12-24T08:52:37+00:00. S ingle A mino- A cid V ariant Encyclo pedia :. User Guide Y.-M. Kang 2018-11-28T11:06:16+00:00. The SAAVpedia is a comprehensive proteogenomic interpretation platform that identifies, annotates, and retrieves SAAVs from proteomic and genomic sequence data to discover true pathogenic variant candidates. SAAVpedia provides a proteogenomic analysis pipeline to prioritize and interpret SAAVs. The SAAVpedia is a platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. Identification, functional annotation, and retrieval of single amino-acid variants for proteogenomic interpretation
Open Source Software for the Real-Time Control, Processing, and Visualization of High-Volume Electrochemical Data | This repository contains the master script for the SACMES program and all updates | All updates for the Standard Operating Procedure (SOP) can be viewed here: https://www.dropbox.com/preview/NetzLab%20SACMES%20SOP/2019_11_13%20SACMES%20SOP.docx?role=personal
SAD contains efficient algorithms for sampling feasible sets of abundance distributions.
High-speed device synchronization in optical microscopy with an open-source hardware control platform | Check out the preprint at https://doi.org/10.1101/533349 for more details | This project has been developed in house by the Paszek and Zipfel labs at Cornell University over a few years and several revisions. The primary developer has been Marshall Colville (mjc449@cornell.edu) with assistance from Warren Zipfel and Matt Paszek | Given the scope of the project, the multiple revisions and adaptations that the hardware and software have gone through, and the fact that we are not electrical or software engineers the code tends to change styles and not follow typical conventions
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch
classifying clinical short notes using background knowledge from unlabeled data. Short and Long Text Classifier using clustering-based enrichment. .. :Travis: image:: https://travis-ci.com/bagheria/saltclass.svg?token=fYbdQUbpnoucyHyb3fs2&branch=master .. _Travis: https://travis-ci.com/bagheria/saltclass. saltclass (Short and Long Text Classifier) is a Python module for text classification built under the MIT license. The project was started in 2018 at the Department of Methodology & Statistics, Utrecht University
Denoising of Aligned Genomic Data. Universal denoiser for genomic sequencing. SAMDUDE is a genomic sequence denoiser that operates on aligned SAM files. It both denoises individual bases in reads as well as updates the corresponding quality scores
Single-cell Aggregated Clustering via Mixture Model Ensemble. SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. SAMEclustering (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. Although several methods have been recently developed to cluster single-cell RNA-seq (scRNA-Seq) data, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments
SAMIRIX is a custom-developed intraretinal segmentation pipeline. It modularly includes import filters for OCT data, a 3rd-party segmentation algorithm, a user interface for controlling and correcting segmentation results, and batch-operations for processing multiple OCT images.
A Semi-Automated Tool for the Visualization of Metabolic Networks. Semi-Automated Metabolic Map Illustrator. SAMMI is a web-based tool for the visualization of metabolic networks and related data. Networks can be uploaded directly from KEGG annotated pathways or using constraint-based metabolic reconstructions
Web server for predicting SAM binding residues of a protein from its amino acid sequence.
A Machine Learning Recommendation Method and Webtool for the Prediction of Functional Post-Translational Modifications | ABSTRACT Post-translational Modifications (PTMs), chemical or proteinaceous covalent alterations to the side chains of amino acid residues in proteins, are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof and the lack of effective means for experimentalists to prioritize PTMs by functional significance, currently less than ~2% of all PTMs have an assigned biological function. Here, we describe a new artificial neural network model, SAPH-ire TFx for the functional prediction of experimentally observed eukaryotic PTMs. Unlike previous functional PTM prioritization models, SAPH-ire TFx is optimized with both receiver operating characteristic (ROC) and recall metrics that maximally capture the range of diverse feature sets comprising the functional modified eukaryotic proteome
Matlab package for incorporating spatial-anatomical similarity into the VGWAS framework to detect significant biomarkers in both genetic and imaging data of neurodegenerative diseases.
SAUCIE is a python object that loads data from a numpy matrix and produces numpy matrix output for the reconstruction, visualization, and/or clusters.
Data denoising with transfer learning in single-cell transcriptomics | R package for transfer learning of single-cell RNA-seq denoising | SAVER-X – Laboratory for single Cell data science | R package for transfer learning of scRNA-seq denoising. Take a look at our free SAVER-X web-server for the transfer learning online computation! We also encourage you to read our pre-print manucript for more information. You can also refer to our earlier denoising method SAVER | Laboratory for single Cell data science | Where Statistics, Biology and Computer Science Meet | Uploading Data is as Easy as 1-2-3: | Researchers can directly upload their data of UMI counts to the web portal as a (gene x cell) matrix stored in a .csv, .txt or .rds file. Our cloud service does not store the user’s data or use it for any other purpose besides denoising | In most single cell transcriptomics (scRNA-seq) studies, the data are extremely sparse and noisy, hindering downstream analyses
Modeling multidomain protein structures using small-angle X-ray scattering data. This is a bioinformatics tool to use SAXS data to assemble protein domain structures into full-length structural models. Installation (tested on CentOS Linux 7 (Core)). (3) Compile SAXSDom from source code (required). running /data/jh7x3/SAXSDom/db_tools/tools/cmake-2.8.12.2/bin/cmake -E create_symlink "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" 2>&1
> CORRECT NAME OF TOOL COULD ALSO BE 'statistical analysis docking results', 'affinity', 'protein-targeted', 'machine-learning' | A Computational Tool for Docking | Molegro Virtual Docker for Docking | Machine Learning to Predict Binding Affinity | Make molecular docking reliable, fast, easy, free, and funny with SAnDReS. It is the easiest way to run dependable protein-ligand docking simulations. SAnDReS takes a different approach to docking; it focuses on the simulation of a system composed of an ensemble of crystallographic structures for which ligand binding affinity data is available
Coordinate Descent Approach for Sparse Bayesian Learning in High Dimensional QTL Mapping and Genome-wide Association Studies.
Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models | SBM-for-correlation-based-networks
SBML2Modelica is a tool which translates biochemical models written in System Biology Markup Language (SBML) Version 3 Level 2 into well-structured, user-intelligible, easily-modifiable Modelica models.
SBMLLint is a collection of tools for linting reactions. The initial focus is detecting mass balance errors. The tool takes as input a model expressed in either SBML (Systems Biology Markup Language, a standard format for biochemical models) or the Antimony language (a human readable representation of chemical reaction models).
> MEDIUM CONFIDENCE! | Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq | Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" manuscript | Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" by Valentine Svensson, Eduardo Beltrame and Lior Pachter | The workflow has 4 steps. The output data after each step can be downloaded from CaltechDATA at https://data.caltech.edu/records/1276 | 1) FASTQ Subsampling and processing with kallisto bus
SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Single-cell ATAC-seq analysis via Latent feature Extraction. SCALE neural network is implemented in Pytorch framework. Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang & Qiangfeng Cliff Zhang. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, (2019).
Set of tools for SCoring, ANnotating and VISualizing splice junctions using annotation details (gencode or other).
An Open Source Physical Layer for the DARPA Spectrum Collaboration Challenge.
The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database
SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database (IEDB) and clusters them based on antigens, receptors and epitopes to generate benchmark datasets. Users can customize structural quality and clustering parameters (e.g. resolution, R free factors, antigen or epitope sequence identity) to generate these datasets based on their need.
consensus approach to contig filtering and genome prediction from single cell sequencing libraries of uncultured eukaryotes. SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries. Please note that this version of SCGid constitutes an early-release version that is currently under active development toward a stable version coinciding with the release of the accepted manuscript introduing it. I am now porting SCGid to python 3 and stabilizing it for full release as SCGid (v1.0) within the next few weeks. This development is taking place on a separate branch. In the mean time, this beta version is working and available for use. I am available to assist with any problems you run into while using this branch of SCGid as well as patch bugs. If you encounter a bug or confusing error while running the beta version of SCGid, please open an issue on this repositiory
Schema is a general algorithm for integrating heterogeneous data modalities, with application to multi-modal single-cell biological datasets.
Inference of clonal selection in cancer populations using single-cell sequencing data | Single Cell Inference of FItness Landscape | We propose a computational method for in vivo inference of clonal selection and estimate of fitness landscapes of heterogeneous cancer cell populations from single cell sequencing data | matlab -nodisplay -nodesktop -r "n=<number>;m=<number>;gv_file='<input_gv_tree>';output='<output_file>';method='<method_name>';nRep=<number>;theta=<number>;SCIFIL"
Identifying critical source areas using multiple methods for effective diffuse pollution mitigation | A framework for modelling and mapping diffuse pollution risk across landscapes | SCIMAP - Diffuse Pollution Risk Mapping | To identify the locations that are a problem, we developed SCIMAP. This project was originally jointly developed between Durham and Lancaster Universities. SCIMAP is supported by the U.K.’s Natural Environment Research Council, the Eden Rivers Trust, the Department of the Environment, Food and Rural Affairs and the Environment Agency. Following this project SCIMAP has been supported by Durham University, the Rivers Trust and the Environment Agency
Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
Ab initio marker selection for single cell transcriptome profiling. Marker gene selection from scRNA-seq data. SCMarker performs cell-type-specific marker selection from single cell RNA sequencing data. It provides users a tool for selecting features from tens of thousands of genes for further cell-type clustering analysis
a genomics portal for the soybean cyst nematode (Heterodera glycines). All supporting analyses required for SCNBase data
SCOC database is a large, open, and global database with sediment community oxygen consumption rates.
SCOM applies three criteria (significantly synergistic competition for mRNAs, significantly positive correlation, and significantly sensitive correlation conditioning on synergistically competed mRNAs) to predict ncRNA synergistic competition network from gene (ncRNAs acting as ceRNAs, and target mRNAs) expression data and predicted ncRNA-related ceRNA networks.
Software for COrrelated Phenotype Analysis.
Tool for sample size calculations for single-cell sequencing experiments.
Single-cell RNA-seq imputation constrained by bulk RNA-seq data.
a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data. Please run Rscript --vanilla fitSCRIBE.R [expression file] [batch index file] [biological group index file] [output file]
accurate and partner type-specific prediction of protein-binding residues from proteins sequences | SCRIBER - web server from Biomine lab
SCSsim is a tool designed for emulating single-cell genome sequencing data. It consists of three modules: 1) “simuVars” module aims to generate single cell genome from a given reference sequence by inserting user-defined genomic variations into genomic loci; 2) “learnProfile” component is developed to infer sequencing platform dependent profiles from real data; 3) “genReads” utility is provided to mimic single-cell genome amplification and read generation procedures based on the results of “simuVars” and “learnProfile”.
Statistical test of structured continuous trees based on discordance matrix.
Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing | Abstract A single neuron and its synapses define the fundamental structural motif of the brain but the underlying gene expression programs that specify individual neuron types are poorly understood. To address this question in a model organism, we have produced a gene expression profile of >90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes
A web-based platform for analyzing Small-Angle Scattering curves of lyotropic liquid crystals. Small Angle Scattering Crystallographic Peak Treatment and Analysis. To access SCryPTA, click here . The instructions to use SCryPTA can be found here
Adding noise to Markov cohort state-transition models.
Splice graph based differential transcript expression analysis tool for population data.
A Sequence Distance Graph framework for genome assembly and analysis | Sequence Distance Graph framework: graph + reads + mapping + analysis | The Sequence Distance Graph (SDG) is a framework to work with genome graphs and sequencing data. It provides a workspace built around a Sequence Distance Graph, datastores for paired, linked and long reads, read mappers, and k-mer counters. It can be used to perform different types of sequence analyses | Index of /opendata/data/sdg_datasets | Welcome to SDG’s documentation! — SDG documentation | Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live | Websites for you and your projects | Hosted directly from your GitHub repository. Just edit, push, and your changes are live | Ready to get started? Build your own site from scratch or generate one for your project
A Web-Based Integrative Machine-Learning Framework for Predicting 6mA Sites in the Rice Genome | Welcome to the Home Page of SDM6A | For the convenience of users, particularly for the vast majority of experimental scientists, a publicly accessible web-server for SDM6A has been established. Moreover, to maximize users' convenience, given below a step-by-step guide on how to use it to get the desired results without the need to through the above mathematical details
A GRASS tool for the Sediment Delivery Ratio mapping. This work involves a tool implementation for evaluating Sediment Delivery Ratio (SDR) in a river basin, through GRASS GIS software. The definition of a spatially distributed value of SDR is a very important task as the sediment routing can affects solid transport in stream channels, water quality degradation, and frequency increase of natural disasters such as debris flows and mudflows. For such reason the SDR evaluation, coupled with GIS approach, has been extensively used in scientific literature. Geographic information systems provide a fundamental support for a better prediction of SDR, since it can consider the space variability of factors influencing the sediment routing processes. Actually a specific GIS module to estimate the spatial variability of SDR does not exist.
The Swine Disease Reporting System (SDRS) consists of multiple projects that aggregates data from participating veterinary diagnostic laboratories (VDLs) in the United States of America, and reports the major findings to the swine industry.
> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations | BACKGROUND:The detection of protein complexes is of great significance for researching mechanisms underlying complex diseases and developing new drugs. Thus, various computational algorithms have been proposed for protein complex detection. However, most of these methods are based on only topological information and are sensitive to the reliability of interactions. As a result, their performance is affected by false-positive interactions in PPINs. Moreover, these methods consider only density and modularity and ignore protein complexes with various densities and modularities
Relative sea-level data from the SEAMIS database compared to ICE-5G model predictions of glacial isostatic adjustment.
the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis results are downloadable, you can provide the given link here, in order to upload the output to this system and compare them with publically available datasets. SEA (also SEAweb) is a searchable database for the expression of small RNA (miRNA, piRNA, snoRNA, snRNA, siRNA) and pathogens. Publically available sRNA sequencing datasets were analysed with Oasis 2 pipelines and the results are stored here for easy and comparable search. Our curated, ontology connected metadata enables powerful searches within this database. Learn more in the documentation and publication
A bioinformatics pipeline for the rapid and user-friendly processing of Illumina sequences, from raw reads to alignments. A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments. Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics. SEquence CApture PRocessor (SECAPR). Sorry, something went wrong. Reload?. Sorry, we cannot display this file. We are now teaching a free 1-week intensive course on target enrichment data, including practical exercises for all functionalities of the SECAPR pipeline. See course overview from last year and contact tobias.andermann@bioenv.gu.se in case you are interested. Sorry, this file is invalid so it cannot be displayed
Webserver and deep neural network design tool for hierarchical biological sequence classification.
A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes. A tool for simulating CNVs for WES data. It simulates rearranged genome(s), short reads (fastq) and BAM file(s) automatically in one single command. SECNVs 2.7.1 (SimulateCNVs 2.7.1). SECNVs (Simulator of Exome Copy Number Variants) is a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors | SED: Screening for Lasso of ECFPs and Deep Neural Nets | SED was developed to predict ligand bioactivities and to recognize key substructures associated with GPCRs through the coupling of screening for Lasso of long extended-connectivity fingerprints (ECFPs) with deep neural network training
SEGAN is a novel diversity-generated image inpainting adversarial network with a newly designed style extractor for diversity image inpainting tasks. For a single input image with missing regions, our model can generate numerous diverse results with plausible content. Experiments on various datasets have shown that our results are diverse and natural, especially for images with large missing areas.
SELVa (Simulator of Evolution with Landscape Variation) - simulator of sequence evolution that allows the fitness landscape to vary according to user-specified rules.
> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/gddp (RESEARCH.CCHMC.ORG) | > CORRECT NAME OF TOOL COULD ALSO BE 'CONCLUSION:SEMA' | Graphical data mining of cancer mechanisms with SEMA | SEMA is a graphical hypothesis testing platform for multidimensional cancer genomics data | SEMA is a graphical hypothesis testing platform for multidimensinoal cancer genomics data, written in R Shiny and JavaScript. SEMA uses Structural Equation Modeling (SEM) for the analyses of graphical models | Free HTML5 Template by FreeHTML5.CO | Graphical data mining from cancer genomic datasets
Predicting the effects of SNPs on transcription factor binding affinity | MOTIVATION:GWAS have revealed that 88% of disease associated SNPs reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). RESULTS:SEMpl estimates transcription factor binding affinity by observing differences in ChIP-seq signal intensity for SNPs within functional transcription factor binding sites genome-wide. By cataloging the effects of every possible mutation within the transcription factor binding site motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci
Now to predict the experimentally measured affinity between protein monomers in solution, we just need the 3D structure of the suggested PBP on one subunit of the proposed dimer.
benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines. SEPATH template pipelines optimised for UEA high performance computing cluster. SEPATH - Searching for Pathogens Computational Pipeline. A repository containing scripts and results required for the SEPATH manuscript. SEPATH is a software designed to obtain accurate taxonomic classifications from within host tissue sequences. It is implemented in python 3 and relies on the Snakemake workflow management system. SEPATH was produced specifically to provide researchers with the ability to conduct ultra high throughput metagenomic studies from raw data to classification and has been benchmarked on simulated human cancer whole genome sequence datasets
SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500.
web-based visualization of Arabidopsis thaliana iCLIP and RNA-seq data in an interactive python framework. SEQing: interactive web-based tool for visualization of iCLIP and RNA-seq data. The file requirements.txt can be used to install all needed needed dependencies for the project. Python 3.5 or higher is required and we recommend to setup a virtual environment for this project. If your current python points to a python2 version, please put python3 instead of just python before running SEQing
Modularized and customizable pipeline framework for NGS processing in R package.
SEQualyzer (Structure-profiling Experiment Quality Analyzer ) - interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.
The Standard European Vector Architecture (SEVA) platform is a web-based resource and a material clone repository to assist the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes.
SF-Matching(SubFragment-Matching) is a machine-learning based approach to predict compounds from tandem mass spectra.
SFLA IWSSr is an Efficient hybrid filter-wrapper metaheuristic-based gene selection method for high dimensional datasets.
a comprehensive and interactive database of the silkworm | Silkworm Genome Informatics Database | e.g. FIBH or KWMTBOMO15365 or BGIBMGA005111 or silk fibroin heavy chain &nbspBrowse in Gene Lists | Search by sequence alignment against genomes or genes | With the Exponential increasing of sequencing data in genomics, transcriptomics and epigenetics, and the development of data analysis methods, a serious of informatics database with integrated analysis tools have been constructed, like the Flybase and TAIR. Silkworm, as a domesticated insect, lacks an online analysis platform. On the basis of previous efforts, including Silkbase, SilkDB and Ensembl Insects, we constructed the silkworm genome informatics database, SGID. Hopefully, it will assist to bioinformatics analysis of silkworms in the future
A novel method for tumor classification via support vector machine with sparse group Lasso. At present, with the in-depth study of gene expression data, the significant role of tumor classification in clinical medicine has become more apparent. In particular, the sparse characteristics of gene expression data within and between groups. Therefore, this paper focuses on the study of tumor classification based on the sparsity characteristics of genes. On this basis, we propose a new method of tumor classification-Sparse Group Lasso (least absolute shrinkage and selection operator) and Support Vector Machine (SGL-SVM). Firstly, the primary selection of feature genes is performed on the normalized tumor datasets using the Kruskal-Wallis rank sum test. Secondly, using a sparse group Lasso for further selection, and finally, the support vector machine serves as a classifier for classification. We validate proposed method on microarray and NGS datasets respectively
> MEDIUM CONFIDENCE! | A graphical tool for generating hybrid ground-truth spiking data for evaluating spike sorting performance | SHYBRID is a graphical user interface that allows for the easy creation of hybrid ground truth extracellular recordings. This README file contains information on how to install the program, as well as information on how to get started making extracellular spiking ground truth data. If you have any further questions feel free to contact me
Software for Structural Identifiability ANalysis of ODE models.
SIIM is a professional organization at the nexus of medical imaging informatics and healthcare technologies. SIIM provides an unparalleled opportunity to not only hear from the best, brightest and most forward thinkers in imaging space but talk to them face to face in a collegial setting.
a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. SIMLIN: an improved bioinformatics approach based on multi-stage ensemble learning model for S-sulphenylation prediction
Survival-significant Isoform Networks By Altered Domain-inclusion.
Tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.
Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant.
Robust Moiety Model Selection Using Mass Spectrometry Measured Isotopologues.
The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching.
Scalable software tool for gene network reverse engineering from big data.
Yu Lab in the Department of Computational Biology at St. Jude Children's Research Hospital
Computing Skin Cutaneous Melanoma Outcome from the HLA-alleles and Clinical Characteristics. Skin Cutaneous Melanoma High-Risk Prediction(SKCMhrp) webserver can be used to distinguish high risk SKCM patients from low risk SKCM patients from their HLA-superallele and clinical characteristics. The risk estimation is based on statistical and survival analysis on recent SKCM datasets. See general section for more information.
Facilitating knowledge discovery in life sciences by machine-aided skim reading. SKIMMR - a research prototype for machine-aided skim reading (includes back-end code for generating a graph-like knowledge base from texts and a standalone HTTP server-based UI)
Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.
Single-sample landscape entropy reveals the imminent phase transition during disease progression.
Systems-Level Interactive Data Exploration (SLIDE) - web-based tool for interactive visualization of large-scale – omics data.
Web application for the reproducible processing of environmental DNA metabarcoding data.
a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme | A scaffold assemble pipeline for stLFR reads | This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds | git clone --recursive https://github.com/BGI-QingDao/SLR-superscaffolder.git YOUR-DOWNLOAD-DIR --depth 10 | Here is an illustration of this pipeline:
Database of Chemical Constitutents of Smokeless Tobacco Products.
Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.
Using Python® language for the validation of the CCI soil moisture products via SM2RAIN.
SMAGEXP (Statistical Meta-Analysis for Gene EXPression) - galaxy tool suite for transcriptomics data meta-analysis.
an interactive web application for comprehensive DNA methylation analysis and visualization. BACKGROUND:Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. RESULTS:To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project
Ultra-fast de novo assembler using long noisy reads
A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes | R codes for sample size calculation to detect dynamic treatment regime (DTR) effects based on changes in CAL outcomes from a non-surgical chronic periodontitis treatments study. The experiment is performed under a SMART design. The clustered tooth (sub-unit) level CAL outcomes are skewed, spatially-referenced, and non-randomly missing. The imple… | A SMART design for non-surgical treatments of chronic periodontitis with spatially-referenced and non-randomly missing skewed outcomes | devtools::install_github("bandyopd/SMARTp") | # Install from CRAN (when available)
Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.
> HOMEPAGE MISSING! | > NAME EQUAL TO (PUB. DIFFERENT) bio.tools/smog | A Lightweight Tool for Object-Spreadsheet Mapping | In the life science domain, experts are usually familiar with spreadsheet software and often use it in their daily work to collect and structure required domain knowledge. The processing and analysis of spreadsheet data is an important task that must be supported by efficient software solutions. A typical application scenario is for example an integration of spreadsheet data (specified or derived) in an ontology to provide reasoning or search. Different converter tools were developed to support a spreadsheet-to-ontology transformation. Such tools allow often only a relatively simple structure of the spreadsheet template or they require complex mapping processes to map the spreadsheet and ontological entities
Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. Sequence-Mask-Search framework and SMSNet model for de novo peptide sequencing. SMSNet's predictions for HLA peptidome and human phosphoproteome datasets. SMSNet's training datasets (WCU-MS-BEST, DeepNovo, ProteomeTools). SMSNet's training datasets (WCU-MS-ALL). Two models for SMSNet are provided here. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and phosphoproteome dataset (PRIDE accession PXD009227) can be found on FigShare. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and human phosphoproteome dataset (PRIDE accession PXD009227)
Identifying Brain Region Connectivity using Steiner Minimal Tree Approximation and a Genetic Algorithm Web-based tool to find a connectivity path among a given set of brain regions. Specifically, this tool uses a genetic algorithm to find a better connectivity path among the brain regions than SMT-Neurophysiology.
Multi-SNP mediation intersection-union test.
R package for visualization and analysis of single-molecule localization microscopy data.
a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing | SNAPPy is a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing | This is the repository for SNAPPy, a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing. SNAPPy allows high-throughput HIV-1 subtyping locally while being resource efficient and scalable. This pipeline was constructed using Snakemake , and it uses MAFFT and for multiple sequence alignment, BLAST for similarirty querys, IQ-TREE for phylogenetic inference, and several Biopython modules for data parsing an analysis. For in-depth information on how the tool works please visit the documentation page. SNAPPy was design for Linux based operative systems | Welcome to snappy’s documentation! — SNAPPy-HIV1-Subtyping 1.0.0 documentation | Free document hosting provided by Read the Docs
Web-based browser with comprehensive, scientifically validated clinical healthcare terminology. Enables consistent representation of clinical content in electronic health records.
> HOMEPAGE BROKEN! | a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers | Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3' untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3'UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified
Modular workflow for standardizing molecular simulation and functional analysis of protein variants.
SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence.
high-throughput tissue-specific functional annotation of single nucleotide variants. Tissue-specific variant annotation pipeline. This pipeline annotates variants based on multiple sources of prior knowledge, including the GWAS literature, tissue-specific open chromatin, tissue-specific modulation of gene expression, and clinical pathogenicity. To download and prepare annotation files
Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL | By using SNP-Seek, you abide by the data use license stated | Query for SNPs from the 3000 genome project | - Mansueto, et al. Rice SNP-seek database update: new SNPs, indels, and queries . Nucl. Acids Res. (2017) 45 (D1): D1075-D1081. doi: 10.1093/nar/gkw1135 This paper describes new features and datasets added to SNP-Seek in 2015-2017 as well as software and database updates | This site provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.)
Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data. SNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium. SNiPloid assumes that short reads datasets (i.e. samples) derived from distinct accessions (diploid or polyploid) have been separately preprocessed as described here.
Synthetic Oligo Library Quality Control Tool. SOLQC - Synthetic Oligo Quality Control tool. SOLQC is a novel analysis tool, which enables fast and comprehensive analysis of synthetic oligo libraries enabling the user comprehensive information and insights about the quality and state of the library
SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins.
Python library implementing the full self-organizing map (SOM) analysis workflow.
Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models.
Using Apache Spark on genome assembly for scalable overlap-graph reduction. Scalable Overlap-Graph Reduction Algorithms for Genome Assembly using Apache Spark on Cloud. Please go to the Wiki pages, https://github.com/BioHPC/SORA/wiki, to learn about SORA
SPAG is a tool for predicting the spatial distribution of adaptive genetic variants under future climatic conditions.
Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning.
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.
SPARSim is a count data simulator for scRNA-seq data.
> HOMEPAGE MISSING! | Alignment of Long Diverged Molecular Sequences to Assembly Graphs | A bstract Background Graph-based representation of genome assemblies has been recently used in different applications from gene finding to haplotype separation. While most of these applications are based on the alignment of molecular sequences to assembly graphs, existing software tools for finding such alignments have important limitations. Results We present a novel SPAligner tool for aligning long diverged molecular sequences to assembly graphs and demonstrate that SPAligner is an efficient solution for mapping third generation sequencing data and can also facilitate the identification of known genes in complex metagenomic datasets. Conclusions Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem
Structural and physico-chemical interpretation of QSAR models
Data Model for Variants and Applications at NCBI.
Learning-to-rank technique based on ignoring meaningless ranking orders between compounds | SPDRank is stochastic pairwise descent RankSVM method with ignoring meaningless ranking orders that used on Learning-to-Rank Technique based on Ignoring Meaningless Ranking Orders between Compounds
A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data | Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry
Tool that computes point-based models using a parametric boundary description for the computing of Shape analysis.
Disentangling microbial associations from hidden environmental and technical factors via latent graphical models.
Targeted insertional mutagenesis libraries for deep domain insertion profiling. SPINE: Saturated Programmable INsertion Engineering. Protein domain insertion via programmed oligo libraries
Simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.
Statistical Parametric Mapping (SPM) software for the analysis of brain imaging data sequences.
To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. Protein sequence profile prediction aims to generate multiple sequences from structural information to advance the protein design. Protein sequence profile can be computationally predicted by energy-based method or fragment-based methods. By integrating these methods with neural networks, our previous method, SPIN2 has achieved a sequence recovery rate of 34%. However, SPIN2 employed only one dimensional (1D) structural properties that are not sufficient to represent 3D structures. In this study, we represented 3D structures by 2D maps of pairwise residue distances. and developed a new method (SPROF) to predict protein sequence profile based on an image captioning learning frame. To our best knowledge, this is the first method to employ 2D distance map for predicting protein properties.
SPROUTS has two general functions. The first is to provide existing mutation data given a protein specified by a PDB ID. This is Query mode. The second is to generate new mutation data based on a new PDB ID or a user input. This is Submit mode.
R package for filtering of spatially related peaks in mass spectrometry imaging data.
SPar-K (Signal Partitioning using K-means) is a modified version of a standard K-means algorithm designed to cluster vectors containing a sequence of signal (that is, the order in which the elements appear in the vectors is meaningful). In order to detect a possible phase shift or orientation inversion between two vectors, this program allows computing distances between two vectors by shifting and flipping them.
Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ.
High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data | A python application for MALDI-TOF MS dereplication | python SPeDE.py <Path\to\ppmc_interval_index.csv> <Project_directory> <Output_directory> [-d <density>] [-c <cluster>] [-l <local>] [-m <cutoff>] [ -o <output_format>\] [-p <peak-count>] [-n <name>] [-q <validation_name>] [-v] [-e] | Command driven processing (Windows and Linux supported, MacOS unknown) | This program cannot be run on a Linux subsystem in Windows
SProCoP is a set of statistical process control aids for visualize, detect, and identify of assignable causes of variation in chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution); and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts and boxplots.
The Prevalence and Impact of Model Violations in Phylogenetic Analysis | tests of stationarity, reversibility, and homogeneity for sequence alignments | This just deletes (with rm -rf, so be careful), /data/srh/processed_data/SRH_tables/ and /data/srh/processed_data/IQtree/ | All scripts have hard-coded input and output destinations. If you want to run them for yourself, you will need to adjust these destinations in each script as you go | This will calculate SRH stats and IQtree input files for all datasets in SRHtests/datasets. It requires python 3.6.x or higher and dependencies as in the header of srh.py. Input and output files are hardcoded near the end of the script, change them if you need to. This script creates two output folders, each of which contains one folder for each dataset in SRHtests/datasets
> MEDIUM CONFIDENCE! | Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) for autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) | Spectral unmixing methods attempt to determine the concentrations of different fluorophores present at each pixel location in an image by analyzing a set of measured emission spectra
SSEThread is an Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method.
accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. binding affinity change estimation. SSIPe is a method to calculate binding affinity changes (ΔΔGbind) of protein-protein interactions (PPIs) upon mutations at protein-protein interface. Please direct questions and inquiries to our Service System Discussion Board or contact Dr. Estimation of binding affinity change upon mutations at protein-protein interface
A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16) | a GUI to Simplify the Generation of Sequence Similarity Networks | SSNpipe is a Python program, and independent all-inclusive executable binary files for most popular operating systems are freely available in release page | Please be aware that SSNpipe and all python Tkinter applications are unable to run on MacOS Mojave 10.14.6, due to an unidentified bug in the MacOS system. This issue should be patched in the soon to be released MacOS Catalina 10.15, click here for more information)
Scaled Simplex Representation for Subspace Clustering.
Secondary Structure based End-to-End Learning model for Protein-Ligand Interaction Prediction. Abstract Computational prediction of bioactivity has become a critical aspect of modern drug discovery as it mitigates the cost, time, and resources required to find and screen new compounds. Deep Neural Networks (DNN) have recently shown excellent performance in modeling Protein-Ligand Interaction (PLI). However, DNNs are only effective when physically sound descriptions of ligands and proteins are fed into the network for further processing. Furthermore, previous research has not incorporated the secondary structure of the protein in a meaningful manner. In this work, we utilize secondary structure information of the protein which is extracted as the curvature and torsion of the backbone of protein to predict PLI. https://github.com/ekraka/SSnet
Subjective Evaluation of the Spectral Temporal SIMilarity (ST-SIM) Measure for Vibrotactile Quality Assessment. Recent standardization efforts for Tactile Internet (TI) and haptic codecs have paved the route for delivering tactile experiences in synchrony with audio and visual interaction components. Since humans are the ultimate consumers of tactile interactions, it is utmost important to develop objective quality assessment measures that are in close agreements with human perception. In this work, we present the results of a large-scale subjective study of a recently proposed objective quality assessment approach for vibrotactile signals called ST-SIM (Spectral Temporal SIMilarity). ST-SIM encompasses two components: perceptual spectral and temporal similarity measures. Two subjective experiments were conducted to validate ST-SIM, and elicited subjective ratings are used to create a VibroTactile Quality Assessment (VTQA) database.
2D and 3D constrained Total Variation using the Split Bregman formulation
HGGM-LIM Split-Bregman-ST-Total-Variation-MRI
Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. Changes in blood flow velocity and distribution are vital in maintaining tissue and organ perfusion in response to varying cellular needs. Further, appearance of defects in microcirculation can be a primary indicator in the development of multiple pathologies. Advances in optical imaging have made intravital microscopy (IVM) a practical approach, permitting imaging at the cellular and subcellular level in live animals at high-speed over time. Yet, despite the importance of maintaining adequate tissue perfusion, spatial and temporal variability in capillary flow is seldom documented. In the standard approach, a small number of capillary segments are chosen for imaging over a limited time. To comprehensively quantify capillary flow in an unbiased way we developed Spatial Temporal Analysis of Fieldwise Flow (STAFF), a macro for FIJI open-source image analysis software
New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches. Simple Tool for Analysis of Replication Timing with R. Visit our website : https://thomasdenecker.github.io/START-R/. We use Docker to develop and manage START-R. We invite you to verify that the following requirements are correctly satisfied before trying to bootstrap the application:
An Open Source Tool for Disease Modeling | The Eclipse Foundation - home to a global community, the Eclipse IDE, Jakarta EE and over 350 open source projects, including runtimes, tools and frameworks | The Spatiotemporal Epidemiological Modeler (STEM) Project | Some Eclipse Foundation pages use cookies to better serve you when you return to the site. You can set your browser to notify you before you receive a cookie or turn off cookies. If you do so, however, some areas of some sites may not function properly. To read Eclipse Foundation Privacy Policy click here | The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases
Probabilistic genotyping software that combines biological modelling and mathematical processes to interpret a wide range of complex DNA profiles.
A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity. codes for the membrane transporter paper. codes for membrane transporter paper:. model_training_*.py are codes for parameter tuning in a server
Tool for analysis and visualization of spatial transcriptomics datasets.
accurate and ultrafast genomic profiling with exact sequence matches. Ultrafast sequence typing and gene detection from NGS raw reads. See the full documentation at: https://sting.readthedocs.io/
Visualize the human surface proteome (surfaceome) and load your own expression data to inspect and uncover cellular phenotypes and new surfaceome markers.
Risk-based surveillance for meat-borne parasites. There is a plethora of meat-borne hazards - including parasites - for which there may be a need for surveillance. However, veterinary services worldwide need to decide how to use their scarce resources and prioritise among the perceived hazards. Moreover, to remain competitive, food business operators - irrespective of whether they are farmers or abattoir operators - are preoccupied with maintaining a profit and minimizing costs. Still, customers and trade partners expect that meat products placed on the market are safe to consume and should not bear any risks of causing disease. Risk-based surveillance systems may offer a solution to this challenge by applying risk analysis principles; first to set priorities, and secondly to allocate resources effectively and efficiently.
StrUctural Susceptibility PrEdiCTion on BDQ.
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Spatial Variance Components Analysis (SVCA). NB: If you are already a limix user, we recommend you install svca_limix and svca in a dedicated conda environment so there is no interference between your limix versions
Genotyping structural variations with long reads. SVJedi : Genotyping structural variations with long read data. SVJedi is a structural variation (SV) genotyper for long read data. Based on a representation of the different alleles, it estimates the genotype of each variant in a given individual sample based on allele-specific alignment counts. SVJedi takes as input a variant file (VCF), a reference genome (fasta) and a long read file (fasta/fastq) and outputs the initial variant file with an additional column containing genotyping information (VCF)
Impact prediction tool for structural variation.
SVants – A long-read based method for structural variation detection in bacterial genomes. Config file input files and parameters. Output from LastalAlignToGenome.sh. git clone https://github.com/EpiBlake/SVants.git
Genome-wide Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants using the long-fragment information from the 10x Genomics platform.
Tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight.
Counting Kmers for Biological Sequences at Large Scale. This is a distributed kmer counting tools for TB-PB sequencing dataset
An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis | Introduction： As the number of the MS/MS spectra increases rapidly, the excessive computation time taken by MS/MS spectra data analysis has become a critical concern in computational biology. In this work, we designed and implemented SWPepNovo, an efficient de novo peptide sequencing tool for large-scale MS/MS spectra data analysis using a novel peptide-spectrum matches (PSMs) algorithm. To achieve the high performance, we designed an improved scoring algorithm to reduce the time complexity and eliminate the data dependence to enable all possible locality and vectorizations. Performance is also tuned by pre-fetching, double buffering mechanism, and an optimized memory access scheme, to achieve an optimum performance and best utilization of various computing resources within neo-heterogeneous many-core architecture
Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. A software for single particle tracking which includes intensity ratiometric measurements and analysis. Unpack the zip file to a folder of your choice. follow the instructions in the manual in order to get started
Database containing 4.373 video, 18.212 still images and 7.771 labels concerning sampled that were prepared and stored from 1910 at the “Stazione Zoologica Anton Dohrn di Napoli (SZN)”. Moreover, the digitised version of 38 documents (totalling 8406 pages) with important information about taxonomy, ecology and phylogenetic is also included.
Sage is a proteomics database search engine to match tandem mass spectra to peptides. Sage also performs retention time prediction, quantificaiton and FDR control.
a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait
> MEDIUM CONFIDENCE! | a novel method for selecting parameters for gene functional annotation routines | Novel strategy for selecting best parameters for gene functional annotation routines in merlin | readme instructions updated · 81b3a5a9
Modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.
Genome-wide copy number variants (CNV) calling from off-target reads.
ScType is a tool for fully-automated cell type identification from single-cell RNA-seq data. ScType provides a complete pipeline for single-cell RNA-seq data analysis (including data processing, normalization and clustering) and cell-type annotation.
Accurate reference-based transcript assembler.
Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
Mapping the RNA structural landscape of viral genomes. ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by first scanning a single input sequence to identify regions which generate negative thermodynamic z-scores (a hallmark of functional RNA sequences), and subsequently identifying the specific base pairs which we…. Welcome to the ScanFold web server. Using the ScanFold web server you can identify regions of an RNA sequence which generate unusually stable secondary structures (one of the hallmarks of a functional RNA)
ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation
A pipeline for recovery of unaligned reads utilising similarity with aligned reads | Rescue potential false negative unmapped reads in alignment tools | Manuscript available now on bioRxiv: https://www.biorxiv.org/content/early/2018/06/13/345876 | python3 usage: scavenger.py [options] -G/--genome_file <genome_file> -i/--input -at/--aligner_tool <aligner>
Sci-Hub provides access to nearly all scholarly literature. Source code and data analyses for the Sci-Hub Coverage Study. Analyses for the Sci-Hub Coverage Study. Manuscript for the Sci-Hub Coverage Study. Manuscript source for the Sci-Hub Coverage Study. Data for the Sci-Hub Stats Browser. removing barriers in the way of science. Din bedste informationskilde om sci hub. This project investigates the coverage of scholarly literature in the Sci-Hub and LibGen scimag repositories. It's based on using DOIs to uniquely identify articles. For more information, see the corresponding study:. This is the manuscript source for the study titled Sci-Hub provides access to nearly all scholarly literature. Sci-Hub is a pirate website that provides access to full texts from the scholarly literature, including paywalled articles. The first pirate website in the world to open mass and public access to tens of millions research papers
Modeling framework for studying population-scale family trees that combines techniques from the animal and plant breeding literature and from human genetics literature.
A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data. MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we developed SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results. Based on the SciApps workflow platform, we generated new components to support the complete cycle of the MaizeCODE data management
Sequence analysis of the cytochrome c oxidase subunit 1 gene of Sarcoptes scabiei isolated from goats and rabbits in East Java, Indonesia | Software for the Molecular Biologist | Welcome to the Sci Ed Software website
Accurate and Efficient Cell Lineage Tree Inference from Noisy Single Cell Data | Cell tree inference and genotype calling from noisy single cell data | ScisTree is a computer program for inferring cell tree and calling genotypes from uncertain single cell genotype data. If you use ScisTree, please cite: | The key feature of ScisTree is that it works with uncertain genotypes with individualized probability. That is, you can specify for each genotype (at a row/cell or column/site) different probabilities of being a particular genotype state. ScisTree allows both binary or ternary genotypes. Here is an example for binary genotypes. Note: don't include blank rows in the input genotype file
SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions.
Annotation of secondary structure elements in proteins.
Accurate tool for somatic structural variation and virus integration detection.
PyTorch-based deep learning library for sequence data.
Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks (command line version of FORECasT).
discovery of differential chromatin interactions via a self-similarity measure | SELFISH (Discovery of Differential Chromatin Interactions via a Self-Similarity Measure) is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way. For more information read the full paper: Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure. A Python implementation of Selfish is available at Ay-lab
SeneQuest contains information on gene-to-senescence associations is crucial for increasing our understanding of the molecular mechanisms driving senescence.
Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy | As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important
Radar vision in the mapping of forest biodiversity from space.
A Generic Practice for Generating Dual-pol Covariance Matrix Elements in SNAP S-1 Toolbox.
Web-based feature extraction tool which computes protein and DNA sequence driven features. It can calculate 252 protein- based and 42 DNA- based descriptors.
a python tool to evaluate genomic prediction in complex scenarios | SeqBreed.py is a python3 software to simulate populations under (genomic) selection. It inherits most of funcionality from SBVB (Perez-Enciso et al., 2017, https://github.com/miguelperezenciso/sbvb1) and pSBVB (Zingaretti et al. 2018, https://github.com/lauzingaretti/pSBVB) softwares but code has been completely rewritten. It is now much more user friendly and adds numerous new features such as easy selection implementation (BLUP, GBLUP, SSTEP), plots (PCA, GWAS)..
Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.
rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode)
Web server for the extraction of DNA or protein sequences from next-generation sequencing data.
Modeling aspects of the language of life through transfer-learning protein sequences. Modelling the Language of Life - Deep Learning Protein Sequences. Repository for the paper Modeling aspects of the language of life through transfer-learning protein sequences. Holds pre-trained SeqVec model for creating embeddings for amino acid sequences. Also, contains checkpoint for fine-tuning
making graph genomes intuitive to commuters | displays multiple genomic sequences in the form of a tube map | A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg | Link to working demo: https://vgteam.github.io/sequenceTubeMap/ | Run Sequence Tube Maps On Your Own | If you are using vg and want visualize the graphs it generates, the online version is limited to small file sizes. For visualizing bigger data sets you can run Sequence Tube Maps on your own. You can either run Tube Maps completely on your local (Linux) machine or use your local browser to access Tube Maps running on any other (Linux) machine you have access to
The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in Finns. It provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map.
Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing | Pneumococcal serotype quantification using NGS reads | SeroCall can identify and quantitate the capsular serotypes in Illumina whole-genome sequencing samples of S. pneumoniae, calculating abundances of each serotype in mixed cultures. The software is written in Python (compatible with Python 2 or 3), and is freely available under an open source GPLv3 license
an open source tool to infer epidemiological and immunological dynamics from serological data | Inference framework for serological data | serosolver is a modelling and inference package that uses a dynamic model to infer antibody dynamics and infection histories from cross-sectional or longitudinal serological data. The model infers individual-level infection histories, historical attack rates, and patterns of antibody dynamics by accounting for cross-reactive antibody responses and measurement error
Evaluation of Cell Type Deconvolution R Packages on Single Cell RNA-seq Data.
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci | [posMatrix,retVals]=ShNeigh(heatmapMatrix,method_type)
RNA SHAPE prediction using graph kernel | SHApe simulation with graph KERnels | import shaker.rna_tools.rna_io as rio
Platform-agnostic data harmonizer for gene expression data.
Fast tool for mapping-free gene separation of reads, using Bloom filter.
Shift-T is a server for an automated Variable-Temperature NMR Data Analysis.
App developed in Shiny and usable in R environment that allows to visualize, explore, filter and extract data from FoodMicrobionet.
ShinyGO is a graphical enrichment tool for animals and plants.
A software framework for performing benchmarks of machine-learning classification algorithms
Precise, high-performance FlowSOM-style cytometry data analysis in a browser, in an R Shiny app.
ShuTu is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining.
Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Accumulation and selection of somatic mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity. Recently developed single-cell DNA sequencing (SCS) technologies promise to resolve ITH to a single-cell level. However, technical errors in SCS data sets, including false-positives (FP) and false-negatives (FN) due to allelic dropout, and cell doublets, significantly complicate these tasks. Here, we propose a nonparametric Bayesian method that reconstructs the clonal populations as clusters of single cells, genotypes of each clone, and the evolutionary relationship between the clones
A general response process theory for situational judgment tests. Situational judgment tests (SJTs) have emerged as a staple of assessment methodologies for organizational practitioners and researchers. Despite their prevalence, many questions regarding how to interpret respondent choices or how variations in item construction and instruction influence the nature of observed responses remain. Existing conceptual and empirical efforts to explore these questions have largely been rooted in reflexive psychometric measurement models that describe participant responses as indicative of (usually multiple) latent constructs. However, some have suggested that a key to better understanding SJT responses lies in unpacking the judgment and decision-making processes employed by respondents and the psychological and contextual factors that shape how those processes play out. To this end, the present article advances an integrative and generalizable process-oriented theory of SJT responding
Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Sierra is an R package designed for detecting differential transcript usage analysis from polyA-enriched single cell RNASeq data. Sierra identifies coordinates of read pileups (i.e. peaks) and performs UMI counting, followed by differential usage analysis between defined cell populations. Please read vignette for a demonstration on how to use this software
Web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.
scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies.
Tool for visualizing and exploring patterns of small mutational events.
signal peptide recognition based on semantic segmentation. A signal peptide predictor based on deep learning. For CPU: pip3 install -r requirement.cpu.txt. For GPU (suggest): pip3 install -r requirement.gpu.txt
integrated 'omics knowledgebase for mammalian cellular signaling pathways. A multi-omics knowledgebase for cellular signaling pathways. Welcome to the Signaling Pathways Project. The Signaling Pathways Project is a multi-omics knowledgemine based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench relevant to cellular signaling pathways. Learn more ». 1555 datasets found. Use the filter to narrow the listings. Transcriptomic Cistromics (ChIP-Seq)
package for cancer mutational signatures | SigsPack R/Bioconductor package for mutational signature estimation | SigsPack provides estimations of a sample's exposure to mutational processes described by a set of known mutational signatures (for example from COSMIC). The exposure stability is quantified by bootstrapping the mutational catalogue
Automated Spatially Targeted Optical Micro Proteomics (autoSTOMP) to determine protein complexity of subcellular structures | Automate what you see on a computer monitor | What is it? For what is it? Get it? Use it? Get help? Contribute? | Latest stable version: 2.0.0 —— Nightly builds: 2.1.0-SNAPSHOT | Both left the project at Sikuli-X-1.0rc3 during 2012, when I decided to take over development and support and name it SikuliX | SikuliX automates anything you see on the screen of your desktop computer running Windows, Mac or some Linux/Unix. It uses image recognition powered by OpenCV to identify GUI components. This is handy in cases when there is no easy access to a GUI's internals or the source code of the application or web page you want to act on
SiliS-PTOXRA (DRY-in Silico Screening & Prediction of Toxic Hazard and Risk Assessment) for the prediction of toxicological endpoints.
An open-source Simulink library for developing closed-loop brain signal interfaces in animals and humans | Simulink Brain Signal Interface (SimBSI) | SimBSI is an open-source graphical environment for the rapid prototyping of animal and human brain-computer interfaces (BCIs). SimBSI is designed as a library on top of the graphical programming environment of Simulink with three goals in mind:
Bayesian Linear Mixed Models for Motif Activity Analysis. Simulate gene expression data where gene expression is determined by a linear inlfuential factor, such as motifs.
Software tool enabling confident phosphosite assignment.
an R package to simulate genetic sequence data for pedigrees. Simulate Genetic Sequence Data for Pedigrees. Methods to simulate genetic sequence data for pedigrees, with functionality to simulate genetic heterogeneity among pedigrees. Christina Nieuwoudt, Angela Brooks-Wilson, and Jinko Graham (2019) <doi:10.1101/534552>
alternative splicing-aware simulation of biological sequence evolution. To add a sequence you need to click the "Add sequence" button is the top left corner of the main application screen. Sequences must be in the arc-annotated format: first line starts with > and following is the sequence header. Next line is the RNA Sequence and then the secondary structure inforamtion. You can add multitude sequences at the same time. The sequences will be added to the list in the side menu. To delete sequences, you can click on those you want deleted and click the "Delete selected" button to remove them. If you want to clear the whole list, the button "Delete all" will do it. The buttons "Select All" and "Unselect All" are used to make this easier when working with multiple sequences
> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'vessel pathlines', 'vessel', 'FCNN', 'vessel pathline' | Accelerating cardiovascular model building with convolutional neural networks | The only fully opensource software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis | Blood velocity distribution in CABG simulation | Blood velocity in coronary aneurism | SimVascular components svModel, svMesh, svPre, and svPost are provided under the full BSD license subject to the terms below: | Copyright © 1998-2007 Stanford University, Charles Taylor, Nathan Wilson, Ken Wang. See SimVascular Acknowledgements file for additional contributors to the source code
fast and resource frugal de novo comparative metagenomics | Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets | This github directory stores Simka and SimkaMin software. This readme focuses on Simka features. All information about SimkaMin is located in the simkaMin directory
An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces.
A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions | Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time
Interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database.
> HOMEPAGE MISSING! | A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species | Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by searching for combinations of genes that have previously been implicated as being cell-type specific, an approach that is not quantitative and does not explicitly take advantage of other single-cell RNA-seq studies. Here, we describe our tool, SingleCellNet, which addresses these issues and enables the classification of query single-cell RNA-seq data in comparison to reference single-cell RNA-seq data. SingleCellNet compares favorably to other methods in sensitivity and specificity, and it is able to classify across platforms and species
Inference of intercellular networks from single-cell transcriptomics.
Linked Data Services platform for decentralized knowledge base | LodView is a powerful RDF viewer, IRI dereferencer and opensource SPARQL navigator | It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English | Lorem Ipsum is simply dummy text of the printing and typesetting industry
A single-sample circadian biomarker that performs across populations and platforms. SkinPhaser is a Shiny app of predicing the circadian phase using expression values of 12 biomarker genes from human epidermis samples
Automated sleep stage scoring with sequence to sequence deep learning approach.
A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome | Free Bootstrap 4 Pingendo Aquamarine template for unique events
> MEDIUM CONFIDENCE! | Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ | scripts used in the Smart-3SEQ paper
Two predictive precision medicine tools for hepatocellular carcinoma.
Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data. Soft Windowing on Linear Regression. The main function in the package utilizes a windowing function in the form of an exponential weighting function to linear models. The bandwidth and sharpness of the window are controlled by two parameters. Then, a series of tests are used to identify the right parameters of the window (see Hamed Haselimashhadi et al (2019) <https://www.biorxiv.org/content/10.1101/656678v1>)
Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568
A Case Study in Deploying Weak Supervision at Industrial Scale. Programmatically Building and Managing Training Data. Build Training Sets Programmatically. Labeling and managing training datasets by hand is one of the biggest bottlenecks in machine learning. In Snorkel, write heuristic functions to do this programmatically instead!
Web-server framework to explore and visualize large genomic variation data in lab and its applications to wheat and its progenitors.
Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research.
Identification and resolution of plant taxonomic names.
SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.
A graphical model approach to identify primary genes in perturbed biological pathways. Topological gene-set analysis has emerged as a powerful means for omic data interpretation. Although numerous methods for identifying dysregulated genes have been proposed, few of them aim to distinguish genes that are the real source of perturbation from those that merely respond to the signal dysregulation. Here, we propose a new method, called SourceSet, able to distinguish between the primary and the secondary dysregulation within a Gaussian graphical model context. The proposed method compares gene expression profiles in the control and in the perturbed condition and detects the differences in both the mean and the covariance parameters with a series of likelihood ratio tests.
The South Green platform is a local network of scientists gathering Bioinformatics skills based on the Agropolis campus that hosts research institutes such as CIRAD, IRD, INRA, SupAgro, Alliance of Bioversity international and CIAT. Based on this strong local community in the field of agriculture, food, biodiversity and environment, this network of national and international scope, develops bioinformatics applications and resources dedicated to genetics and genomics of tropical and Mediterranean plants. South Green relies on the computer technical platforms of its partner institutes.
The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).
Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data | SoyCSN (Soybean Context Specific Network) - | SoyCSN (Soybean Context Specific Network) | SoyCSN computes and visualizes any of the 14 soybean context specific networks both at the expression and interactome level. Users can compare the gene-gene relationship differences at different confidence levels across all the soybean tissues
A Soybean mine instance with genomic data from the Legume Information Systems (LIS) multi-species chado database and genetic data pulled from Soybase
> HOMEPAGE MISSING! | Towards a fast and reliable clustering for potentially divergent biological sequences | This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed package was also intensively evaluated on simulated and real genomic and protein data sets. The clustering results were compared to the most known traditional tools, such as UCLUST, CD-HIT and DNACLUST
integrating tissue morphology and spatial gene expression to predict disease cells. SpaCell has been developed for analysing spatial transcriptomics (ST) data, which include imaging data of tissue sections and RNA expression data across the tissue sections. The ST data add a novel spatial dimension to the traditional gene expression data from dissociated cells. SpaCell is desinged to integrates the two histopathological imaging and sequencing fields, with the ultimate aim to discover novel biology and to improve histopathological diagnosis in a quantitative and automated way
Apache Spark based Read Clustering tool to cluster a large number of DNA/RNA sequences generated from next-generation sequence technologies, including Illumina and PacBio.
Encouraging durable memory using spaced testing in pediatric radiology.
Spaniel Spatial Transcriptomics Analysis.
Apache Spark is a unified analytics engine for big data processing, with built-in modules for streaming, SQL, machine learning and graph processing. Melanoma expression analysis with Big Data technologies.
Production-quality memory-efficient Apache Spark based genome analysis framework. SparkGA2 is an Apache Spark based scalable implementation of the best practice DNA analysis pipeline by Broad Institute, which is an improvement over the similar SparkGA1 (https://github.com/HamidMushtaq/SparkGA1.git)
a database for spatially resolved transcriptomes. Welcome to SpatialDB! click thumbnails to quickly browse the spatial gene expression profiles. Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology
A new approach to estimating pairwise sequence alignments. SimpleFastaParser from Bio.SeqIO.FastaIO. To create filtered datasets run Bacterial_pipeline_part1.py and Bacterial_pipeline_part2.py
SpikeInterface is an unified framework for spike sorting. Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.
A software tool for quantitative analysis of nanoscale spine morphology | Abstract Super-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ comes with an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology
ab initio prediction of splice sites using convolutional neural network. This is the source code for SpliceFinder
a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data. RNAseq pipeline for alternative splicing junctions. SpliceLauncher is a pipeline tool to study the alternative splicing. It works in three steps:. SpliceLauncher comes with a ready to use config.cfg file. It contains the paths of software and files used by SpliceLauncher. The INSTALL mode of SpliceLauncher updates this config.cfg file. If you define the path to GFF (v3) file and path to the FASTA genome, the INSTALL mode will extract all necessary information from this GFF and indexing the STAR genome. This informations are stored in a BED file that contains the exon coordinates, in a sjdb file that contains the intron coordinates and a text file that contains the details of transcript structures. You need to define where these files will saving by the -O, --output argument
Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.
SpliceVec: Distributed feature representations for splice junction prediction
Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks. SpliceVisuL: Visualization of Bidirectional Long Short-term Memory Networks for Splice Junction Prediction
Integrative, scalable tool for the discovery of splice-altering variants.
> MEDIUM CONFIDENCE! | Genome-wide epistasis and co-selection study using mutual information | SpydrPick is a command line tool for performing 'direct coupling analysis' of aligned categorical datasets. It constructs a coupling graph based on thresholded node-pair Mutual Information (MI) scoring, followed by pruning of edges that represent indirect couplings using the ARACNE algorithm | Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure | Home: https://github.com/santeripuranen/SpydrPick | License: GNU Affero General Public License
Software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences.
A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction | This is our model of MBD pulldown alignments generated from SssI-treated DNA proposed in the publication entitled "A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction". Please read through the instructions in the README before using the software. Test files are provided in the "source" folder. Links to the indexes of CpGs in hg18 and the corresponding yi Λ file, generated from that list using our experimental presets and summed on 10bp windows, are also given
R Package for Stacking with Applications to Scenarios Involving Sequential Addition of Samples and Features.
A stacking based prediction of protein-carbohydrate binding sites from sequence.
Interscholastic Network To Generate LexA Enhancer Trap Lines in Drosophila.
Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent years whole genome shotgun sequencing of clinical isolates has become common. As of August 2017 there were over 44,000 publicly available S. aureus sequencing projects in EBI's ENA database. Staphopia aims to provide rapid analysis of these whole-genome datasets as well as useful S. aureus specific results, such as genotype, antibiotic resistance and virulence gene profiles.
Extendable software package for Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates.
Stereological and Automated Analysis Platform for Assessing Histological Labelling in Cleared Tissue Specimens.
Evaluation and Classification of Peak Profiles for Sequencing Data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets
A phylogenetic tool to construct pathogen transmission networks | Welcome to the StrainHub Repo - Files and Data - StrainHub Online: | Strainhub is designed as a web-based software to generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata. The software maps the metadata onto the tree and performs a parsimony ancestry reconstruction step to create links between the associated metadata and enable the construction of the network. Users also have the option to skip the StrainHub ancestry reconstruction step by generating a maximum clade credibility tree (MCC) through BEAST phylogeography | Generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata
a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. Stress predicting framework with microarray data based on CMCL and logical correlation model. Stress Predictor based on Machine Learning. python learn.py dataset/dataset_learn_v2_005.limma.csv dataset/dataset_learn_v2_005.label.csv --reduce_updown --save output/model_v2 --save_csv output/model_v2 --epoch_count 1000 --batch_size 0. --reduce_updown Use this parameter if dataset is separated into up and down column
This is a tool for analysis of video data of mice engaged in string-pulling. It analyses Phenotyping motor behavior of mice for sensory, whole-body and bimanual skilled hand function.
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Genotyping low-coverage whole-genome sequencing intercross pedigrees from outbred founders' | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders | Whole-genome genotyping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing | Carlborg's Lab (Yanjun Zan, Thibaut Payen, Örjan Carlborg) - BMC - Uppsala University | Experimental intercrosses of divergent lines are useful to map loci (quantitative trait loci; QTL) contributing to phenotypic variation using the recombinant founder mosaic genotypes in the F2 generation | git clone https://github.com/CarlborgGenomics/Stripes
Program for alignment of structures of DNA-protein complexes.
Tool for 3D protein structure profiling.
a pipeline for building custom databases for common metagenome profilers | Ley Lab MetaGenome Profiler DataBase generator | de la Cuesta-Zuluaga, Jacobo, Ruth E. Ley, and Nicholas D. Youngblut. 2019. “Struo: A Pipeline for Building Custom Databases for Common Metagenome Profilers.” bioRxiv. https://doi.org/10.1101/774372
StudyPortal combines the free sources ClinicalTrials.gov, PubMed, OpenStreetMap and Geonames.org to provide you an integrated search for visualization of suitable clinical studies and scientific articles that match your search criteria.
A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces | SuAVE: Surface Assessment Via grid Evaluation
RDKit-based overlap measure that combines volumetric shape and pharmacophoric features to give a combined overlap score similar to OpenEye's Tversky Combo and Malhotra and Karanicolas' COS measure.
predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. MOTIVATION:Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder, and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. RESULTS:We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction
Random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph.
Intuitive and fast interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences or quality images.
The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.
SulfAtlas describes the family and sub-families of structurally-related sulfatases. Sub-families are created based on phylogenetic analyses and essentially correspond to different substrate specificities
Software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies.
An R package for summarizing multiple enrichment analysis results.
Tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics.
Image Super-Resolution as a Defense Against Adversarial Attacks | super-resolution-adversarial-defense | We use wavelet denoising and image super resolution as pre-processing steps to defend images against adversarial attacks. If you find our work useful in your research or publication, please cite our work:
Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Super CRF toolbox for training an conditional random field in combination with super pixel annotations
A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM | A Super Clustering Approach for Single Particle Picking in cryo-EM Images
Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data.
Pipeline for high-throughput extraction of cell contours from 3D image stacks.
P01.152 Evaluation of Factor V Leiden variant as risk a factor for venous thromboembolism in glioblastoma patients | The Swedish Frequency resource for genomics (SweFreq) is a website developed to make genomic datasets more findable and accessible in order to promote collaboration, new research and increase public benefit. You can contact swefreq@scilifelab.se if you want to find out more about this resource and how it could benefit you and your research | {{ mainCtrl.msg.level }}! {{ mainCtrl.msg.msg }}
A fast, memory-efficient, multiple genome orthology classifier. A high performance tool to identify orthologs and paralogs across genomes. SwiftOrtho is orthology analysis tool which identifies orthologs, paralogs and co-orthologs for genomes. It is a graph-based approach
> LOW CONFIDENCE! | Nonparametric expression analysis using inferential replicate counts | R scripts used in the Swish paper
System for Quality-Assured Data Analysis (SyQADA) - workflow management system that seeks to improve reproducibility in as simple a framework as feasible.
SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.
Symbolic computing in Python. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select domain specific submodules. The supplementary materials provide additional examples and further outline details of the architecture and features of SymPy. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem.
evaluation of free management platforms for synthetic biology designs | Web application enabling users and software to browse, upload, and share synthetic biology designs | Dumps all sequences from SynBioHub instances as FASTA | A parts repository for synthetic biology | SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources
An Automatic Tool to Quantify Synapses from Microscopy Images. A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images. SynQuant is a Fiji plugin that automatically quantify synapses from fluorescence microscopy images. Try SynQuant Now!. SynQuant performs better than peer unsupervised methods [5-8] for all the three data sets we tested (3D in-vivo [2], array tomography [3], neuron-astrocyte coculture [4])
Specific tools for pre-processing datas in order to use them in SynTView.
SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships in twelve primate species, including human
The JAX Synteny Browser for mouse-human comparative genomics. An interactive web-based conserved synteny browser application. The Jackson Laboratory Synteny Browser. An interactive web-based conserved synteny browser application, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genomes based on the biological attributes of the features. The current implementation for the browser supports the reference genomes of the laboratory mouse and human. Show true orientation of comparison genome relative to reference Always show gene symbols Show anchors. Reference species (outer ring) Mus musculus Homo sapiens
Improved target gene prediction. Abstract Motivation Identifying the genes regulated by a given transcription factor (its “target genes”) is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TF’s binding site and the expression of the gene across a set of tissues. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene. Results We present the T-Gene algorithm, which overcomes these limitations. T-Gene can be used to predict which genes are most likely to be regulated by a TF, and which of the TF’s binding sites are most likely involved in regulating particular genes.
Automated data extraction software for medical summary using text mining (T-Library). Library project of Physician’s empirical knowledge. Automatic extraction of medical information from medical record. Yamada T, Kondo Y, Momosaki R. 2019. Automated data extraction software for medical summary using text mining (T-Library) PeerJ Preprints 7:e27685v1 https://doi.org/10.7287/peerj.preprints.27685v1
Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis | temporal multi-task sparse canonical correlation analysis | T-MTSCCA: temporal multi-task SCCA model for longitudinal brain imagign genetics
an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Release 3: Maria Bogaerts maria.bogaerts@ibe.upf-csic.es, Josefa Gonzalez josefa.gonzalez@ibe.upf-csic.es. T-lex is a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data. Problems during installation? Try our DOCKER file.
user friendly database of tRNA sequences and structures. Discover the best tRNA database available!. There is simplified list of what you can do:. Search by sequence, structure and other properties. See available and generated models
> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'mDAD', 'T1DToolkit.org' | Designing Online and Mobile Diabetes Education for Fathers of Children With Type 1 Diabetes | T1D Toolkit – Manage Diabetes Better | Research QuestionBlog Post FeedbackTech Support | This field is for validation purposes and should be left unchanged
T1TAdb is a database of Type I Toxin-Antitoxin systems.
TACITuS is a portal, which deals with data pre-processing, selection and, eventually, integration of transcriptomic data coming from diverse sources, such as ArrayExpress.
A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. TAD-Lactuca is a tool to predict Topologically Associating Domains(TAD) boundary using histone marks information. It was written in Python language, using Random Forests(RF) and Multilayer Perception(MLP)
phylogenetic augmentation of microbiome samples enhances phenotype classification | TADA is a new data augmentation technique for classifying phenotypes based on the microbiome. Our algorithm, TADA, uses available data and a statistical generative model to create new samples augmenting existing ones, addressing issues of low-sample-size. In generating new samples, TADA takes into account phylogenetic relationships between microbial species. Adding these synthetic samples to the training set improves the accuracy of downstream classification, especially when the training data have an unbalanced representation of classes
Genome-wide supervised learning of non-coding loci associated to complex phenotypes.
Tool for analysis of the morphology of microbial colonies.
Tool for alternative polyadenylation site analysis.
Pipeline for TARgeted VIRal strain reconstruction from metagenomic data.
BLAST service for the entire “TARA OCEANS” collection, an international project to which many researchers of the institute cooperated. It includes assembled sequences of prokaryotic and eukaryotic fractions.
Package for Calibrated Flow Cytometry Analysis.
An in-silico method for predicting the thermal activity for xylanases from GH10 and GH11 families. a multi-step method for the classification of xylanases from glycoside hydrolases families 10 and 11 based on their optimum temperature of activity. TAXyl: An in-silico method for predicting the optimum temperature of activity for xylanases from GH10 and GH11 families. Xylanases are involved in lignocellulosic biomass degradation and the enzyme optimum temperature is an essential factor to be considered for choosing an appropriate biocatalyst for specific usage
Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign. International partnership for clinical informatics. and advanced research in tuberculosis. Leveraging clinical, genomic, and imaging data.
Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.
> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'tree-child', 'BTC' | Generation of Binary Tree-Child phylogenetic networks | Supplementary files for "Generation of Tree-Child phylogenetic networks" | If you have pipenv installed, the requirements can be installed by executing pipenv install. Notice however that graphviz must be installed previously (only needed to run the Jupyter notebook). Once installed, the jupyter notebooks can be run with pipenv run jupyter-notebook, and the scripts with pipenv run python script.py | The jupyter notebook can also be run without installing anything:
A Network Pharmacology Approach for Uncovering the Osteogenic Mechanisms of Psoralea corylifolia Linn.
T Cell Relation Extraction (TCRE) - Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature.
The TCRex web tool provides a user-friendly interface to predict the recognition of pathogenic & cancer epitopes by human T cell receptors (TCRs). It can predict TCR–epitope binding based on TCR beta chain information from full repertoire data files from standard files (Immunoseq, MiXCR, etc), and calculates appropriate statistics.
Structural modelling of TCR-pMHC class I complexes. Structural modeling tool of TCR-pMHC class I complexes. TCRpMHCmodels predicts the three-dimensional structure of TCR-pMHC class I complexes using comparative modelling. Upon submission, this tool automatically selects the best templates and provides within minutes a complete three-dimensional model. The input must include all protein chains from the TCR-pMHC complex (the TCR alpha chain, the TCR beta chain, the peptide chain and the MHC chain), separated by a fasta header. The tool will automatically detect the chain types
> CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:TCSM' | Modeling clinical and molecular covariates of mutational process activity in cancer | Tumor Covariate Signature Model (TCSM) | This repository contains the code for reproducing the results on real data from the paper Modeling Clinical and Molecular Covariates of Mutational Process Activity in Cancer, which implements the Tumor Covariate Signature Model (TCSM)
A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations.
analysis of single and comparative transcriptomes | Download TCW package: www.agcol.arizona.edu/software/tcw or from this site | Transcriptome Computational Workbench | AGCoL : TCW Home : Doc Index : singleTCW Guide : DE Guide : multiTCW Guide : Tour | Description: For single-transcriptome (singleTCW) - similarity search against annotation databases, GO annotation, ORF finding and differential analysis. For multi-transcriptome (multiTCW) - compute similar pairs, provide statistics for pairs, compute clusters, provide statistics for clusters. Both singleTCW and multiTCW provide graphical interfaces for extensive query and display of the results | TCW provides analysis and query for sequences (transcriptome, proteome), and comparison of species sequences. TCW uses Java, mySQL, optionally R, and various External packages. It has been tested on Linux and Mac
Multiple sequence alignment program. The main characteristic is that it will allow you to combine results obtained with several alignment methods.
Multiple sequence alignment that combines several alignment methods.
A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.
> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Betti', 'resting-state' | Exact topological inference of the resting-state brain networks in twins | Exact Topological Inference (ETI) for Brain Networks | The data/codes presented here is published in [4,5,6]. Using the data, we will show how to construct Betti plots from weighted brain graphs, where the weights are Pearson correlations. Then show how to perform the exact topological inference and obtain the p-value on the Betti plots. The Betti plots are the basic data visualization technique in persistent homology but statistical inference procedure has been lacking in the field [1,2,3]. New exact topological inference framework is developed for determining statistical significance of Betti plots | The codes have been tested with MacBook Pro with MATLAB 2016
> HOMEPAGE MISSING! | A Software to Identify Complete and Truncated T-DNA Insertions | Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software
TDimpute is a novel transfer learning-based neural network to impute missing gene expression data from DNA methylation data. In the tool, the pan-cancer dataset from TCGA was utilized for training a general model for all cancers, which was then fine-tuned on the target cancer dataset for imputation.
TE-Tracker is a program for detecting germline transposition events through whole-genome resequencing.
A Verification Checklist to Reduce Errors in Models and Improve Their Credibility. This is the model verification repository. An application example is uploaded on the repository. This example will be updated further and with other elaborated examples. The TECH-VER checklist consists of five domains: (1) input calculations; (2) event-state (patient flow) calculations; (3) result calculations; (4) uncertainty analysis calculations; and (5) other overall checks (e.g. validity or interface). In health economic literature, checklists or best practice recommendations on model validation credibility always declare verification of the programmed model as a fundamental step, such as ‘is the model implemented correctly and does the implementation accurately represent the conceptual model?’ However, to date, little operational guidance for the model verification process has been given
Graph-based computational method for decomposing protein structures into closed loops.
Prediction of essential proteins by integrating network topology, subcellular localization information, gene expression profile and GO annotation data.
TEMPO (TEmporal Modeling of Pathway Outliers) - method for modeling and detecting gene sets with disruption of some temporal pattern of expression.
TEffectR is an R package for studying the potential effects of transposable elements on gene expression with linear regression model.
> CORRECT NAME OF TOOL COULD ALSO BE 'maizeTE_variation' | Transposable elements contribute to dynamic genome content in maize | Structural transposable element (TE) annotation of multiple maize genomes | TEs along a region of the genome: | We reconstruct the history of TEs nesting into each other. For example, the blue TE on the left inserted first, and then was disrupted by the insertion of green and yellow TEs
lineage-level classification of transposable elements using conserved protein domains. Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH
an expanded motif database for DNA shape features of transcription factor binding sites. Responsive Bootstrap 4 Admin & Dashboard Template. TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs). These structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. The DNA shape features were predicted using our recently published high-throughput method (Zhou et al. NAR 2013) and visualized in the form of heat maps. Users can download these DNA shape feature data and perform further analysis, for example, to identify which DNA shape feature(s) at which position(s) in the target DNA contribute to the DNA binding specificity of a TF. Users can also compare DNA shape profiles, both qualitatively and quantitatively, between two TF datasets from the database, or between a set of uploaded sequences and a TF from the database
Constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. It seems like you are using Internet Explorer, which is not supported yet. Please switch to Chrome , Firefox , or Safari
TFregulomeR comprises of a comprehensive compendium of transcription factor binding sites (TFBSs) derived from the MethMotif and GTRD, as well as the ready-to-use functionality in R language facilitating data access, integration and analysis. The binding motifs predicted in-silico from MethMotif and GTRD describe cell specific transcription factor (TF) binding propensities, while the DNA methylation profiles from MethMotif portray a second epigenetic dimension in TF binding events. The whole toolbox allows a better understanding of the TF binding propensities in a cell-specific manner.
TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.
Rapid Reconstruction of Time-varying Gene Regulatory Networks with Limited Main Memory | Abstract Reconstruction of time-varying gene regulatory networks underlying a time-series gene expression data is a fundamental challenge in the computational systems biology. The challenge increases multi-fold if the target networks need to be constructed for hundreds to thousands of genes. There have been constant efforts to design an algorithm that can perform the reconstruction task correctly as well as can scale efficiently (with respect to both time and memory) to such a large number of genes. However, the existing algorithms either do not offer time-efficiency, or they offer it at other costs memory-inefficiency or imposition of a constraint, known as the ‘smoothly time-varying assumption’
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries | *: Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human body parts are crucial for building medical text mining applications. To achieve this, we establish a mapping system consisting of a Wikipedia-based scoring algorithm and a named entity normalization method (NEN). The mapping system makes full use of information available on Wikipedia, which is a comprehensive Internet medical knowledge base
Testing Haplotype Effects In Association Studies
Bioinformatics pipeline for the analysis of TILLinG mutants in conjunction with the new optimised reference sequence for tetraploid wheat. This tool consists of TILLING populations developed in tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and John Innes Centre.
A Code for Modeling and Generating Electric Fields-Features and Applications to Enzymatic Reactivity. TITAN (elecTric fIeld generaTion And maNipulation) is being developed by:
Computational tool to assess titin’s role as a disease gene.
The use of patient-specific equipoise to support shared decision-making for clinical care and enrollment into clinical trials | Total Knee Replacement (TKR) Decision Support | TMC Total Knee Replacement (TKR) Math Equipoise | Welcome to the Knee Arthritis Treatment Tool
Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion | TM-IMC: Text Mining and Induce Matrix Completion for GPCR function prediction | TM-IMC is an algorithm for automated annotation of Gene Ontology (GO) term for G protein-coupled receptors (GPCRs) using features derived from text mining and induced matrix completion of GPCR-GO associatation matrix
A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments.
Phylogenetic Tree-based Microbiome Association Test | Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals
> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'iBIOMES', 'Lite', 'iBIOMES Lite', 'nucleosome' | TMB Library of Nucleosome Simulations | Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 μs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library
A Web Tool for Predicting Stability of Transmembrane α-Helix Association.
improving reference-free cell composition estimation by cross-cell type differential analysis | Tools for the analysis of heterogeneous tissues | This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. improve variable selection in reference-free deconvolution | DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation.
database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavioral, morphological, phenological, and physiological traits coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. We ultimately aim to provide an inclusive and accessible data resource to facilitate advances in fish research
Proton Monte Carlo platform for research and clinical applications.
Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.
Dose-Response Metabolomics to Understand Biochemical Mechanisms and Off-Target Drug Effects with the TOXcms Software. Job opportunities are available
measuring functional diversity across scales based on TPD with R | Methods for Measuring Functional Diversity Based on Trait Probability Density | Tools to calculate trait probability density functions (TPD) at any scale (e.g. populations, species, communities). TPD functions are used to compute several indices of functional diversity, as well as its partition across scales. These indices constitute a unified framework that incorporates the underlying probabilistic nature of trait distributions into uni- or multidimensional functional trait-based studies. See Carmona et al. (2016) <doi:10.1016/j.tree.2016.02.003> for further information
Software to quantify mRNA abundance of genomic features.
TPOT stands for Tree-based Pipeline Optimization Tool. Consider TPOT your Data Science Assistant. TPOT is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.
Institute for Systems Biology "Trans-Proteomic Pipeline"
a scalable workflow for predicting cancer of unknown primary based on next-generation transcriptome profiling | Cancer of unknown primary site (CUP) accounts for 5% of all cancer diagnoses. These patients may benefit from more precise treatment when primary cancer site was identified. Advances in high-throughput sequencing have enabled cost-effective sequencing the transcriptome for clinical application. Here, we present a free, scalable and extendable software for CUP predication called TRANSCUP, which enables (1) raw data processing, (2) read mapping, (3) quality report, (4) gene expression quantification, (5) random forest machine learning model building for cancer type clas-sification. TRANSCUP achieved high accuracy, sensitivity and specificity for tumor type classifica-tion based on external RNA-seq datasets. It has potential for broad clinical application for solving the CUP problem
TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.
Software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing.
The TRAX Light-Rail Train Air Quality Observation Project. - Department of Atmospheric Sciences. Department of Atmospheric Sciences. College of Mines and Earth Sciences. Monitoring Air Quality Along UTA TRAX Lines.
Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data.
T-cell Receptor/Immunoglobulin Profiler (TRIP)
Chromosome-scale sequence assembly of Triticeae genomes with open-source tools.
Web-tool for prediction of protein–protein Interactions in human Transcriptional Regulation.
Tool for visualizing and analyzing cancer hallmarks in signaling networks.
Mapping spatio-temporal dynamics of single biomolecules in living cells. TRamWAy helps analyzing single molecule dynamics. It infers the diffusivity, drift, force and potential energy across space and time
Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains.
a trait-tissue association map for human complex traits and diseases. deTSDB, deTS, TSEA, tissue-specificity. TSEA-DB provides a comprehensive reference for trait-associated tissues. A systematic tissue-specific enrichment analysis (TSEA) has been conducted using deTS to infer tissues in which trait-associated genes are enriched. Two reference tissue panels are collected: the GTEx v7 panel (47 tissues) and the ENCODE panel (44 tissues). A total of 5019 GWAS summary statistics data sets for human complex traits and diseases (435 + 161 GWAS data sets from the non-UKBB panel and 4423 data sets from the UKBB panel) have been analyzed for their causal tissues. Content 1. 1. Collection and processing of GWAS summary statistics for complex traits and diseases. The Multi-Trait Collection (MTC) traits were previously reported in the work by Liu et al., 2019
Translational Bioinformatics Tool Suite For Network Analysis And Mining. An R software for Gene Co-Expression Analysis. Gene co-expression network (GCN) mining aims to mine gene modules with highly correlated expression profiles across sample cohorts. It may help to reveal latent molecular interactions, identify novel gene functions, pathways and drug targets, as well as providing disease mechanistic insights on for biological researchers. TSUNAMI is developed to allow biological researchers with no programing background to perform GCN mining themselves. Users can get access to our online service from http://spore.ph.iu.edu:3838/zhihuan/TSUNAMI/
A computational tool for the specific prediction of tumor T cell antigens | Nowadays, cancer is considered a global pandemic and millions of people die every year because this disease remains a challenge for the world scientific community. Even with the efforts made to combat it, there is a growing need to discover and design new drugs and vaccines. Among these alternatives, antitumor peptides are a promising therapeutic solution to reduce the incidence of deaths caused by cancer. In the present study, we developed TTAgP, an accurate bioinformatic tool that uses the random forest algorithm for antitumor peptide predictions, which are presented in the context of MHC class I. The predictive model of TTAgP was trained and validated based on several features of 922 peptides
A FIJI Macro for quantifying pattern in extracellular matrix. Welcome to The Worklfow Of Matrix BioLogy Informatics (TWOMBLI). Twombli is a Fiji plugin. To get started download the TWOMBLI folder to your computer. Your browser does not support the video tag
In the TXG-MAPr, users can analyze dose- and time-response curves, compound correlation plots and functional annotation of the WGCNA modules to derive mechanistic information of the toxicity. In addition, we included the prediction of transcription factor activities, as well as physical interactions between downstream proteins encoded by the transcriptome, which might be useful in analyzing the perturbations triggered by exposure with toxic compounds. Users can investigate module perturbation of the TG-GATEs compounds by looking at the module eigengene scores (EGS)
In situ structure determination at nanometer resolution using TYGRESS. TYGRESS:Tomography-Guided 3D Reconstruction of Subcellular Structures. Tomography-Guided 3D Reconstruction of Subcellular Structures (TYGRESS) is a hybrid method, which combines the advantageous features of both cryo-electron tomography and single particle cryo-EM to achieve higher resolution than before of complex subcellular structures within their native environment. Back to UT Southwestern Back to UTSW Labs
Automated high-throughput platform for state-of-the-art genome-based taxonomy.
A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms. The "tranucleotide-derived Z-value Manhattan Distance” (TZMD) approach profiles genomic composition with high resolution, which can distinguish bacteria at even strain level
Targeted Bisulfite Sequencing Analysis Pipeline A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform. TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length, number of mismatches etc. are adjustable -The output gives heatmap with categories.
Web platform for taxonomic profile-based fungal gene prediction.
open-source mobile software for distributed studies of hearing. TabSINT is an open source platform for administering tablet based hearing-related exams, as well as general-purpose questionnaires. It is meant to be flexible, easy-to-use, and useful for administrators who manage studies of all sizes. Open source platform for hearing assessments,and general purpose questionnaires
A Tool to Analyze the Binding Affinity | Taba: Tool to Analyze Binding Affinity | Taba is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. You can use a higher version as well
Computational tool that reveals vast protein modification landscapes from large tandem mass spectrometry datasets.
Tool for predicting conserved microRNA targets and target mimics in plants.
Long noncoding RNA ZFAS1 promotes tumorigenesis and metastasis in nasopharyngeal carcinoma by sponging miR-892b to up-regulate LPAR1 expression. Search for predicted microRNA targets in mammals. 1. Select a species Human Mouse Rat Chimpanzee Rhesus Cow Dog Opossum Chicken Frog. 2. Enter a human gene symbol (e.g. "Hmga2"). TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer , 7mer , and 6mer sites that match the seed region of each miRNA.
Connecting genetics and drug discovery | This is the Target Gene Notebook source-code repository | to build TGN backend against git repository:
in-field counting of wheat spikes with context-augmented local regression networks. This is the repository for TasselNetv2, presented in:
An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples.
An Atlas of the Subcellular Proteome of Human T Cells. This is a curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively.
Deconvolving the effects of pervasive and autonomous transcription of transposable elements | TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data | #About TeXP is a pipeline for quantifying abundances of Transposable Elements transcripts from RNA-Seq data. TeXP is based on the assumption that RNA-seq reads overlapping Transposable Elements is a composition of pervasive transcription signal and autonomous transcription of Transposable Elements
A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows.
Telescope is an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. It allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Moreover, output files are rendered in HTML in real time, allowing the use of markdown and rich-text features. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted.
Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq. It can be used for Statistical Performance of TE Quantification Methods. All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.
In silico estimation of telomere content and composition from cancer genomes.
Package to study genetic variation in tera-scale genotypes as it performs PCA of large-scale datasets.
Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. This repository contains data and materials linked to the Terminome-Seq project. The preprint of the manuscript is 2019_Terminome-Seq.pdf or it can be downloaded from the Bioarxiv website here https://www.biorxiv.org/content/10.1101/621938v2
Terra Populus' Architecture for Integrated Big Geospatial Services | Boundaries are missing for the selected sample geography. Please select a different sample geography
a set theoretical utility for exploring sequence variant data | Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data | Tersect is a command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data. The tool generates index files based on provided variant data (VCF files) which can then be used to rapidly execute flexible set theoretical queries and output the resulting lists of variants in selected regions
A Set of Stata Commands for Confirmatory Tetrad Analysis | This respository contains three Stata commands for conducting Confirmatory Tetrad Analysis (CTA). In addition, the repository is set up so that the commands can be installed within Stata. Simply type "net install tetrad, from(https://github.com/sbauldry/tetrad/raw/master) replace" without the quotes in Stata's command window. These commands are introduced in Bauldry and Bollen (2016)
a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia. ThalPred: Development of Decision Model for Discriminating Thalassemia Trait and Iron Deficiency Anemia
ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more.
The Great Genotyper is an alignment-free population genotyper of small and structural variants. It begins by preprocessing raw sequencing data to create a Counting Colored De Bruijn Graph (CCDG). Then it uses the succinct CCDG to genotype any list of phased or unphased variants, leveraging the population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art with unprecedented performance. It took 100 hours to genotype 4.5M variants in 4.2K whole genome human samples using one server with 32 cores and 145GB of memory.
Web-based data management tool for health and medical research.
the Therapeutic Structural Antibody Database | The Structural Antibody Database | (Therapeutic Structural Antibody Database) | Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link] | SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]
High-throughput analysis software for non-invasive thermal assessment of laboratory mic.
Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction | This is a TensorFlow implementation accompanying our paper. This codebase is based on Shreshthgandhi's Tensorflow implementation of the cdeepbind model. The framework of model training and testing have beed adopted with minor changes. Other code files have been modified and re-structured with changes specific to our model. And the folder, scripts/RNAsubopt is a copy of RNAsubopt from the ViennaRNA project | We used two datasets to evaluate our model. The following datsets were used for training our models | You can download the datasets from the corresponding website. After that, you should prepare the data used in the training code according to the steps below. We use the CLIP-seq dataset as an example | BTW, The ThermoNet implementation is available at invitro bin deepbind_model utils_update.py
Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML
quantifying phosphopeptide positional isomers | The human phosphorylation regulatory network represents a complex signaling cascade where proteins can be phosphorylated at multiple sites resulting in different functional states. Here we present Thesaurus, a hybrid search engine that detects, localizes, and quantifies novel positional isomers using site-specific fragment ions directly from data independent acquisition mass spectrometry experiments. This software works for several PTMs in addition to phosphorylation. Check out our paper describing Thesaurus and what it can do at Nature Methods (Searle et al, 2019)!
Spatial transcriptomics integrates transcriptomics data with histological tissue images, offering deeper insights into cellular organization and molecular functions. However, existing computational platforms mainly focus on genomic analysis, leaving a gap in the seamless integration of genomic and imaging modalities. Thor is a comprehensive spatial transcriptomics analysis tool designed to bridge this gap by enabling efficient co-analysis of gene expression profiles and high-resolution tissue images. It provides scalable workflows for spatial feature extraction, cell segmentation, gene–spatial correlation, and visualization, facilitating multi-omic insights into tissue architecture and cellular heterogeneity.
Tool for determining the threshold in short RNA-seq datasets.
Software for scalable execution of portable pipelines on the cloud.
efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain | TideHunter is an efficient and sensitive tandem repeat detection and consensus calling tool which is designed for tandemly repeated long-read sequence (INC-seq, R2C2, NanoAmpli-Seq)
Time-energy measured data on modern multicore systems running shared-memory applications.
Scripts for analyzing transposon sequencing data used by the Whiteley lab | Custom scripts for analyzing (parsing, mapping, and tallying) Tn-seq reads and determining differentially abundant transposon insertion mutants | The scripts contained herein can be used to automatically analyze high-throughput (Illumina) sequencing reads derived from transposon-genome junctions
Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.
Generic Web framework for rendering an information block.
Genome browser for tomato (cultivar Heinz 1706 version 2.50) that includes RNAseq tags, EST and Tentative Consensus sequences to investigate the functional and structural annotation of the tomato genome.
Tool for selecting high-quality top-down proteomics mass spectra.
A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models.
R package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.
a graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology. Topological-tumour-graphs
A post sequencing QC tool for Oxford Nanopore sequencers.
> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'agonist', 'RXR' | Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library | Concentration 5-30% of expected value
A method for merging multiple independent neuronal traces.
Track-Control is an automatic video-based real-time closed-loop behavioral control toolbox.
TrackFind is a FAIR genomic tracks search and curation engine. It supports crawling of the TrackHub Registry and other data portals to fetch track metadata. Crawled metadata can be accessed through hierarchical browsing or by search queries, both through a web-based user interface and as a RESTful API. TrackFind supports advanced SQL-based search queries that can be easily built in the user interface, and the search results can be browsed and exported in JSON or GSuite format. The RESTful API allows downstream tools and scripts to easily integrate TrackFind search, currently demonstrated by the GSuite HyperBrowser and EPICO.
Genome-wide tool for preliminary assessment of therapeutic target druggability.
A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity | Files needed to build a Singularity container to run the TractoFlow pipeline | Singularity related files for TractoFlow | The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram
Machine learning tool for microscopy pixel classification.
NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. The second version of NanoSim (v2.0.0) uses minimap2 as default aligner to align long genomic ONT reads to reference genome. It leads to much faster alignment step and reduces the overall runtime of NanoSim. We also utilize HTSeq, a python package, to read SAM alignment files efficiently.
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
De novo transcriptome assembler that uses line graph iteration.
a novel machine learning approach for eukaryotic promoter prediction. Approach for prediction of eukaryotic transcription start sites. A deep learning approach for precise prediction of eukaryotic transcription start sites. Our approach offers significant improvement over existing promoter prediction methods. We provide the full basis for the comparison and encourage users to freely access our computational method to facilitate and streamline their own analyses. ./data/ contains some data files. TSS_MSU.txt was used for TSS sequence taking. Rice genome can be downloaded from MSU rice experiment official page
Software for the prediction of orthologs between two species, based on transcripts sequence similarities. A procedure to extend BLAST alignments and to define orthologs based on the “Bidirectional Best Hit” approach was implemented.
Fast and Reliable Tool for QSAR. Transformer CNN for QSAR/QSPR modelling. The repository contains the source code for a new Transformer-CNN method described in our paper http://arxiv.org/abs/1911.06603. First, we trained the Transformer model on SMILES canonicalization task, e.g., given an arbitrary SMILES, the model converts it to a canonical one. Second, we use the internal representation of the Transformer (the output of the encoding stack with shape (BATCH, LENGTH, EMBEDDING)) as SMILES embeddings and build upon them CharNN model (Convolution and HighWay as it is done in DeepChem). The resulting model works both in classification and regression settings
A Computational Theory for the Discretized Entorhinal Cortex.
A Code for Computing Kinetic and Related Parameters in Chemical Transformations and Transport Phenomena | Recent advances in phenomenological descriptions of the kinetics of rate processes (Aquilanti et al., 2010, 2017, 2018) motivated this code based on detailed formulations given in previous works | Theoretical and Computational Chemistry
Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models.
Tree-Weighting for Multi-Study Ensemble Learners.
Clustering biological sequences using phylogenetic trees | Efficient phylogenetic clustering of viral sequences | TreeCluster is a tool that, given a tree T (Newick format) and a distance threshold t, finds the minimum number of clusters of the leaves of T such that some user-specified constraint is met in each cluster. The user can also specify a branch support threshold s such that no pair of leaves in any cluster can be connected by branches with support less than or equal to s. Note that all leaves given a cluster of -1 are singletons, meaning they did not cluster with any other leaves (i.e., each leaf with a cluster of -1 is in its own cluster)
R package that performs analyses of expression evolution from RNA-seq data, including optimized input formatting, normalization and pair-wise distance evaluation, expression character tree inference and preliminary phylogenetic network analysis.
Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. Computational Biology Research Laboratory. TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts. TreeFix-TP is designed for scenarios where multiple strain ... Our websites may use cookies to personalize and enhance your experience. By continuing without changing your cookie settings, you agree to this collection. For more information, please see our University Websites Privacy Notice . TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts
a new method for improving the scalability of species tree estimation methods | TreeMerge is a tool for scaling phylogengy estimation methods to large datasets. TreeMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). TreeMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2019)
Treerecs is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence.
> CORRECT NAME OF TOOL COULD ALSO BE 'TreeshrewDB v2.0' | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome | Symbol Accession number Full gene name | &nbspFan Y, Yu D et al., 2014. Tree shrew database (TreeshrewDB): a knowledge base for Chinese tree shrew genome biology. Scientific Reports, 4: 7145 | 2019-09-05 Upgrading, some functions are not available
Software tool to prioritize important genes in pathways and their non-coding regulators.
Efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species.
A tool for interactive visualization and comparison of genetic maps. Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices
TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis.
Toolkit for rapidly simulating ChIP-seq data using statistical models of the experimental steps.
Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs.
Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, which consists of four genera and 19 extant species. The members of the genus Tupaia , which are colloquially referred to as the tree shrews, were first recorded in a sketch by William Ellis on a voyage with Captain Cook in 1780. Tree shrews are similar in appearance to squirrels, and their body weight ranges between 120-200 g. The natural habitat of the tree shrews consists of the tropical rainforests in South East Asia, where they feed on fruits, insects, and small vertebrates
Protein MD Setup tutorial using BioExcel Building Blocks - a Jupyter Notebook tutorial.
The UK Adult Twin Registry Update | If you would like access to data or samples from the Department Of Twin Research & Genetic Epidemiology or are interested in proposing a collaboration with us, please first follow the link DTR Policy Document for data access which will give you the necessary background information | You will then need to complete a “Data Access Proposal Form” (links below) and email the completed form to the Data Access Manager Victoria Vazquez or fax to +44 (0)20 7188 6718 for consideration by the Department of Twin Research Executive Committee | No attempt should be made to link or combine the data provided under this agreement to other information or archived data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, unless specific permission to do so has been received from the TwinsUK TREC | The proposal should specify the data and or samples required clearly
a tool to genotype mobile element insertions from whole genome resequencing data. Genotyping of segregating mobile elements insertions. This pipeline is developped by Jainy Thomas (University of Utah) and Clement Goubert (Cornell University). Elaborated with the collaboration of Jeffrey M. Kidd (University of Michigan). TypeTE is a pipeline dedicated to genotype segregating Mobile Element Insertion (MEI) previously scored with a MEI detection tool such as MELT (Mobile Element Locator Tool, Gardner et al., 2017). Please adress all you questions and comments using the "issue" tab of the repository
> CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:U-PASS' | unified power analysis and forensics for qualitative traits in genetic association studies | GWAS power calculator / generic power calculations for large scale association tests. Built with R Shiny | U-PASS: a Unified Power Analysis of Association Studies
Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.
Unified Biological Dictionaries (UniBioDicts) is a set of software packages that unite many of the most important biological controlled vocabularies, database vocabularies, and ontologies, under a common query-interface. These packages can access these disparate biological resources, and map their vocabulary data onto a common representation consisting of terms (which biocurators prefer to use), a unique identifier (which computers can reason with), and various descriptive metadata. This cross-resource infrastructure is essential for an efficient, modernized biocuration process, as it directly enables the autocomplete-based curation of particularly context-rich annotations, that combine terminology from across biological niches.
Utilities for handling sequences and assemblies from the UCSC Genome Browser project.
The Upper Gastrointestinal Cancer Registry (UGICR) is a clinical quality registry, that collects information about the diagnosis, treatment and outcomes of individuals with upper gastrointestinal cancer. The registry is managed by the Cancer Research Program part of Public Health and Preventive Medicine , Monash University.
> MEDIUM CONFIDENCE! | A Model Based Tool to Detect Tandem Repeats | ULTRA Locates Tandemly Repetitive Areas | To contribute to ULTRA development, you want to be on the develop branch, which is where we are currently integrating feature branches. For more information, see the ULTRA wiki
a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries | UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries
Efficient algorithms to discover alterations with complementary functional association in cancer.
Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing.
An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. A unified environment for DNN-based automated segmentation of neuronal EM images. Check the following pages after installation. Click the link "main.exe" in [UNI-EM] to launch the control panel. Urakubo, H., Bullmann, T., Kubota, Y., Oba, S., Ishii, S., UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. Scientific Reports 9, 19413 (2019) doi:10.1038/s41598-019-55431-0
a web tool for the integration and visualization of biomolecular networks for protein function prediction | In order to execute an experiment, you must first create an experiment design | {{ experiment.name }}-{{ experiment.newid }}
Big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardized biobanking.
Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation. Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018. UNet++: A Nested U-Net Architecture for Medical Image Segmentation. UNet++ is a new general purpose image segmentation architecture for more accurate image segmentation. UNet++ consists of U-Nets of varying depths whose decoders are densely connected at the same resolution via the redesigned skip pathways, which aim to address two key challenges of the U-Net: 1) unknown depth of the optimal architecture and 2) the unnecessarily restrictive design of skip connections
Unsupervised Online Video Object Segmentation With Motion Property Understanding | Tao Zhuo, Zhiyong Cheng, Peng Zhang, Yongkang Wong, and Mohan Kankanhalli | Results on DAVIS-2016 TrainVal Dataset (50 videos)
A Convolution Neural Network (CNN) model to classify publications with accession annotations according to UniProtKB categories
an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific peroxygenases (UPOs) present in the fungal kingdom. The fungal UPOs in this database are obtained by searching against all the fungal genomes present in the Ensembl database. This server uses profile hidden Markov models (HMMs) for homology search and incorporates clustering algorithms to group the most similar sequences
Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates.
Sample sizes and population differences in brain template construction. Caucasian and Chinese Brain templates [US200 CN200]
Clinical and pharmacological application of multiscale multiphysics heart simulator, UT-Heart | Cardiotoxicity Hazard Map/ECG Data Base NEW | The world’s leading technologies open the new door for:
User-friendly Transcriptome Analysis Pipeline.(UTAP) is open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data.
The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans . The database provides detailed information on 3'UTR structures and alternative polyadenylation for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar ) as well as new annotations generated by others. 3'UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of 3'UTRs we are building a 3'UTR database for C. elegans .
The Unified Variant Pipeline (UVP) is used to identify variants and assign lineage from Mycobacterium tuberculosis sequence data.
visualization and enhanced analysis of circular RNAs via back and canonical forward splicing | An R-shiny app that provides backsplice and canonical splicing analysis for both circRNA and parental transcripts | An R package that provides analysis and visualisation of canonical and backsplice junctions. Takes output provided by the STAR aligner as well as CIRI2 and circExplorer2 output and enables circRNA downstream analysis | Ularcirc manuscript now available through Nucleic Acids Research | Author and maintainer: David Humphreys (d.humphreys at victorchang dot edu dot au) | Ularcirc can annotate circRNA with overlapping gene information. This is obtained from available bioconductor databases. Use the following command to identify what databases to download:
Geothematic open data in Umbria region. Carta di pericolosità sismica locale dell’Umbria. Benvenuti nel Portale Open Data dell' Umbria. I dati della Pubblica Amministrazione umbra a disposizione dei cittadini. www.regione.umbria.it leggi di più. La cartografia di pericolosità sismica vettoriale della Regione Umbria è stata ultimata nel 2013 utilizzando tutti gli originali d'autore delle carte di pericolosità sismica locale realizzate alla scala 1:10.000, riviste ed omogeneizzate
Unified rational protein engineering with sequence-based deep representation learning. UniRep model, usage, and examples. UniRep, a mLSTM "babbler" deep representation learner for protein engineering informatics. Analysis and figure code from Alley et al. 2019. git clone https://github.com/churchlab/UniRep-analysis.git. First clone or fork this repository and navigate to the repository's top directory (cd UniRep). We recommend using our docker environments. Install docker to get started
Top ‱ cited papers from PUBMED. Unicorn Papers are based on an equal contribution (EC) citation model in which the total number of citations had been divided by the number of the authors. Currently, the list contains 3405 papers with ECcit ≥ 847.0 (updated monthly since 2020). ‱ - permyriad, literally meaning "for (every) myriad (ten thousand)"
Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Retrieving Information of Proteins from Uniprot. Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information. UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProtknowledgebase). M. Soudy, A. Anwar, E.A. Ahmed, et al., UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase), Journal of Proteomics (2019), https://doi.org/10.1016/j.jprot.2019.103613
Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola | Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola
Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS. Implementation of a visualization prototype for molecular structures and networks using the Unity3D game engine. Implementation of numerous graphical methods as spheres, particle systems, bond, etc.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.
Classification and annotation of viral sequences based on RefSeq annotation.
High-throughput variant antigen profiling in African trypanosomes of livestock | Variant Antigen Profiling for Trypanosoma congolense and Trypanosoma vivax | Trypanosomes are important human and veterinary parasites that cause potentially lethal blood infections and a chronic wasting disease (African trypanosomiasis). These organisms use antigenic variation to evade the host immune response, for which their genomes contain many hundreds of variable antigen genes. Making sense of this hypervariable repertoire is a major challenge in genome analysis and a bottleneck in vaccine development | the VAPPER code for the first time, please type:
Search for Drug Transporter Entries: | Examples: P-glycoprotein 1 ; BCRP ; OATP1B1 ; Oxaliplatin ; Lung cancer .. | Search Drug Transporter by Transporter Name: | J. Y. Yin, W. Sun, F. C. Li, J. J. Hong, X. X. Li, Y. Zhou, Y. J. Lu, M. Z. Liu, X. Zhang, N. Chen, X. P. Jin, J. Xue, S. Zeng * , L. S. Yu * & F. Zhu * . VARIDT 1.0: Variability of Drug Transporter Database. Nucleic Acids Research . doi: 10.1093/nar/gkz779 (2020). PMID: 31495872
sampling complementary RNA reads from the sequence read archive. VARUS: Drawing Diverse Samples from RNA-Seq Libraries. VARUS was originally written by Willy Bruhn as a Bachelors' thesis supervised by Mario Stanke. This repository is a copy of https://github.com/WillyBruhn/VARUS made in November 2018 and contains many bugfixes, an incremental intron database feature and an extension for using HISAT al alternative alignment program
VASE is a web-tool for visualizing alignments on a protein structure. It allows you to enter the ID of a protein structure in PDB format for which VASE will generate an interface. VASE will show a set of homologous sequences, aligned to the sequence of your structure, along with entropy/variability data and a 3D interface. Here's an example: 1CRN.
A Visual Analytics Toolkit for Social Spambot Labeling | Visual Analytics Toolkit for Social Spambots Labeling | The server is currently busy. Please wait. | Thank you for your participation | You have completed all the sessions | Label as Spambot Label as Genuine | Please express your opinion about VASSL:
A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data | In this article, we introduce the variant call format-diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators
A web-based visualization tool for high-throughput variant data mining and management.
a one-click client-side software to construct population phylogeny from genome-wide SNPs. VCF2PopTree is a client-side software written in Javascript and it runs. purely within the user’s computer/browser. VCF2PopTree is compatible
SNP/Indel Variant Calling Pipeline and data management tool used for analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer’s Disease Sequencing Project.
Use of three points to determine the accuracy of guided implantation.
an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers easy searching of genotype and haplotype data inferred from AIRR-seq datasets. From these data we can explore the variability of the genomic loci of the Ig and TR encoding genes across populations
VDJdb is a database extension, new analysis infrastructure and a T-cell receptor motif compendium.
a Variant Filtering tool based on Ensemble methods. Variant Ensemble Filter, an ensemble based filter for VCF files. VEF is designed for filtering variants of single non-cancerous samples. This bash script calls example script vef_clf.py and vef_apl.py located in the example/ directory to train and apply the filter, respectively. After running test.sh, there will be 2 filter models in example/data with the .clf extension, along with 2 filtered VCF files with the .vef.vcf extension
An Open-Source Matlab-Based Toolbox for the Collection and Analysis of Electromyography Combined With Transcranial Magnetic Stimulation. The combination of electromyography (EMG) and transcranial magnetic stimulation (TMS) offers a powerful non-invasive approach for investigating corticospinal excitability in both humans and animals. Acquiring and analyzing the data produced with this combination of tools requires overcoming multiple technical hurdles. Due in part to these technical hurdles, the field lacks standard routines for EMG data collection and analysis. This poses a problem for study replication and direct comparisons. Although software toolboxes already exist that perform either online EMG data visualization or offline analysis, there currently are no openly available toolboxes that flexibly perform both and also interface directly with peripheral EMG and TMS equipment
Performs intersectional genetics-related operations to find VEnCodes using databases provided by the FANTOM5 consortium, namely the CAGE enhancer and transcription start site (TSS) databases. For more information on the VEnCode technology, please refer to Macedo and Gontijo, bioRxiv 2019
Virtual Grid Engine (VGE) is a kind of middleware for running bioinformatics software pipelines on large-scale supercomputers which do not support any grid engine survices. VGE employs master-worker model. It first reserves processors and/or cores by running the job which is parallelized by MPI, then asign divided small tasks onto its worker processes. VGE is written in python.
The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited. The VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.
Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. Virus Identification By iteRative ANnoTation. Discovery Environment Applications List. Created by upendra_35, last modified on Nov 04, 2019. If you find VIBRANT useful please consider citing our preprint on bioRxiv:. Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387. VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies. The QuickStart tutorial provides an introduction to basic DE functionality and navigation. Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions
a computational tool for assessing clinical impacts of somatic variants | A Computational Tool for Assessing Clinical Impacts of Somatic Variants Following the AMP-ASCO-CAP 2017 Guidelines | Variant Interpretation for Cancer (VIC) | Clinical Interpretations of Variants in Cancer | java -jar target/VIC-1.0-jar-with-dependencies.jar [-b ] [-d ] [-h] [-input_type ] [-i ] [-cancer_type ] [-convert2annovar ] [-l ] [-skip_annovar] [-o ] [-annotate_variation ] [-table_annovar ] [-s ] [-otherinfo ] [-db ]
A precision virtual crossmatch decision support system for interpretation of ambiguous molecular HLA typing data | VICTOR: VIrtual CrossmaTch for mOleculaR typing data | This prototype tool computes virtual crossmatch using the candidate’s unacceptable antigens including high resolution alleles and molecular HLA typing of the donor | Web services interface information for Transplanttoolbox
ontology classification and study of vaccine responses given various experimental and analytical conditions. VIO: Vaccine Investigation Ontology. Statistics of Vaccine Investigation Ontology. IRI: https://raw.githubusercontent.com/vaccineontology/VIO/master/src/ontology/vio.owl. VIO and its usage in studying Yellow Fever vaccine-induced host response were presented in the VDOS-2018 workshop: https://sites.google.com/site/vdosworkshop/VDOS-2018. Note: This version of statistics metrics does not include any instance data yet. This feature will be added in the future
VIPER is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT tag approach. The software allows one to display the data as a two-dimensional plot of spectrum number (i.e. elution time) vs. mass. It can read MS data from several file formats: .PEK, .CSV (Decon2LS format), .mzXML, and .mzData.
a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resource, UTHealth, SBMI, Zhongming Zhao
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells | ValIdated Systematic IntegratiON of hematopoietic epigenomes | The VISION project aims to harvest truly valuable information from the flood of epigenomic data on hematopoietic cells as
Haplotype-aware structural variants simulator for short, long and linked reads
a Variant-Information Search Tool for precision oncology | The Variant Information Search Tool developed @ WBI
VMD Plugin to Browse, Discover, and Install VMD Extensions. In this page, you can find all the possible alternatives to install the VMD Store extension. 1. Install VMD Store through VMD Tk Console This installation process can be used ... Biomolecular SIMulations Research Group
Virtual Metabolic Human (VMH) database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data.
Vascular Network Analysis (VNA) is a novel analysis protocol based on freely available or commonly used software to generate vascular data from μCT scans.
Untargeted Metabolomics Feature Clustering Approach for Clinical Breath Gas Chromatography. Metabolic profiling of breath analysis involves processing, alignment, scaling and clustering of thousands of features ex-tracted from Gas Chromatography Mass spectrometry (GC-MS) data from hundreds of participants. The multi-step data processing is complicated, operator error-prone and time-consuming. Automated algorithmic clustering methods that are able to cluster features in a fast and reliable way are necessary. These accelerate metabolic profiling and discovery plat-forms for next generation medical diagnostic tools. Our unsupervised clustering technique, VOCCluster, prototyped in Py-thon, handles features of deconvolved GC-MS breath data. VOCCluster was created from a heuristic ontology based on the observation of experts undertaking data processing with a suite of software packages.
visual analysis of disease-associated microbiome-immune system interplay | Visualization of Linear Regression Elements | Visualization of linear regression elements comparing microbiome and immune system readouts
VOLPES (Visualization Of PhysicochEmical Sequence properties) - interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences.
Variational projection for accurate clustering of single-cell transcriptomic data.
A Customizable Variant Prioritization Ordering Tool for Annotated Variants. VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT provides various functions for the purpose of speeding up variant discovery
Exploring Drugbank in Virtual Reality Chemical Space. VRTK is a toolkit to rapidly build VR solutions. VRTK is a collection of useful, reusable solutions to common problems found when building for virtual reality. VRTK aims to help productivity by speeding up the creation process from prototyping ideas to building complete solutions
Transcriptional profiling aligned with in situ expression image analysis reveals mosaically-expressed molecular markers for GABA neuron sub-groups in the ventral tegmental area | VTA Expression Data Extractor
Deep learning for clustering of multivariate clinical patient trajectories with missing values. Deep learning for clustering of multivariate short time series with potentially many missing values. This repository contains code for a new method for clustering multivariate short time series with potentially many missing values (published here), a setting commonly encountered in the analysis of longitudinal clinical data, but generally still poorly addressed in the literature. Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values". Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values"
Allele Min-Set Cover Software. To facilitate reference-material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and preselection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of reference samples from the 1000 Genomes Project to cover 237 variants considered putatively pathogenic (of which 12 were classified as pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG). The number of samples, number of alleles, and processing time were measured in subsets of the 237 target alleles.
VarFish is an easy-to-use web-based database system designed for empowering geneticists in the analysis of clinical and whole exome sequencing variant data sets for individuals and families. It provides a set of tools for supporting the full workflow from (i) variant data quality control, (ii) variant filtration and (iii) efficient assessment of variants based on visual alignment inspection and annotation data such as functional and frequency annotation.
VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones.
VarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses.
Tool for mapping a list of chromosome coordinates, and their variants, to the corresponding protein residues in the canonical UniProt protein sequence.
Package for variable selection in model-based clustering of mixed-data with missing values.
prioritizing clinically reported variants with binary classification algorithms. VarSight is a collection of scripts used to test the application of classification algorithms for identifying variants that will be returned on a clinical report. VarSight relies on Codicem to perform common clinical pipeline pre-processing, namely variant annotation and filtering. In addition to data available in Codicem, it also uses gene rankings that are based on Human Phenotype Ontology (HPO) terms using both a built in calculation (cosine score) and the external tool PyxisMap. The classifiers in VarSight ingest a total of 95 features that are run through a feature selection process to get the top 20 features. Those 20 features are used to test both classification of reported variants and prioritization of reported variants in a larger filtered list. Results from the latest version of VarSight tests are available in the folder labeled "paper"
Disease variants and protein structure. Disease Variants and Structure
heuristic-free alignment for assessing linear and graph read aligners. Vargas computes optimal alignments of short reads to a directed acyclic graph (DAG). After building a graph, reads are aligned using a SIMD-vectorized version of the Smith-Waterman dynamic programming algorithm, with 16 -- 64 reads per vector depending on the instruction set
Benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction.
A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCarta is a database of human DNA genetic variants found in individuals diagnosed with Autism Spectrum Disorder (ASD) and reported in peer-reviewed scientific literature.
Building large updatable colored de Bruijn graphs via merging | VARI-merge is a pair of tools (vari-merge and color-merge) capable of merging the succinct colored de Bruijn graphs produced by VARI. The VARI-merge branch includes all of VARI | Cosmo is a fast, low-memory DNA assembler that uses a succinct de Bruijn graph | VARI is an extension to Cosmo and supports offline construction of succinct colored de Bruijn graphs. It can be found in the VARi branch, however all the components are also in this branch. You should use this branch for the VARI tools because it includes an important bugfix: Palendromes are not duplicated during the revcomp generation phase of succinct de Bruijn graph construction
A Large-Scale Genomic Variant Search Index.
VariantValidator is a user-friendly software tool designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Sequence Variant Nomenclature. VariantValidator ensures that users are guided through the intricacies of the HGVS nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately inter-converts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF) VariantValidator interfaces with the hgvs package to parse, format, and manipulate biological sequence variants. See https://github.com/biocommons/hgvs/ for details of the hgvs package VariantValidator is a highly functional platform enabling high-throughput and embeddable utilisation of functionality of https://variantvalidator.org/
VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. A variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). VarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. VarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel. You can use it through the online tool ORVAL: https://orval.ibsquare.be.
Variant Combination Pathogenicity Predictor (VarCoPP) 2.0
Variant Score Ranker (VSR) - web application for intuitive missense variant prioritization.
Variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.
a complete and efficient tool to support NGS data analysis. High precision on genetic analysis
Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables
venn diagram based network propagation analysis framework for comparing multiple biological experiments. Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee and Sun Kim. Handles I/O between front-end & back-end. Currently, Venn-diaNet uses String DB
R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures.
a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity | The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study
An innovative visualization R package to ensure behavioral raw data reliability and transparency. Background In recent years, the scientific community encouraged the use of raw data graphs to improve the reliability and transparency of the results presented in papers. However, methods to visualize raw data are limited to one variable per graph and or only small samples. In behavioral science as in many other fields, multiple variables need to be plotted together to allow insights of the behavior or the process observations. In this paper, we present ViSiElse, an R-package offering a new approach in raw data visualization. Methods. ViSiElse was developed with the open-source software R to provide a solution for the complete visualization of the raw time data. Results. ViSiElse grants a global overview of a process by combining the visualization of multiple actions timestamps for all participants in a single graph. Individuals and or group behavior can easily be assessed
Accelerating structure-function mapping using the ViVa webtool to mine natural variation | If Autoforward does not work, follow this link to go to Clay's ViVa website..
VICTOR is an interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering outputs.
Vienna Graph Clustering. The graph clustering framework VieClus -- Vienna Graph Clustering. The main project page of to open source framework VieClus -- Vienna Graph Clustering. This is the release of our memetic algorithm, VieClus (Vienna Graph Clustering), to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. In our experimental evaluation, we show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration in a small amount of time. In fact, for most of the small instances, we can improve the old benchmark result in less than a minute. Moreover, while the previous best result for different instances has been computed by a variety of solvers, our algorithm can now be used as a single tool to compute the result. VieClus - Vienna Graph Clustering is a memetic algorithm
A C ++ Variant Integration Kit for Next Generation Sequencing Association Analysis. Documentation for VikNGS — VikNGS 0.0.1 documentation. Free document hosting provided by Read the Docs
The method is essentially an EM algorithm.
a Fiji macro for automated assessment of viral plaque statistics. Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user's needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed
Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
> HOMEPAGE MISSING! | a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data | MOTIVATION:The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation
a stand-alone program for visualizing and analyzing statistical features of biological sequences | For Microsoft Windows platform, just download the VisFeature-win32-x64.zip package from https://github.com/wangjun1996/VisFeature/releases. Unpack it to your favorite location and then open VisFeature.exe | We have tested these codes on Windows10-64bit platform and Ubuntu 16.04.5 LTS platform. There is no guarantee that these codes can be compiled and executed on other platforms without modifications
A framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise.
Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS | Single test file Multiple test files | If you use VisioProt-MS for your research please cite: | Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux; VisioProt-MS: interactive 2D maps from intact protein mass spectrometry, Bioinformatics, bty680, https://doi.org/10.1093/bioinformatics/bty680 | You are in test mode. Click on a button to select a single test file or multiple test files. Uncheck to exit and upload your own data
Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.
Web-Assisted Symbolic Plasmid Synteny Server.
Tool for improving the design of drugs based on protein-water interactions.
WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.
This code is implementation of an algorithm to segment the nucleus of white blood cells (WBCs)
An Efficient Technique for White Blood Cells Nuclei Automatic Segmentation
weighted bipartite network projection for microRNA-disease association prediction | BACKGROUND:Recently, numerous biological experiments have indicated that microRNAs (miRNAs) play critical roles in exploring the pathogenesis of various human diseases. Since traditional experimental methods for miRNA-disease associations detection are costly and time-consuming, it becomes urgent to design efficient and robust computational techniques for identifying undiscovered interactions. METHODS:In this paper, we proposed a computation framework named weighted bipartite network projection for miRNA-disease association prediction (WBNPMD). In this method, transfer weights were constructed by combining the known miRNA and disease similarities, and the initial information was properly configured. Then the two-step bipartite network algorithm was implemented to infer potential miRNA-disease associations
Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison.
Pipeline for detecting whole genome duplication events using the genome or transcriptome annotations.
WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.
A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. A cost-effective approach to diploid assembly for single samples and trios. It includes the following steps: construct sequence graph from illumina, align long reads to the graph and partition these long reads to two haplotypes.
Fast and Memory Efficient Approach for Mapping NGS Reads to a Reference Genome.
A Tool for Within-Taxon Operational Taxonomic Unit Diversity Analysis. A Tool for Within-Taxon Operational Taxonomic Unit (OTU) Diversity. Please copy the OTU Table and the rep_set.fna file into the same directory of witod.py and util directory
a multi-dimensional program organised around World Pneumonia Day | There are limited examples of population-based approaches that engage a broad range of stakeholders for prevention of pneumonia. In 2010, a multi-dimensional public-private partnership was established around World Pneumonia Day (WPD) in Seoul, Korea and included the following components: a) formation of an expert advisory group, b) creation of educational materials tailored for lay persons, c) creation of a dedicated WPD internet website in the local language, d) organisation of a WPD venue in central Seoul, e) creation of video and social networking messages for wide distribution, and f) engagement of parents, health-care professionals, public health agencies and policymakers
Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server. If you use WPMIAS, please cite this article: Yuhan Fei, Yiyang Mao, Chengji Shen, Rui Wang, Hongsheng Zhang, Ji Huang, "WPMIAS: Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server", Bioinformatics, 2019, in press. DOI:10.1093/bioinformatics/btz820
A Python Package for the Design of Materials for Harnessing Heat. Pioneering the design of materials to harness heat. WPTherml stands for William Paterson University's tool for Thermal Energy and Radiation management with Multi Layer nanostructures. Project maintained by FoleyLab Hosted on GitHub Pages — Theme by mattgraham. WPTherml stands for William Paterson University’s tool for Thermal Energy and Radiation management with Multi Layer nanostructures.
Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion. 2D-wavelet-for-protein-structural-classes-prediction We constructed a prediction model based on wavelet denoising using different feature expression methods. A new fusion idea, first fuse and then denoise, is proposed in this article. Two types of pseudo amino acid compositions are utilized to distill feature vectors. Then, a two-dimensional (2-D) wavelet denoising algorithm is used to remove the redundant information from two extracted feature vectors. The two feature vectors based on parallel 2-D wavelet denoising are fused, which is known as PWD-FU-PseAAC. The project includes three original datasets, source code for two-dimensional wavelet denoising and source code for feature vector prediction
Wannier90 is a tool for obtaining maximally localized wannier functions from DFT calculations.
Real-time cryo-electron microscopy data preprocessing with Warp. If you just want to use Warp, all tutorials and binaries can be found at http://www.warpem.com. Continue reading this README only if you're interested in compiling Warp from source
WebAnno is a general purpose web-based annotation tool for a wide range of linguistic annotations including various layers of morphological, syntactical, and semantic annotations.Additionaly, custom annotation layers can be defined, allowing WebAnno to be used also for non-linguistic annotation tasks.
Cleavage sites analysis tool for natural and unnatural substrates from diverse data source.
WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS)) and compound concentrations.
An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser. 1 Abstract Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download install an executable file and to run that file from a Unix- or DOS-like command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers. We have created Webina, a new version of Vina, to address these challenges. Webina is a JavaScript WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking calculations take place on the user’s own computer rather than a remote server
Web application for the analysis of fluorescent reporter gene data.
a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BACKGROUND:CRISPR Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION:We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat
This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. The WheatIS search is an implementation of DataDiscovery.
Time series of heat demand and heat pump efficiency for energy system modeling. This repository contains scripts that compile heat demand and COP time series for European countries.
Whisper is a tool for an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement.
Automatic white blood cells detector using differential evolution (DE)
White blood cells detection using differential evolution (DE)
Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data | large scale GC-MS data preprocessing workflow | WiPP - A Workflow for improved Peak Picking - Quick Start Guide | WiPP is an open source large scale GC-MS data preprocessing workflow built in Python 3 that uses machine learning to optimise, automate and combine the peak detection process of commonly used peak picking algorithms
An indoor multi-camera multi-space dataset with contextual information and annotations for people detection and tracking. Nowadays, camera networks are part of our every-day life environments, consequently, they represent a massive source of information for monitoring human activities and to propose new services to the building users. To perform human activity monitoring, people must be detected and the analysis has to be done according to the information relative to the environment and the context. Available multi-camera datasets furnish videos with few (or none) information of the environment where the network was deployed. The proposed dataset provides multi-camera multi-space video sets along with the complete contextual information of the environment. The dataset regroups 11 video sets (composed of 62 single videos) recorded using 6 indoor cameras deployed on multiple spaces
Complete genome assembly of the Wolbachia endosymbiont of the horn fly Haematobia irritans irritans.
To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. This Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network.
Interactive web-based platform presenting global cancer statistics , which can be used for cancer research.
Immunostainings in Nervous System Development of the Nematode C. elegans | Embryo series courtesy of Einhard Schierenberg | WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes. Wormbook also contains: WormMethods, a collection of protocols for nematode researchers; WormHistory, personal perspectives on C. elegans research; and the Worm Breeder's Gazette, an informal, non-refereed, biannual newsletter for the interchange of ideas and information related to C. elegans and other nematodes. Additional chapters can be found in GENETICS
open-source robotics platform for survival and behavior analysis in C. elegans. WormBot, C. elegans lifespan robotic image aquisition platform. Homepage UW Pathology Seattle, Washington, USA. WormBot is an open hardware and open software robotic microscopy screening platform designed for C. elegans behavior and survival analysis. This site contains links and information for building the WormBot, an open hardware project designed for automatted survival analysis in the nematode C. elegans. The WormBot is an extremely simple and inexpensive robotics platform that captures timelapse images and realtime movies of nematodes in standard tissue culture plates
Intermine data mining platform for C. elegans and related nematodes
an interactive platform for systems genetics in Caenorhabditis elegans | eQTL visualization and investigation | All eQTL patterns for a single trait
Massive XML-based biological data management platform.
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data | Wiki for programs and pipelines for sequencing data analysis | 3. XAEM: step by step instruction and explanation | Annotation reference: XAEM requires a fasta file of transcript sequences and a gtf file of transcript annotation. XAEM supports all kinds of reference and annotation for any species. In the XAEM paper, we use the UCSC hg19 annotation:
Inferring the three-dimensional structures of the X-chromosome during X-inactivation. 3D cubic lattice, 3D structure of the X-chromosome, Xist lncRNA, X-chromosome inactivation. 3D-XCI is a lattice-based 3D modeling tool for generating accurate and stable high-resolution 3D chromosome structures based on population Hi-C data
An algorithm for extracting ion chromatograms.
> HOMEPAGE MISSING! | an eXtreme Gradient Boosting based method for identifying pseudouridine sites | As one of the most popular post-transcriptional modifications, pseudouridine (Ψ) participates in a series of biological processes. Therefore, the efficient detection of pseudouridine sites is very important in revealing its functions in biological processes. Although experimental techniques have been proposed for identifying Ψ sites at single-base resolution, they are still labor intensive and expensive. Recently, to fill the experimental method's gap, computational methods have been proposed for identifying Ψ sites. However, their performances are still unsatisfactory. In this paper, we proposed an eXtreme Gradient Boosting (xgboost)-based method, called XG-PseU, to identify Ψ sites based on the optimal features obtained using the forward feature selection together with increment feature selection method
extended gradient descent algorithm for lattice finding | Directory Algorithm documentation | Directory precomputedSamplePoints
Putative biomarkers for predicting tumor sample purity based on gene expression data.
XIBD (X chromosome Identity by Descent) performs pairwise identity by descent (IBD) mapping on the autosomes and the X chromosome.
multi-dimensional NMR analysis software. Xipp (pronounced zip) is an NMR analysis software package created and supported by Dr. Daniel S. Garrett in the lab of Dr. G. Marius Clore. This software package is designed to study labeled proteins and nucleotides and is a complete re-write and extension of the PIPP package using Java. Xipp uses the same file format for Peak-Pick files and assignment tables as was used in PIPP. In addition many of the keyboard and mouse commands are the same as used by PIPP. The primary differences between PIPP and Xipp is that Xipp allows multiple NMR experiments to be viewed and overlayed at same and has built-in ability to aid in backbone assignment. The most important difference is that PIPP is no longer supported while Xipp is actively supported
XL-mHG is a Semiparametric Test for Enrichment in Ranked Lists.
Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. WM tract atlases for the human (HCP and UK Biobank) and Macaque brain and connectivity blueprint atlases for the human (HCP) and macaque brain. Reference: Warrington S, Bryant KL, Khrapitchev AA, Sallet J, Charquero-Ballester M, Douaud G, Jbabdi S, Mars RB*, Sotiropoulos SN* (in prep.) XTRACT - Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. XTRACT - a command-line tool for automated tractography. XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152)
Search and retrieve integrated Xenopus tropicalis and Xenopus laevis data
Cloud-based BAM cleansing tool for RNA and DNA from Xenograft. A cloud-based tool for mouse read cleansing in xenograft samples. XenoCP is a tool for cleansing mouse reads in xenograft BAMs. XenoCP can be easily incorporated into any workflow, as it takes a BAM file as input and efficiently cleans up the mouse contamination. The output is a clean human BAM file that could be used for downstream genomic analysis. St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal. Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore
Integrative pharmacogenomics analysis of patient-derived xenografts.
A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images. XitoSBML - the spatial SBML plugin for ImageJ. XitoSBML: Spatial SBML Plugin for ImageJ. XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images. XitoSBML is not just a converter, but also a spatial model editor so that users can add molecules(species), reactions, and advection/diffusion coefficients to the converted Spatial SBML model
Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material.
Better quality score compression through sequence-based quality smoothing. YALFF (Yet Another Lossy FASTQ Filter) is a smoother for FASTQ files which uses an FM-Index to store the k-mer database. The compressed index greatly reduces the amount of memory required compared to other tools such as QUARTZ. This is because the dictionary of k-mers can be linearized into contigs
Identification of a novel long non-coding RNA within RUNX1 intron 5 | This site uses cookies. By continuing to browse the site you are agreeing to our use of cookies. Find out more here . {{alert.msg}}
Fast and interpretable segment-based alternative splicing and gene expression analysis | Transcript Segment Library Construction for RNA-Seq Quantification | Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene
Search and retrieve S. cerevisiae data, populated by SGD and powered by InterMine
Accurate and parameter-free web segmentation for microscopy images of yeast cells.
Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.
Yosshi (YOur web-server for S-S bond HarvestIng) - web server for disulfide engineering by bioinformatic analysis of diverse protein families.
Antibody high-density alignment visualization and analysis platform with an integrated database.
Application for quantification of spontaneous tail movement in zebrafish embryos.
ZebrafishMine is powered by the InterMIne data warehouse system, and integrates biological data sets from multiple sources. It currently includes updates of data from ZFIN, the zebrafish model organism database. There is also data from the Panther database.
Zebrafish is an online database of standardized Zebrafish (a marine vertebrate model) neuroanatomy, accessible via an interactive interface for 3D visualisation.
An automated quantitative image analysis pipeline of in vivo oxidative stress and macrophage kinetics | Zebrafish leukocyte tracking pipeline in Matlab | Zebrafish leukocyte tracking pipeline in Matlab. Version 1.4
A phylogenetic simulator of trees, genomes and sequences that accounts for dead linages | Evolution simulator with extinct lineages | Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages | Zombi is a flexible platform of genome evolution which can be of great interest to those who want to test different evolutionary hypotheses under simulations and need to use a fast and easy-to-use tool to generate species trees, gene trees or sequences. Zombi's output is especially simple and easy to read, understand and parse
R package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation.
Large-Scale Structural Refinement and Screening of Zirconium Metal-Organic Frameworks for H2S/CH4 Separation. You can find more than 182 experimentally synthesized guest-free and disorder-free Zirconium-based metal-organic frameworks (Zr-MOFs), which contain no less than 10 coordinated Zr6O8 inner cores. These structures are optimized by a combination of periodic density functional theory (DFT) and molecular mechanics method, and are given in cif format
Python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.
A web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation.
A method that simultaneously identifies and optimizes hit/lead molecules by integrating chemical- and protein-space-driven architectures and stands for an automated-hit identification and optimization tool (A-HIOT).
This R package is designed for computing alternative individualized treatment recommendation (A-ITR).
Open source web application and gene chip analysis automation framework for annotation-based meta-analysis of data from public repositories (NCBI GEO). It allows retrieval, annotation, organization and analysis of gene expression data from public repository. It automates several analysis steps to be accomplished to setup a working environment for conducting meta-analyses, without giving up power and flexibility.
Exploiting orthology and de novo transcriptome assembly to refine target sequence information.
A pipeline to automatically process and analyze simultaneously acquired EEG-fMRI data for sleep research
Protein structure modeling using MSA transformer
An active learning platform for expert-guided, data efficient discovery of behavior
A platform for research in biomedical literature search and benchmarking.
A2Sign (Agnostic Algorithms for Signatures) a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution.
A2TEA is a software workflow facilitating identification of candidate genes for stress adaptation based on comparative genomics and transcriptomics. It combines differential gene expression with gene family expansion as an indicator for the evolution of adaptive traits.
A3D Database is a database for structure-based protein aggregation predictions for the human proteome
Exploring structural aggregation propensities in the yeast proteome.
A3FE is an open-source package implementing an automated workflow for alchemical absolute binding free energy calculations, designed to reduce computational cost and human intervention.
Suite of R packages for analysis of Affymetrix microarray experiments.
An R package of the "a4" packages collection. It comprises of basic funtionalities needed to analyse Affymetrix microarray experiment results.
An R package of the "a4" packages collection. It comprises of commands using machine learning algorithms for classification work to analyse Affymetrix microarray experiment results.
An R package of the "a4" packages collection. It is made to allow for easy interopetability with the nlcv R package.
Aggrescan4D (A4D) is a web server for predicting pH-dependent protein aggregation and engineering protein solubility. It builds on the A3D method, offering evolutionary-informed mutation protocols and integrating precalculated results and structure retrieval from AlphaFold.
An R package of the "a4" packages collection. It is used for microarray data preprocessing where annotation information is added to experimental result data.
An R package of the "a4" packages collection. It provides reporting functionality.
A5 is an integrative pipeline for genome assembly that automates sequence data cleaning, error correction, assembly, and quality control by chaining a number of programs together with additional custom algorithms.
De novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system
aCLImatise is a Python library and command-line utility for parsing the help output of a command-line tool and then outputting a description of the tool in a more structured format, for example a Common Workflow Language tool definition.
Using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data.
Contact Map Overlap maximization (CMO) solver. Given two protein structures represented by two contact maps, it computes the amino-acid alignment which maximize the number of common contacts.
A command line tool for protein-ligand binding affinity prediction
AA_stat is a tool for shotgun proteomics that uncovers the unexpected modifications of amino acid residues in the protein sequences, as well as possible artefacts of data acquisition or processing, in the results of proteome analysis.
A manually curated database for tracking and predicting genes of Abdominal aortic aneurysm (AAA).
Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
Set of tools implementing different conservation scores.
Manually collected database for combinations of antibiotics with adjuvants.
Automated Augmentation for Domain Generalization (AADG) is a data manipulation based domain generalization method that can sample data augmentation policies that generate domains and diversify the training set from an appropriate search space.
AAgAtlas is a database of human autoantigens extracted from biomedical literature.
A comprehensive database of anti-aging peptides.
Extract amino acid property data from AAINDEX.
Machine-learning-based algorithm that uses amino acid index to predict protein subcellular localization based on its sequence.
AAindexNC is a bioinformatics tool and database that estimates the physicochemical properties of non-canonical amino acids derived from protein structures and the PDBechem databank, building upon the existing AAindex database.
AARDVARK is an R package that identifies reversion mutations in DNA sequence data.
FileSender is an open source web application for sending files of any size, quickly and securely. FileSender is available to all institutions affiliated with the Australian Access Federation (AAF). You can use your institution login details to access and use FileSender.
The Anchor Alignment-Based Small RNA Annotation (AASRA) Pipeline is a comprehensive solution for small RNA alignment.
Automated bioinformatics pipeline to analyse SNP containing DNA sequences mainly for finding SNPs which cause a change in the splicing pattern.
Matteo Ramazzotti - matteo dot ramazzotti at unifi.it
It is a suite of perl scripts aimed at scannig a properly formatted set of protein sequences and their corresponding coding sequences and extract from them imperfect homopetidic repeats of a given amino acid. The user can define the nature of such residue and the maximal length and proportion of insertions tolerated, together with other search parameters.
An adaptive attention U-net (AAU-net) to segment breast lesions automatically and stably from ultrasound images.
Machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains.
A curated database for binding affinity and neutralization profiles of coronavirus related antibodies.
Identifying sequence-dissimilar antibodies that bind to the same epitope.
AB12PHYLO is an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data.
ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.
Identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions. Applied to a whole SNP dataset, the tool gives as output a list of SNP-sets associated with the disease and, for each SNP-set, the list of significant SNPs.
Approach to predicting antibody-antigen complex structures from sequence.
The package is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses.
A deep learning method for predicting antibody-antigen interactions based on sequence information.
A comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.
The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species.
An R package which functions provide an automated pipeline to perform expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis. A GUI interface is also provided.
Abasy (Across-bacteria systems) Atlas contains the most comprehensive collection of reconstructed and meta-curated bacterial gene regulatory networks having enough quality to allow system-level analyses.
abawaca (A Binning Algorithm Without A Cool Acronym) is a binning program that can take advantage of different types of information such as differential coverage and DNA signature.
Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly.
Computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs.
A containerized web server for the identification and topology prediction of ABC proteins. ABC-Finder i.e., A Docker-based package for the identification of ABC proteins in all organisms, and downstream analysis and visualization of the topology of ABC proteins using an interactive web browser.
A web application for analysis of breast cancer GWAS variants.
abc4pwm is a software tool for clustering of pwms, classficiation of pwms to their DNA binding Domain, motif search, and other supportive modules.
The atlas of biosynthetic gene clusters in the human microbiome.
ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis.
Providides pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5 - 30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans).
An Alzheimer's Disease Biomarker Comprehensive Database for Humans. It includes the information for all the genetic parameters like mitochondrial genes, polymorphic genes (SNP's), transcription factors, proteins, miRNAs, Associative pathway, and AD brain images.
Alzheimers Disease Biomarker Comprehensive Database (ABCD)
The Aliment to Bodily Condition knowledgebase (ABCkb) is a database connecting plants and human health.
Aliment to Bodily Condition knowledgebase (ABCkb)
An automatic data mining tool based on a consistent voting method with a user-friendly graphical interface. In order to extract useful information from a huge amount of biological data nowadays, simple and convenient tools are urgently needed for data analysis and modeling. In this paper, an automatic data mining tool, termed as ABCModeller (Automatic Binary Classification Modeller), with a user-friendly graphical interface was developed here, which includes automated functions as data preprocessing, significant feature extraction, classification modeling, model evaluation and prediction. In order to enhance the generalization ability of the final model, a consistent voting method was built here in this tool with the utilization of three popular machine-learning algorithms, as artificial neural network, support vector machine and random forest.
Adaptive Bezier-Curve Network for Real-time End-to-end Text Spotting.
AbCPE web server implements a multi-label classification algorithm that predicts antibody class(es) for epitopes. This data driven machine learning based algorithm offers prediction of epitopes potentially recognised by an individual or multiple classes of antibodies viz. IgG, IgE, IgA and IgM (excluding IgD).
Server to predict linear B cell epitope regions in an antigen sequence, using an artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research.
ABCpred is a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors.
Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein.
ABCstats is an R package for metabolomics data transformation. Adaptive Box-Cox (ABC) transformation improves the data normality for statistical analysis.
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.
Integrated online application for identification of optimal immunizing peptides for antibody production using peptide-based strategy.
AbDev is a machine learning tool for predicting 12 biophysical properties of monoclonal antibodies using variable region sequences. It combines deep learning (DeepSP) with machine learning techniques and offers a web application interface for predictions.
AbDiver is a tool to explore the natural antibody landscape to aid therapeutic design.
Prediction of active antimicrobial compounds using supervised machine learning techniques.
ABDS is an R tool suite designed for analyzing biologically diverse samples, specifically addressing challenges with missing data imputation, signature gene detection, and differential pattern visualization. It provides tools for mechanistic imputation, group-wise testing, and heatmap visualization.
Calculates partial atomic charges for small organic molecules, drug-like molecules.
ABEILLE (ABerrant Expression Identification empLoying machine LEarning from sequencing data) is a variational autoencoder (VAE) based method for the identification of AGEs from the analysis of RNA-seq data without the need of replicates or a control group.
Web server for the prediction of antibody epitopes.
Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.
abi2link is designed to create linkage files out of ABI genotype and phenotype files.
abi2xml is a command line utility to convert an abi trace file to an xml file. Abi trace files contain DNA sequence data and are e.g. produced by ABI PRISM TM 377 DNA sequencers.
Pipeline for chemical exposome integration and analysis with biotic data
Display the trace in an ABI sequencer file.
This tool reads in an ABI sequence trace file and graphically displays the results.
An antibody language model for completing antibody sequences.
Automated Brain Lines Extraction Based on Laplacian Surface Collapse.
ABM (Anaerobic Biodegradation Model). A mechanistic model of methane emission from animal slurry with a focus on microbial groups.
Employing agent-based model (ABM) tool to simulate brain tumor growth that includes an EGFR signaling pathway together with a related cell-cycle pathway, angiogenesis and tyrosine kinase inhibitors (TKIs) treatment. The users can apply this tool to predict the responses of brain cancer to TKIs, and to reveal the dual role of angiogenesis during TKI treatment.
Portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.
abmR is an R package for agent-based model analysis of large-scale movements across taxa. Agent-based modeling (ABM) shows promise for animal movement studies. However, a robust, open-source, and spatially explicit ABM coding platform is currently lacking. We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein-Uhlenbeck (OU) model. The theoretical background for abmR is discussed and the main functionalities are illustrated using two example populations. Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with other R movement modeling packages
ABNER (A Biomedical Named Entity Recognizer) is a software tool for molecular biology text analysis.
Aboria is a powerful and flexible C++ library for the implementation of particle-based numerical methods. The particles in such methods can represent actual particles (e.g. Molecular Dynamics) or abstract particles used to discretise a continuous function over a domain (e.g. Radial Basis Functions).
Automatic blood oxygen saturation signal analysis software. This software automatically detects desaturation and following recovery events from the blood oxygen saturation signal. The software calculates numerous event-specific metrics for each scored event.
Web application for documentation and analysis of substitutants.
abPOA can perform multiple sequence alignment (MSA) on a set of input sequences and generate a consensus sequence by applying the heaviest bundling algorithm to the final alignment graph.
Realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.
Annotated regulatory binding sites from orthologous promoters.
Performs alanine scanning mutagenesis for a given protein-ligand complex.
Simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated.
An in-silico method to predict the aggregation kinetics of native proteins.
Perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files.
Absolute and Comparison Analysis for Affymetrix Data
Automated R tool to efficiently analyse region-specific CpG methylation from bisulfite sequencing PCR.
An R package which provides RNA-Seq analysis based on modelling absolute expression differences.
abstcal is a a Python package to calculate abstinence results using the timeline followback interview data.
De novo genome sequence assembler using short reads.
AC-Caps is a deep learning method used for predicting the RBP binding sites on lncRNA chains.
Adjustment for Confounding factors using Principal Coordinate Analysis (AC-PCoA) is a R package that adjust for confounding factors using principal coordinate analysis.
AC2 is an efficient protein sequence compression tool using artificial neural networks and cache-hash models.
ac4C-AFL is a bioinformatics tool for high-precision identification of human mRNA N4-acetylcytidine (ac4C) sites based on adaptive feature representation learning. A web server is available at the provided URL.
Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE.
Genome mining for anti-CRISPR associated genes.
A Fast Sequence Mapper and Aligner based on the Seed–Embed–Extend Method. Accel-Align does base-to-base alignment by default.
A adjacent context coordination network (ACCoNet) to explore the coordination of adjacent features in an encoder-decoder architecture for RSI-SOD.
Accucopy is a CNA-calling method that extends our previous Accurity model to predict both total (TCN) and allele-specific copy numbers (ASCN) for the tumor genome. Accucopy adopts a tiered Gaussian mixture model coupled with an innovative autocorrelation-guided EM algorithm to find the optimal solution quickly. The Accucopy model utilizes information from both total sequencing coverage and allelic sequencing coverage.
Accurate enhancer prediction by integration of multiple cell type data with deep learning. Enhancers are one class of the regulatory elements that have been shown to act as key components to assist promoters in modulating the gene expression in living cells. accuEnhancer utilize DNase data to build a deep learning model for predicting the H3K27ac peaks as the active enhancers in selected cell types. Moreover, we also tested joint training for multiple cell types to boost the model performance.
AccuVIR -- an Accurate VIRal genome assembler and polisher -- utilizes path searching and sampling in sequence alignment graphs to assemble or polish draft assembly of viral genomes.
Tool to search a knowledge base of the most commonly used chromatographic columns to locate those with the properties best-suited to the separation at hand. The Column Selector database contains information for 254 characterized columns, along with results for >4800 systematic experiments.
Implementation of an augmented drug synergy prediction algorithm.
Automated cell type discovery and classification through knowledge transfer.
A tool to test next-generation-sequencing (NGS) data from single-cell sequencing for contamination. By using sophisticated dimensionality reduction and clustering methods, it uses tetramer profiles to differentiate between different species in a given sample.
This package provides a multivariate inferential analysis method for detecting DE genes. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR).
Correctly reformat an application ACD file.
Generate an HTML table of parameters from an application ACD file.
Web-server for the generic analysis of large data sets of counts.
Trace processing of an application ACD file (for testing).
Corrects substitution errors in an Illumina archive using a k-mer trie.
Advanced Computational Engine for Molecule (ACE-Molecule) is a quantum chemistry package based on a real-space numerical grid.
In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility.
Optimizing Combinatorial Design of Pooled ELISpot Assays with an Epitope Similarity Model. ACE facilitates (1) generation of ELISpot configurations (peptide-pool assignments) using a deep learning approach to cluster similar peptides and (2) deconvolution of pool spot counts for identification of immunogenic peptides.
It aids gene prediction accuracy evaluation. It uses GFF format to make it easy to convert gene prediction results into an analyzable format. Novel features include isoform accuracy evaluation from either the annotated gene or gene prediction perspective or both at the same time. Masking of genomic sequence which has unknown features allows gene predictions in annotated regions to be analyzed in a genomic context.
Efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data.
ACEapi is the API for the the Advanced Cohort Engine for searching longitudinal patient records.
ACEGEN is a toolkit for generative drug design built using TorchRL, streamlining reinforcement learning for molecular generation. It offers a comprehensive and tested approach, validated through benchmarking and applied in multiple drug discovery case studies, and is available under the MIT license.
PKPD model for ACE inhibition with benazapril or cilazapril; ducational drug dosing app for treatment of high blood pressure
Tool that aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.
ACEP is a deep learning model for high-throughput antibacterial peptide recognition. By loading a pre-trained model, the software can be deployed on a common computer to perform antimicrobial peptide recognition, important motif discovery, and visualization analysis. Both the peptide sequences and PSSM profiles need to be input the model.
AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.
ACES (Analysis of Conservation with Expansive Species). Generates BLAST hits against each of the reference genomes, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.
A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).
The Ancestral Recombination Graph tool is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it.
This tool includes functions for reading aCGH data from image analysis output files and clone information files or creating S3 objects for storing these data. It also incudes basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Application for fast calculation of partial atomic charges of structures from the Alphafold database.
The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.
Acidbio a system for automated testing and certification of bioinformatics file format interoperability.
A database and repository of Acinetobacter strains
A framework for adjusting the threshold parameters according to the image contrast. Three functions include Attention mechanism threshold, Contour equalization, and Lung segmentation (ACL).
This database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization.
Set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is fast and can be applied on whole-genome tiling array experiments easily with enough memory.
The Ambivalent Covariance Models are stochastic homology search tools that support more than one consensus secondary RNA structures.
The Database for Elucidating the Relationships Between Natural Products, Compounds, Molecular Mechanisms, and Cancer Types. ACNPD is an online tool that provides users with a quick search of the pharmacological mechanisms of natural anti-cancer products. The database contains 10 common cancer types, XXX compounds, XXX pharmacological mechanisms, involving PI3K/Akt, PI3K/Akt/mTOR, Wnt/ β-catenin and other signaling pathways. The web interface allows users to query related queries in a variety of ways.
ACO is a lossless quality scores compression algorithm based on adaptive coding order and this software can be used for both encoding and decoding.
A tool for isoform co-usage networks from single-cell RNA-seq data
Clinically Oriented antimicrobial Resistance surveillance Network (ACORN) as a lightweight but comprehensive platform, in which we combine clinical data collection with diagnostic stewardship, microbiological data collection and visualisation of the linked clinical-microbiology dataset.
A Web-Based Automated Ultrasonic Vocalization Scoring Platform.
ACovPepDB is a comprehensive peptides database of anti-coronavirus peptides, which contains 518 enrties with 214 unique ACovPs manually extracted from research articles and public databases.
ACP-CapsPred is a computational framework using capsule networks to identify anticancer peptides and predict their functional activities across different cancer types. The tool integrates protein language models, evolutionary information, and physicochemical properties to expedite ACP development.
Improving the Prediction of Anticancer Peptides Using Data Augmentation.
An Accurate Multi-Headed Deep-Convolutional Neural Network to Predict Anticancer peptides.
A two-level prediction engine for identification of anticancer peptides and multi-label classification of their functional types.
A prediction model of anticancer peptides based on feature extraction.
ACPred-BMF server is used for anticancer peptide (ACP) prediction.
Learning embedding features based on multi-sense-scaled attention architecture to improve the predictive performance of anticancer peptides.
ACPredStackL is a ensemble learning framework using stacking strategy for accurate identification of ACPs. Anticancer peptides (ACPs),known as potential future therapeutics for cancer, have been studied extensively,attribution to their unique ability to target cancer cells without affecting healthy cells directly.Many peptide-based drugs are currently being evaluated in preclinical and clinical trial.
A tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN tools or ARIA.
The ACPYPE web server for small-molecule MD topology generation.
AcrDB is a database of computationally predicted anti-CRISPR (Acr) and Acr-associated (Aca) operon database. Acr (anti-CRISPR) proteins are short proteins usually found in phages prophages and other mobile genetic elements that can turn off the CRISPR-Cas system of their prokaryotic hosts.
A tool to determine anti-CRISPR proteins in the whole genome-scale
Absolute concentration robustness explorer (ACRE) explores combinatorial biochemical networks for the Absolute concentration robustness property.
Absolute concentration robustness explorer (ACRE)
AcrFinder is a tool used to identify Anti-CRISPR proteins (Acr) using both sequence homology and guilt-by-association approaches.
AcrHub is an integrative database to provide an all-in-one user-friendly solution for anti-CRISPR proteins (Acr) investigation, prediction, mapping and relationship analysis. Bacteria and archaea have developed a wide variety of CRISPR-Cas systems to protect themselves from harmful mobile genetic elements (MGEs), such as phages and plasmids.
Predicting anti-CRISPR with deep learning.
An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles.
The Arabidopsis Coexpression Tool (ACT) is based on the coexpression analysis of 21273 Arabidopsis thaliana genes from gene pair correlation data of 3500 Affymetrix Arabidopsis ATH1 Genome Array Chip microarray samples.
A method for inferring the functional identity of cells from their transcriptional profile, classifying them based on their dominant function, and reconstructing regulatory networks that are responsible for mediating their identity.
ACTIVA is a realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders.
Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). Find your mutation or gene of interest. You are viewing an updated version (2021) of the ActiveDriverDB. To view the previous version please visit activedriverdb.org/v2020. cystic fibrosis mutations in CFTR. ActiveDriverDB is a human proteo-genomics database. cancer mutations in CTNNB1 phosphodegron.
This tool finds a set of coordinately activated Transcription Factors (TF) from a given gene expression dataset.
Assembly based Circular RNA validator (ACValidator) is a bioinformatics approach to perform in silico validation of selected circular RNA junction(s).
Adversarial Deconfounding AutoEncoder (AD-AE) is a tool to deconfounding gene expression latent spaces.
Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.
MATLAB script for Alzheimer disease identification and classification
Alzheimer disease identification and classification
The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD).
Responsible sharing of biomedical data and biospecimens via the "Automatable Discovery and Access Matrix" (ADA-M). The Automatable Discovery and Access Matrix (ADA-M) provides a standardized way to unambiguously represent the conditions related to data discovery and access. By adopting ADA-M, data custodians can generally describe what their data are (the Header section), who can access them (the Permissions section), terms related to their use (the Terms section), and special conditions (the Meta-Conditions). By doing so, data custodians can participate in data sharing and collaboration by making meta information about their data computer-readable and hence directly available for digital communication, searching and automation activities.
Adaptive Boltzmann machine learning for Potts models of biological data (adabmDCA) This is an implementation of the Boltzmann machine learning to infer several maximum-entropy statistical models of Potts or Ising variables given a set of observables. More precisely, it infers the couplings and the fields of a set of generalized Direct Coupling Analysis (DCA) models given a Multiple Sequence Alignment (MSA) of protein or RNA sequences. It is also possible to infer an Ising model from a set of spin configurations. The learning is performed via a gradient ascent of the likelihood of the data in which the model observables are computed via a Markov Chain Monte Carlo (MCMC) sampling.
Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
A Tool for Analysing (Dis)similarity among Nucleotide and Protein Sequences Using Minimal and Relative Absent Words. ADACT (The Alignment-free Dissimilarity Analysis & Comparison Tool) measures dissimilarities among several species in an alignment-free manner. ADACT takes several genome sequences and some parameters (e.g. K-mer size, absent word type, dissimilarity index, RC-setting) as input, and outputs distance matrix, sorted species relationship and phylogenetic trees (neighbor joining tree and UPGMA tree) among species.
High-resolution identification of orthologous regulatory elements with Adaptive liftOver.
Model selective breeding schemes for animals using stochastic simulation. The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters for different population structures, genetic models, selection strategies, and mating designs. It can be used to evaluate breeding schemes and generate genetic data to test statistical tools.
Adamant is a JSON schema-based metadata creation tool for various research data management workflows.
A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository.
iIentification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network.
ADAPT is an R package for differential abundance analysis of microbiome metagenomics data, using Tobit models to account for zero counts and an innovative method to identify differentially abundant taxa. It is available on Bioconductor and Github and comes with extensive documentation and installation options.
Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.
Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when operating in high-dimensional settings (). The utilities provided here extend the use of this general methodology to many common data analytic challenges that arise in modern computational and genomic biology.
External validation of machine learning models with adaptive sample splitting
Software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.
ADAS-viewer (Visualization of Alzheimer's Disease Alternative Splicing) is a web-based application for integrative analysis of multi-omics data in Alzheimer's disease.
The database of Allelic Dosage-corrected Allele-Specific human Transcription factor binding sites provides a genomic map of allele-specific binding at hundreds thousands single-nucleotide polymorphisms constructed by meta-analysis of thousands of ChIP-Seq experiments.
Web Tool for Navigating and Plotting SomaLogic ADAT Files.
ADataViewer is an interactive web application for identify cohort data sets that are suitable for their research in regards to the Alzheimer's disease data landscape.
A Novel Data-Adaptive Robust Method for Identifying Tissue Specificity Scores.
ADC is an efficient method to identify highly interrelated genes across datasets.
ADCdb: The database of antibody-drug conjugates.
addFeatures adds spot images to a Bruker SCiLS Lab mass spectrometry imaging dataset from a list of defined mass spectral features (m/z regions)
Addgene is an nonprofit online database for plasmids and plasmid associated information.
AddictedChem is a base of controlled substances and a platform for predicting NPS.
AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants,
AddTag is a two-step approach with supporting software package that facilitates CRISPR/Cas-mediated precision genome editing. CRISPR Cas-induced genome editing is a powerful tool for genetic engineering, however, targeting constraints limit which loci are editable with this method. Since the length of a DNA sequence impacts the likelihood it overlaps a unique target site, precision editing of small genomic features with CRISPR Cas remains an obstacle. We introduce a two-step genome editing strategy that virtually eliminates CRISPR Cas targeting constraints and facilitates precision genome editing of elements as short as a single base-pair at virtually any locus in any organism that supports CRISPR Cas-induced genome editing. Our two-step approach first replaces the locus of interest with an "AddTag" sequence, which is subsequently replaced with any engineered sequence, and thus circumvents the need for direct overlap with a unique CRISPR Cas target site.
ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease.
An integrated platform of age-dependent expression and immune profiles across human tissues.
AdelaiDet is an open source toolbox for multiple instance-level recognition tasks on top of Detectron2. All instance-level recognition works from our group are open-sourced here.
Adenita is a 3D visualization and modeling toolkit for the in silico design of static and dynamic DNA nanostructures. Based on a multiscale data model, it visualizes DNA-based structures on different abstraction levels and enable users to load and create DNA origami structures and combine them with proteins.
Adenosiland represents the first attempt of an integrated bioinformatics and chemoinformatics web-resource dedicated to adenosine receptors. This informatics platform provides a wide-ranging of structure based and ligand based query functions to facilitate the exploration of adenosine receptor structures from primary sequences to three-dimensional architectures. Here, we present an overview of Adenosiland platform describing the most valuable searching tools and their functionalities.
AdEPro (Animation of Adverse Event Profiles) is an app that (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Animation of Adverse Event Profiles (AdEPro)
ADEPT is a tool for a high-sensitivity natural language processing (NLP) pipeline for detecting potential adverse drug events (ADEs) with easily interpretable output for high-efficiency human review and adjudication of true ADEs.
Adverse drug event presentation and tracking (ADEPT)
Adepth web server provides both depth and height representation of an atom in a macromolecule; it is capable of computing isosurfaces for atomic depths and presenting graphical view of marcomolecular shape at some distance away from the surface.
Software package for peptide identification using two different types of MS/MS spectra.
ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases.
ADFinder is an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software would facilitate research of programmed DNA eliminations and all down-stream analyses.
ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.
An attention-based deep hybrid model for protein-protein interaction prediction.
Computation of adherence to medications from Electronic Healthcare Data.
A simple toolbox of two ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro.
A scalable tool to visualize the adjacency matrix with values on the edges, direction, and the sum of value as the node size.
Adjusted-ADJUST is a script for the automatic identification of artifacts in electroencephalograph (EEG) data.
ALC is a dynamic fMRI connectivity toolbox for single-subject validation.
ZMIX is a software tool for estimating ancestry proportions in genome-wide association studies (GWAS) using only association Z-scores. It offers a novel method to overcome the challenge of inaccessible study reference allele frequencies.
A tool for adjusting mass spectrometry peaks in PKL file. User can decide whether to shift all spectra or just a single one of the file.
ADL Workbench is a compiler and IDE for working with the archetypes and templates written in the Achetype Definition Language (ADL), and based on any reference model, including openEHR, ISO 13606 and CIMI.
ADM1F is an open-source platform for fast and stable simulations of anaerobic digestion processes, leveraging PETSc for efficient numerical solutions. It features an iPython interface for model configuration, simulation, data analysis, and visualization, offering a significant speed advantage over conventional methods.
Anaerobic Digestion Model No. 1 Fast (ADM1F)
Validating ADME QSAR Models Using Marketed Drugs.
A manually curated database for the differential methylation in Alzheimer's disease.
Provides a user-friendly, freely available web interface for systematic ADMET evaluation of chemical compounds based on a comprehensive database consisting of 288,967 entries.
Chemical Rules for Optimization of Chemical Mutagenicity via Matched Molecular Pairs Analysis and Machine Learning Methods.
An integrated toolkit and pipeline for genetic analyses of admixed populations.
The Admixture simulator is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.
Program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred.
A method for parsing and filtering VCF files for admixture analysis. The method is able to filters SNPs to allow the delineation of population structure in ADMIXTURE and parses the output for summarization and graphical representation via CLUMPAK.
Provides a convenient interface for performing reproducible population genetic analyses as implemented by command-line programs in the ADMIXTOOLS software suite.
AdmixSim 2 is a forward-time simulator for modeling complex population admixture.
Implements five methods to analyze admixture: the three-population test, D-statistics, F4-ratio estimation, admixture graph fitting, and rolloff. In addition, it computes lower and upper bounds on admixture proportions based on f3-statistics. Contains 6 programs: convertf, qp3Pop, qpBound, qpDstat, qpF4Ratio, and rolloff.
Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates using a fast numerical optimization algorithm.
Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data – for example by comparing the sign of f_4-statistics with the signs predicted by the graph – and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
Alzheimer Disease Map Ontology (ADMO) is an ontology created from a disease map. ADMO is a formal representation of AD pathophysiology at the molecular scale. It was designed to store and link omics biomedical data.
An attention-guided denoising convolutional neural network (ADNet), mainly including a sparse block (SB), a feature enhancement block (FEB), an attention block (AB) and a reconstruction block (RB) for image denoising.
ADNI OASIS is a resource providing MRI data, demographics, and other related information for Alzheimer's disease research. It integrates imaging features and patient demographics for dementia classification.
Bayesian inference using the no-U-turn (NUTS) algorithm.
Tool for detecting positively selected amino acid sites from a set of unaligned nucleotide sequence data.
Intrinsic protein disorder prediction through deep bidirectional transformers.
Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. The Samply.MDR-based ETL tools from ADOPT BBMRI-ERIC.
ADOpy is a Python implementation of Adaptive Design Optimization, which computes optimal designs dynamically in an experiment. Its modular structure permit easy integration into existing experimentation code.
A novel two-layer machine learning predictor to identify antidiabetic peptides and diabetes types using multiview information.
A Global Online Platform on the Management of Children With ADPKD. Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common monogenic causes of kidney failure with an estimated worldwide prevalence of 1 in 500-2500 live births and affecting approximately 13 million individuals worldwide, representing a major socio-economic medical problem in the world. ADPKD is characterized by the progressive development and enlargement of multiple renal cysts in all nephron segments, progressively leading to end-stage kidney disease (ESKD) in 50% of patients by the age of 60 years. ADPKD arises as a consequence of mutations in the PKD1 (80% of patients) or PKD2 (15% of patients) genes, which encode respectively the proteins polycystin-1 (PC1) and -2 (PC2). Together, working on ADPedKD, we will aim at completing these gaps and having a better understanding of the ADPKD pediatric perspective.
ADPenetrance is a calculator for variant penetrance using family history of disease and population data. Penetrance is the probability of developing a particular trait given that a person harbours a certain genetic variant or set of variants. This tool uses population-scale data to allow estimation of the penetrance of risk variants associated with autosomal dominant traits.
Adapted Functional Chi-squared test (AdpFunChisq) is a model-free functional dependency measure that uses function direction and strength as evidence for causal inference.
ADPriboDB is a database to facilitate studies in uncovering insights into the mechanisms and biological significance of ADP-ribosylation. ADPriboDB 2.0 serves as a one-stop repository comprising 48 346 entries and 9097 ADP-ribosylated proteins, of which 6708 were newly identified since the original database release.
Adrenaline is a resource providing insights into the association between concomitant medication and survival in patients with breast cancer. It utilizes a nationwide French cohort study to identify medications associated with survival outcomes, providing hypotheses for drug influence on breast cancer evolution.
Single Cell Brain Atlas in Human Alzheimer’s Disease.
This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
ADTnorm is a normalization and integration method designed for CITE-seq datasets, addressing batch effects in ADT expression. It improves cell-type identification and enables atlas-level analyses by accurately aligning populations and providing utilities for threshold-gating and antibody panel selection.
ADToolbox is a Python package for modeling anaerobic digestion metabolism, incorporating metagenomic information to enhance VFA production accuracy. It provides command-line interfaces, a Python API, and facilitates large-scale metagenomic analyses and modeling simulations.
It can calculate four band and five band resistor's resistance.
Software suite that applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance.
ADViSELipidomics is a novel Shiny app for the preprocessing, analysis, and visualization of lipidomics data.
ADVIT is an Automated Dorsum Vein Identification Tool, which helps to perform human identification through hand dorsum vein images. The program can be requested using the form.
ADVP is a platform for the public community to browse, search and understand Alzheimer's Disease genetics findings easily. .
Program that implements the rarefaction method for analyzing allelic diversity across populations while correcting for sample size differences. Using individual multilocus genotype data on genetic polymorphisms, this tool computes estimates of allelic richness, private allelic richness and private allelic richness for combinations of populations.
A R package for performing adverse event (AE) enrichment analysis by gene enrichment tests.
The AEGeAn Toolkit provides a bundle of software tools for evaluating gene structure annotations and genome organization.
Implementation of AEMDA for inferring potential disease-miRNA associations.
The Atomic Energy NETwork (ænet) package is a collection of tools for the construction and application of atomic interaction potentials based on artificial neural networks (ANN).
eQTL analysis using region-based aggregation of rare genomic variants.
Aequatus is a homology browser to visualise homologous, orthologous and paralogous gene structures from Ensembl Compara and Ensembl Core databases
Facilitates quantitative comparisons of electrostatics in protein families and describes electrostatic contributions of individual amino acids.
Aevol is a computational platform for studying the evolution of digital organisms under different conditions, allowing researchers to understand evolutionary forces and mechanisms shaping genome and transcriptome structures. It was used to test hypotheses relating to mutation rate and population size and their effect on genome reduction.
AFA-Recur, a machine-learning-based probability score predicting 1-year risk of recurrent atrial arrhythmia after AF ablation
Web service for profiling amino acids surrounding ligands in proteins.
AFDB-Cluster provides a representation of protein structural clusters derived from the AlphaFold Protein Structure Database (AFDB) and other datasets, facilitating analysis of protein structure-function relationships. The resource offers a way to explore the shared functional landscape across diverse protein data sources.
AfexCore brings 12 essential bioinformatics tools into one intuitive GUI - built for researchers who need quick, reliable sequence analysis without the complexity (or price tag) of enterprise software.
AFExNet is an adversarial autoencoder for differentiating breast cancer sub-types and extracting biologically relevant genes.
This dataset documents the main forest species encountered in southern and central Benin, West Africa, based on field collections and monitoring efforts. It is intended for forestry research and characterization of species abundance in relation to environmental changes.
Package that parses Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions.
Affy6CNV is a pipeline for calling CNVs from Affymetrix 6.0 genotyping array data.
The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.
Structured corruption of cel file data to demonstrate QA effectiveness.
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.
The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
This tool performs an Affymetrix GeneChip Quality Control by implementing a graphical representation of QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection.
Preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.
Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
A Graphical User Interface for analysis of Affymetrix microarray gene expression data using the affy and limma packages.
Affymetrix_Error_Rate is a simple program that identifies the error rate in files of Affymetrix microarray SNP data
Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.
The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
Aan R based pipeline for parallel pre-processing of Affymetrix TM chips. The pipeline starts from a directory containing raw CEL files files and produces Bioconductor R objects containing gene expression measurements suitable for further analysis.
The package contains functions to perform the PDNN method described by Li Zhang et al.
This tool edits SNP probe classes directly while exporting genotypes in PLINK format.
A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
AffyProbeMiner is to re-define chip definition files (CDFs) for Affymetrix chips taking into account the most recent genomic sequence information. It re-groups probes in Affymetrix chips into probe sets according to a list of non-redundant verified complete coding sequences available in GenBank and RefSeq. Pre-computed CDFs for several chips are available for download.
This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
A tool for automated identification and exclusion of autofluorescent objects from microscopy images.
The Assembly Free Linkage Analysis Pipeline (AFLAP) was designed to build genetic maps using k-mers. This pipeline takes raw reads as an input, compares the composition (Jellyfish hashes) of the two parents and identifies uniquely segregating k-mers. AFLAP may be applied to any organism for which a mapping population is available.
Alignment-free network of 143 Bacteria and Archaea genomes.
Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs.
Prediction of antifreeze proteins (AFPs)
Browser-based visualization tools for AFQ results.
Database of protein mutations responsible for antifungal resistance.
The African Human Microbiome Portal (AHMP) is a public web portal providing curated metagenomic metadata related to African human microbiome samples. It offers search and retrieval operations and supports metadata search and access.
An integrated web-based platform for molecular modeling and screening
AFST(Abnormality Filtering and Sequence Trimming for ESTs)is a software tool using a pattern analysis approach.
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
The AFTM database reports the transmebrane segments identified by AlphaFold structural models of human proteins and compares them to those in the UniProt database and the Human Transmembrane Proteome (HTP) database.
Fungal structural and biochemical database.
Assembling the Fungal Tree of Life (AFTOL)
Automated tool that constructs matrices for phylogenomic analyses. It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.
AgAnimalGenomes.org provides tools based on JBrowse and Apollo that allow livestock genomics researchers to browse and manually annotate livestock genome assemblies. While a login is required to edit and create new annotations with Apollo, anyone can view the genomes and all data tracks (e.g. genes, gene expression, functional annotation, QTL, SNP, repeats).
AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.
A tool to evaluate agreement of differential expression for cross-species genomics.
Tool that implements an algorithm for optimal alignment of sequences with SVs.
AgeAnno is a comprehensive and curated database, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy tissue samples with ages ranging from 0 to 110 years.
AgeGuess is a simple online game in which you can post your photos, have other people guess your age, as well as guess the age of other users.
AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.
AGENT is the the Arabidopsis Gene Regulatory Network Tool for Exploring and Analyzing GRNs.
Computer program for estimating the generation interval, effective size, variances and covariances of lifetime number of offspring of an age structured population with overlapping generations.
This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. It does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity or polyploidy. Taking paired ends mapped to a reference genome as input, it merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account.
Such as phastCons, GERP, binCons, and others for a set of genomic intervals.
aggregateBioVar is a R library for differential gene expression analysis for multi-subject single cell RNA sequencing studies.
This code solves the aggregation problem using global inputs given N particles in a 2D environment.
Aggregation of particles in 2D grid using global control
AggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.
AGHmatrix software is an R-package to build relationship matrices using pedigree (A matrix) and/or molecular markers (G matrix) with the possibility to build a combined matrix of Pedigree corrected by Molecular (H matrix). The package works with diploid and autopolyploid data.
A hash table based high throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process.
Enables the rapid filtering, screening and sorting of variants derived from an exome sequencing experiment, to allow the rapid detection of possible deleterious variants.
AgileFileConverter converts varaint data in tab delimited text files, typically supplied by commercial NGS service providers, into the format used by AgileGeneFilter, AgileVariantViewer and AgileFileViewer
AgileGeneFilter allows sequence variants exported from AgileVariantViewer or AgileAnnotator to be filtered, by first identifying the proteins that are affected by the sequence variants and then performing a textual data search on these proteins, using information downloaded from the UNI-Prot web page.
AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data.
AgilePairedEndReadsCombiner reads a matching pair of fasta or fastq files created from a paired end sequence run which used PCR products as the library template and combines the data to produce a single read file contain data equivalent to the whole PCR product.
Enables the rapid filtering, screening and sorting of indel variants derived from an exome sequencing experiment to allow the rapid detection of possible deleterious variants.
AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter is to remove low quality sequence data before alignment to a reference sequence.
This script normalises a set of gene expression data files against a predefined reference data set. The normalisation uses LOESS regression. The major assumption is that the actual data and the reference set have a similar epxression frequency distribution. Typically, the reference set used the is average of a large number of datasets such as the output of Baseline script in this package.
Processing and Analysis of Agilent microRNA data.
Imputation of scRNA-seq data based on a hybrid GAN with dropouts identification.
The AgiND (Agilent Normalization and Diagnostic Package) R library was developped for diagnosis and normalization of one channel and two channel Agilent microarrays.
Aging Atlas is a curated biomedical database comprising a range of aging-related multi-omics datasets (i.e. transcriptomics, single-cell transcriptomics, epigenomics, proteomics, and pharmacogenomics), as well as bioinformatics tools to query and visualize these datasets.
Single-cell transcriptomic profiling of the aging mouse brain | Methodios Ximerakis, Scott L. Lipnick, Brendan T. Innes, Sean K. Simmons, Xian Adiconis, Danielle Dionne, Brittany A. Mayweather, Lan Nguyen, Zachary Niziolek, Ceren Ozek, Vincent L. Butty, Ruth Isserlin, Sean M. Buchanan, Stuart S. Levine, Aviv Regev, Gary D. Bader, Joshua Z. Levin, and Lee L. Rubin
A manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species.
Curated database of aging regulatory relationships in humans.
A framework called Attention guided Global enhancement and Local refinement Network (AGLN) to improve the encoder-decoder network for image segmentation.
Accurate prediction of protein beta-aggregation with generalized statistical potentials.
Resource to unlock the uncharted regions of the coding sequence space.
AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.
AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” . AGORA is used to generate ancestral genomes for the Genomicus online server for gene order comparison, and has been in constant use in the group since.
A Gene Ontology enrichment tool, specifically designed for the abundance bias in Mass Spectrometry (MS) based proteomics data. This site can be used for functional annotation enrichment for proteomics data. It contains tools for abundance corrected functional enrichment and supports the following categories: GO-terms, UniProt-keywords, KEGG-pathways, Reactome, WikiPathways, InterPro, Pfam, PubMed Publications, Diseaeses, Tissues, and Compartments.
Simple command-line tool that enables rapid and flexible production of text tables tailored for aggregation plots from which users can easily design multiple groups based on user-definitions such as regulatory regions or transcription initiation sites.
Agptools is a suite of tools for performing edits to an AGP file during this manual curation stage of genome assembly.
A Database of Regulatory SNPs for Agricultural Animal Species.
A database storing SNPs and their predicted impact on transcription factor (TF) binding in promoter regions for different crops.
Integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.
Comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.
AgroSeek is a system for computational analysis of environmental metagenomic data and associated metadata.
AgrVATE is a tool for rapid identification of Staphylococcus aureus agr locus type and also reports possible variants in the agr operon.
AGTAR is a program that uses adapted genetic algorithm to assemble and quantify transcripts based on RNA-seq data.
AgTC is an open-source tool that generates comma-separated value file templates for standardized data collection in plant science research. It facilitates data collection and management, offering flexibility for various experimental setups and streamlining the data processing pipeline.
Database of protein structure pairs (apo-holo structure pairs) before and after binding. AH-DB is designed to provide an easy and unified way to prepare apo-holo structure pair data for studies. Data is generated by identifying/mapping molecules in Protein Data Bank (PDB) entries.
A REST service for mapping text analysis results from Averbis Health Discovery to FHIR resources.
Ad hoc learning of fragmentation patterns in mass spectra detects post-translationally modified peptides prior to database search. Deep learning model (Temporal conv net, using dilated conv layers) detects post-translational modified peptides based on their ms/ms spectrum.
This tool offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.
AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.
Webserver & command-line tool for search and alignment of APO (unbound) protein structures from HOLO (bound) forms and vice versa. Features: customizable search of Apo-Holo pairs in the PDB, alignment to the query structure, batch mode for fast parallel dataset processing, visualization via Molstar and PyMol, public documented REST-API.
Manually curated database of experimentally validated Antihypertensive peptides (AHTPs) with comprehensive information that includes: sequence, inhibitory concentration (IC50), log value of inhibitory concentration (pIC50) and toxicity.
AHTpin is an in silico method developed to predict and design efficient antihypertensive peptides.
Accurate prediction of anti-hypertensive peptides based on convolutional neural network and gated recurrent unit
A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion. cloud_download Download test images. To run the AI-biopsy framework please follow these steps:. process and result folders from ML training (Not included in this repository). Pre-trained Models of CNN architectures should be downloaded from the "Pre-trained Models" part of https://github.com/wenwei202/terngrad/tree/master/slim#pre-trained-models and be located in your machine (e.g. GitHub_AI-biopsy/scripts/slim/run/checkpoint). The files for pre-trained models are available under the column named "Checkpoint". For accurate results, we recommend the use of axial images with a visible prostate gland. Also, 7 slices per patient are used in voting system to measure the accuracy of the trained model for individual patients. ||| CORRECT NAME OF TOOL COULD ALSO BE 'h4AI-biopsy'
AI-CT-COVID-19 is a collaborative online AI engine for precise CT-based COVID-19 diagnosis using federated learning to provide people worldwide an effective AI model for precise CT-COVID diagnosis.
AI-Driver (AI-based driver classifier) is an ensemble method for predicting the driver status of somatic missense mutations based on 23 pathogenicity features. AI-Driver is an ensemble method for identifying driver mutations in personal cancer genomes.
AI4AMP is a sequence-based antimicrobial peptides (AMP) predictor based on PC6 protein encoding method and deep learning.
A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.
Lightweight, non-intrusive MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output.
The AIBL Distance-to-Boundary model uses novelty detection and distance metrics to identify individuals at risk of developing Alzheimer's disease based on data from the AIBL study. It includes a GUI for non-technical stakeholders and a distance-to-boundary strategy for risk assessment.
AIBL Distance-to-Boundary Novelty Detection
AID-HS is an open-source pipeline for detecting and lateralizing hippocampal sclerosis in temporal lobe epilepsy, producing clinically-relevant reports based on MRI scans.
AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation producing a final assembly satisfying user-specified inter-domain distance restraints.
Automated Isoform Diversity Detector (AIDD) is pipeline for investigating transcriptome diversity of RNA-seq data. AIDD incorporates open source tools into a static virtualbox to ensure reproducability in RNA-seq analysis. AIDD explores editome by mapping both ADAR and APOBEC editing sites on a global and local level and produces publication ready visualization of ADAR editing landscapes.
AIDE (Annotation-effIcient Deep lEarning) is a deep learning framework for automatic medical image segmentation with imperfect datasets, including those having limited annotations, lacking target domain annotations, and containing noisy annotations. Automatic segmentation of medical images plays an essential role in both scientific research and medical care. Deep learning approaches have presented encouraging performances, but existing high-performance methods typically rely on very large training datasets with high-quality manual annotations, which are normally difficult or even impossible to obtain in many clinical applications.
AIDeveloper is a software tool that allows you to train, evaluate and apply deep neural nets for image classification within a graphical user-interface (GUI).
AIdrug2cov is a network representation learning-based methodology to discover drug mechanism and anti-inflammatory response for patients with COVID-19.
Artificial Intelligence-based Web-App for Virtual Screening of Inhibitors against SARS-COV-2.
An easy-to-use AIHF-nomogram to predict advanced liver fibrosis in patients with autoimmune hepatitis.
Sophisticated framework designed from scratch to be a flexible and scalable infrastructure for computational science. Being able to store the full data provenance of each simulation, and based on a tailored database solution built for efficient data mining implementations, AiiDA gives the user the ability to interact seamlessly with any number of HPC machines and codes thanks to its flexible plugin interface, together with a powerful workflow engine for the automation of simulations.
AILDE (Auto In Silico Ligand Directing Evolution) server is developed according to the CSO (Computational Substitution Optimization) protocol, which was designed to automatically perform computational substitution, energy minimization, and binding affinity evaluation. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead.
The Automatic Image Processing for Microarrays tool is designed for uncalibrated microarray gridding and quantitative image analysis. Uncalibrated microarray image analysis supports integration of expression data from different sources and can improve reproducibility.
Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments.
A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe.
A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk.
AIModules enables you to find transcription factor binding sites (TFBSs) and modules on DNA using own matrices or the JASPAR 2022 database.
This package contains the necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). The assignments could be done on individual samples as well as on dataset of gene expression data.
All-in-one scheme-based biomedical named entity recognition using deep learning.
Package containing several tools, datasets and ML models for (phospho-)proteomics.
An R Package for Augmented Inverse Probability Weighted Estimation of Average Causal Effects
The Atlas of Inflammation-Resolution (AIR) is a web application for capturing an essential part ofacute inflammation and inflammation resolution research.
Accurate identification of RNA-binding proteins using machine learning techniques.
Aird is a new format for mass spectrometry data storage. It is an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate for m/z and intensity pairs. Aird provides a novel compressor call ZDPD for m/z data compression,which makes up an amazing compression rate. Compared with Zip, m/z data is about 55% lower in the Aird on average. Aird is a computational friendly algorithm. Through SIMD optimization, the decoding speed of Aird is much higher than that of Zip. AirdPro is opensource under the MulanPSL2 license.
Cloud-based platform to manage and share antibody-based single-cell research.
AirLift is a pipeline that updates mapped reads from one reference genome to another.
Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.
A Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide.
Github repository for the paper "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases" by Høye et al.
An interactive tool for exploring B-cell receptor repertoires and antibody responses. To run AIRRscape, clone the repo and open the app.R file in your RStudio, then click "Run App". As a Shiny app, it can run as a window of RStudio, or as a tab in a web browser (recommended).
Simulating human B cell receptor repertoire sequences.
Ais is a tomogram segmentation package designed for high performance and accessibility. It streamlines segmentation workflows, including particle picking for subtomogram averaging and generating segmentations of cellular architecture, and is available as a GitHub repository with trained models.
AIScaffold is a web-based tool for scaffold diversification using the deep generative model. AIScaffold can perform large-scale diversification in several minutes and recommend the top 500 molecules. Features such as site-specific diversification are also supported. This tool can facilitate the scaffold diversification process for medicinal chemists, thereby accelerating drug design.
AIscEA (Alignment-based Integration of single-cell gene Expression and chromatin Accessibility) a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency.
Interactive image segmentation tool designed to allow curators of biological specimens to segment and annotate image data with ontology terms.
AITAC is a method for accurately infer tumor purity and absolute copy numbers in a tumor sample by using high-throughput sequencing (HTS) data.
AITANA is a platform to facilitate the investigation, development, training and inference of predictive models of Machine Learning and Artificial Intelligence, optimizing the computing resources with the use of a set of tools and methodologies. AITANA wants to minimize the times of training and find the solution of a Machine Learning project with the use of a complete platform to provide an abstraction for computational resources and infrastructure.
Adversarial Inductive Transfer Learning (AITL) is a deep neural network method for addressing discrepancies in input and output space between the pre-clinical and clinical datasets.
AIUPred is a web server and downloadable package that predicts intrinsically disordered protein regions using a combination of energy estimation and deep learning techniques. It builds upon the original IUPred server and scores among the top three single-sequence-based methods.
Aizynthfinder is a tool for retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable precursors. The tree search is guided by a policy that suggests possible precursors by utilizing a neural network trained on a library of known reaction templates.
Software for adaptative-bandwidth kernel density estimation for high-throughput sequencing data.
AKID is a Deep Neural Network-based method that identifies kinase-specific phosphorylation events at single-kinase level in any given Eukaryotic proteome without prior functional annotation. It automatically detects kinase domains, their residues responsible for target specificity and finally their target peptides.
AKLIMATE is an R package for a stacked kernel learning algorithm that integrates multi-modal data and prior knowledge feature sets.
Statistical method that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data.
Software for parameter inference using Approximate Bayesian Computation.
Web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.
Software that includes powerful bioinformatics applications for genetic analysis and offers a comprehensive solution to the tasks of genomic variants annotation, filtration, interpretation and reporting. It includes Alamut Batch, which is a high-throughput variant annotation engine for NGS data, Alamut Focus, an interactive variant filtration application for NGS analysis and Alamut Visual, a graphical variant interpretation environment used by leading genetic clinicians and researchers around the world.
AlbaTraDIS is a software application for performing rapid large-scale comparative analysis of TraDIS experiments whilst also predicting the impact of inserts on nearby genes. It allows for experiements with multiple conditions to be easily analysed using statistical methods developed in the Bio-TraDIS toolkit.
C program that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. It uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters.
ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.
Alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data.
alder detects and dates population admixtures based on patterns of linkage disequilibrium.
A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.
An efficient genotyper and star-allele caller for pharmacogenomics.
Automated label extraction from GEO metadata.
A toolbox for allele-specific epigenomics analysis
Web server supports homolog collection from diverse animal genomes. An input sequence is passed through the server to collect similar sequences for molecular phylogenetic analysis.
A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.
A software program to generate highly sensitivity seeds
Aletsch is a software resource for assembling RNA-seq data, particularly useful for multiple bulk or single-cell samples. It employs bridging and graph-decomposition algorithms to restore missed junctions and leverage supporting information across samples.
Alternative Expression Analysis by massively parallel RNA sequencing
Pipeline for the automated detection of orthologous gene clusters and subsequent positive selection analysis.
A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.
A biological sequence clustering tool with dynamic threshold
Alfie is an alignment-free, kingdom level taxonomic classifier for DNA barcode data. Alfie classifies sequences using a neural network which takes k-mer frequencies (default k = 4) as inputs and makes kingdom level classification predictions.
BAM Statistics, Feature Counting and Annotation
Distance Estimator for Phylogenetic Inference.
Alfresco‘s (FRont-End for Sequence COmparison) aim is to develop a new visualisation tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualised and used to find corresponding sequence domains.
Computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.
AlgaeFUN - MicroAlgae Functional Annotation Web based Tool.
Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.
Provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
Predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.
AlgPred 2.0 is an updated version of our old server AlgPred developed for predicting allergenic proteins
A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.
Alignment-based sequence extraction software (ALiBaSeq) is designed to retrieve homologous regions from a FASTA file with contigs (e.g., an NGS read assembly file). The retrieval is done based on reading BLAST, HMMER, or LASTZ search tab-delimited output tables or SAM / BAM alignment files and then searching for the results in an assembly file.
Automatic Labeling of Independent Components in Electroencephalography (ALICE) is a toolbox and crowdsourcing platform.
Temporal sequence alignment for clustering longitudinal clinical data.
The Alignment Constrained null set generator is a framework to generate randomized versions of an input multiple sequence alignment that preserve some of its crucial features including its dependence structure.
Trimming and clipping FASTQ-formatted read files.
ALIFRITZ performs statistical multiple alignment and phylogeny reconstruction simultaneously. It implements a strategy based on simulated annealing which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences’ indel history, i.e. their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree.
Framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data.
University of Padua, Department of Biomedical Sciences, BioComputing UP lab
align-cli is a tool to assist manual inspection of mass spectra using alignments, isobaric sequences and other information from mass spectrometry.
A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons.
Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.
Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering.
Improved inference of chromosome conformation from images of labeled loci | chromosome conformation reconstructions based on imaged loci | download the align3d files into the Cicada directory | install the GNU Scientific Library
Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.
Maryanne Fenerjian (HMS Office of Technology Licensing contact)
Software for splitting a protein FASTA file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.
An R-package for alignment of protein-protein interaction networks.
Software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
AlignGraph2 is a tool for genome-assisted reassembly pipeline for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.
AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.
Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.
An application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same dataset.
AlignmentViewer is multiple sequence alignment viewer for protein families with flexible visualization, analysis tools and links to protein family databases. It can handle protein families with tens of thousand of sequences and is particularly suitable for evolutionary coupling analysis, preparing the computation of protein 3D structures and detection of functionally constrained interactions.
A Python package for parsing complex features from high-throughput long-read sequencing. Align sequences and then parse features. alignparse documentation — alignparse 0.1.2 documentation. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features. For each read that passes the filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features
Viewing protein secondary structure predictions within large multiple sequence alignments. The module is part of the ANTHEPROT package.
AlignStat is a web-tool and R package for statistical comparison of alternative multiple sequence alignments.
LC-MS alignment algorithm based on Wasserstein distance.
ALION is a sequence alignment tool. Aligns two protein sequences using Needleman-Wunsch global alignment or Smith-Waterman local alignment methods with variable gap penalties and amino acid substitution matrices. Analogous to GCG GAP and BESTFIT programs.
A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosome conformation capture (Hi-C) data. The ∼1.50 Gb assembled alkaligrass genome encodes 38,387 protein-coding genes, and 54.9% of the assembly are transposable elements, with long terminal repeats being the most abundant. Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass
Chemicals prioritization for topics of interest using gene-related PubMed abstracts.
Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.
All2 is a tool for filtering variants from all2all comparison of multiple clones or single cells. There are no variant allele frequency and mutation spectrum plots for structural variant mode and the format of the output files will be slightly different from the SNV/INDEL analyses.
Curation of ion mobility collision cross-section atlas for small molecules using comprehensive molecular representations.
AllCoPol is a collection of tools for the analysis of polyploids, which allow to infer ancestral allele combinations as well as corresponding subgenome phylogenies.
It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.
The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.
R package to simulate small populations. Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period.
AlleleShift is an R package to predict and visualize population-level changes in allele frequencies in response to climate change.
A Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire.
Provides a framework for allelic specific expression investigation using RNA-seq data.
The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.
Integration of gene expression data, connectivity data and neuroanatomical information for the adult and developing brain in mouse, human and non-human primate.
A comprehensive gene set function enrichment tool for both model and non-model species. This is a tool designed for functional genomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets, or differential epigenomic modification gene sets etc) are continuously generated. AllEnricher incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.
A web server for predicting protein allergenicity potential.
A novel web app for prediction of protein allergenicity.
Fast and accurate sequence-based allergen prediction tool that models protein sequences as text documents and employs support vector machine in text classification for allergen prediction.
Bioinformatics tool for allergenicity prediction based on a novel descriptor fingerprint approach.
Server for in silico prediction of allergens based on the main physicochemical properties of proteins.
AllesTM is an integrated tool to predict almost all structural features of transmembrane proteins that can be extracted from atomic coordinate data. It blends several machine learning algorithms: random forests and gradient boosting machines, convolutional neural networks in their original form as well as those enhanced by dilated convolutions and residual connections, and, finally, long short-term memory architectures.
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
A modern data ecosystem for model organism databases.
The Allelic imbalance meter tool offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.
Identifies potential endogenous or exogenous allosteric modulators as well as their characterization in human allosterome. Automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator–protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. Enables identification of allosteric metabolites for metabolic enzymes and screening of potential allosteric compounds for disease-related targets.
The database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations.
Web server uses normal mode analysis and pocket features to predict allosteric pockets on proteins.
Web server for multiscale analysis of multiple allosteric regulations.
Web server that predicts the binding affinities of allosteric ligand-protein interactions.
A web application for exploring and quantifying the effects of allosteric ligand binding and mutations.
Tool for the prediction of allosteric sites in proteins.
AlloViz is a Python package for computing, analyzing, and visualizing protein allosteric communication networks. It integrates existing methods and facilitates the calculation of consensus-like scores based on multiple structural aspects of allosteric networks.
De novo assembly of whole-genome shotgun microreads.
Short read assembler that works on both small and large (mammalian size) genomes.
RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia.
Open RGB Imaging Workflow for Morphological and Morphometric Analysis
This modelling environment provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
Simplifying quality control of high-throughput sequencing data.
Aln2tbl is a Python script for building a mitochondrial features table from a assembly alignment in fasta format. The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks.
AlnC is an extensive database of long non-coding RNAs in Angiosperms.
alntools processes next-generation sequencing read alignments into a sparse compressed incidence matrix (aka Equivalence Classes) and stores it in a pre-defined binary format for efficient downstream analyses and storage. It enables us to compare, contrast, or combine the results of different alignment strategies.
Alohomora was designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array
alona is a web-based bioinformatics service designed to analyze single cell RNA sequencing (scRNA-seq) data. It is an analysis framework for single cell RNA sequencing data (scRNA-seq) and enables exploratory analysis through a set of Python modules. adobo can be used to create analysis pipelines, facilitating analysis and interpetation of scRNA-seq data.
This program calculates the statistical parameters in the modified Gumbel distribution for BLAST
AlPaCas is a web server pipeline designed to identify and analyze SNV-derived PAMs for allele-specific CRISPR gene editing. It assists in selecting Cas enzymes and proposing mutations to enhance selectivity towards SNV-derived PAMs.
Alpha-Frag is a deep neural network for fragment presence prediction improves peptide identification by data independent acquisition mass spectrometry.
A deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data.
Alpha-XIC is a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry.
Alphabet takes a database of aligned protein sequences in BLOCKS+ format and examines the alignments column-wise looking for groups of amino acids that co-occur in columns more frequently than expected based on overall amino acid composition. These groups of amino acids can form a reduced alphabet for building sequence motifs (eMOTIFs) or for detecting correlations between columns of amino acids (MCSeq).
AlphaCharges is a web server for the calculation of partial atomic charges on protein structures, created by AlphaFold.
Empirical and predicted library search for label-free quantification and DIA multiplexing
Package for simulating genomic selection or GWAS data, that drops simulated haplotypes through a pedigree using MaCS. It can simulate sequence and SNP data, pedigrees, QTL effects, and breeding values. Pre-specified pedigrees can also be supplied.
A database for the comparison of structural models predicted by ESMFold and AlphaFold2 for human proteins.
AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
AlphaFind is a web-based search engine that allows for structure-based search of the entire AlphaFold Protein Structure Database. Uniprot ID, PDB ID, or Gene Symbol is accepted as input – the engine will return the most similar proteins found within AlphaFold DB, with an option for additional search to extend and refine the results. The search results are grouped by their source organism and displayed along with several similarity metrics. 3D visualizations of the structural superposition of the proteins are provided, and text filters can be used to find specific organisms or Uniprot IDs. For details about the methodology and usage, please see the manual. This website is free and open to all users and there is no login requirement.
AlphaFold is an AI system developed by Google DeepMind that predicts protein 3D structures from amino acid sequences, achieving accuracy comparable to experimental methods. It is accessible through the European Bioinformatics Institute (EBI) and a GitHub repository.
AlphaFold2 is an AI system developed by Google DeepMind that predicts protein structures from amino acid sequences with high accuracy. It offers a web interface, API documentation, and Docker containers for users to access and utilize its capabilities in various research areas, particularly drug discovery and structural biology.
AI-guided 3D structure prediction of novel proteins. AlphaFold uses neural networks to predict the tertiary (3D) structure of proteins. AlphaFold accepts an amino acid sequence as an input, which it will then will 'fold' into a 3D model.
Impute and phase genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation to impute alleles and genotypes.
AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values.
AlphaMALIG (ALPHAbet Multiple ALIGnment) is a tool which allows you to align many but no more than 200 sequences. These sequences will be formed by characters of a finite alphabet.
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
Alphamod is a novel pipeline that incorporates AlphaFold2 with MODELLER, a template-based modeling program. Additionally, our tool can drive a comprehensive quality assessment of the tertiary protein structure by incorporating and comparing a set of different quality assessment tools.
Simple software package for simulating data in multi-parent populations.
R implementation of the method for partitioning genetic trends. Partition/Decomposition of Breeding Values by Paths of Information.
A modular deep learning framework to predict peptide properties for proteomics.
This server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.
A Python package for protein-protein interaction screens using AlphaFold-Multimer.
AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment.
AlphaSpace2 is a surface topographical mapping tool.
Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization. High-resolution MS-based proteomics generates large amounts of data, even in the standard LC-tandem MS configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich datasets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole TOF (Q-TOF) platform as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS), and microseconds (TOF). In our open-source AlphaTims package, data are indexed, accessed, and visualized by a combination of tools of the scientific Python ecosystem
AlphaTracker is a multi-animal tracking and behavioral analysis tool which incorporates multi-animal tracking, pose estimation and unsupervised behavioral clustering to empower system neuroscience research. Alphatracker achieves the state-of-art accuracy of multi-animal tracking which lays the foundation for stringent biological studies. Moreover, the minimum requirement for hardware (regular webcams) and efficient training procedure allows readily adoption by most neuroscience labs.
Predicting the pathogenicity of missense variants using features derived from AlphaFold2.
Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.
AlpsNMR is an R package that can load Bruker and JDX samples as well as preprocess them.
A method for imputation of missing values in single cell RNA-sequencing data
Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.
This resource describes a method for generating and releasing synthetic datasets based on the Avon Longitudinal Study of Parents and Children (ALSPAC) data to facilitate transparent and reproducible research while preserving participant anonymity. The approach uses the 'synthpop' package in R and provides guidelines for researchers to follow.
Releasing synthetic data from the Avon Longitudinal Study of Parents and Children (ALSPAC)
Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.
AltaiR is a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data. This method provides alignment-free and spatial-temporal analysis of multi-FASTA data through the implementation of a C toolkit that is highly flexible and with characteristics covering large-scale data, namely extensive collections of genomes/proteomes. This toolkit is ideal for scenarios entangling the presence of multiple sequences from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence(s) in (multi-) FASTA format.
AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).
Convenience data structures and functions to handle cdfenvs.
ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.
Cross-platform and standalone tool for analyzing gene expression datasets to highlight significantly rewired pathways across case-vs-control conditions. The Tool is designed to analyze human gene expression datasets (with Entrez ID).
The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.
Method incorporating alternate reference haplotypes to generate gene- and haplotype-level estimates of transcript abundance for any genomic region where such information is available.
Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. altMOD is a MODELLER (https://salilab.org/modeller/) [1] plugin for improved 3D homology model building. Right now, it allows to incorporate in the program's objective function terms for interatomic distances statistical potentials, such as DOPE [2] and DFIRE [3]. The effect of adding statistical potentials in the objective function of MODELLER is described in Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling" (Janson et al., 2019). In a benchmark with 225 single-template homology models, we found that the inclusion of DOPE in the objective function of MODELLER brings an average improvement of 1.3% and 2.0% in GDT-HA [4] and lDDT [5] and a large improvement of -29.8% in MolProbity scores [6]
Altools is a software package that allows the precise detection of polymorphisms and structural variations.
AltWOA is a novel feature selection algorithm where Altruistic property of candidate whales are embedded to the Whale Optimization Algorithm (WOA).
Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood-Brain Barrier Permeability
A web browser-based tool to analyze lung intravital microscopy.
Fast bam file viewer from the National Cancer Informatics Program.
Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus. In interdisciplinary fields such as systems biology, close collaboration between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest
Alvis is a tool for contig and read ALignment VISualisation and chimera detection. It produces LaTeX and SVG alignment diagrams from a number of common alignment formats.
Selective Neuronal Vulnerability in Alzheimer's Disease.
Selective Neuronal Vulnerability Alzheimer Disease
A tool to discriminate disease-causing and neutral mutations in Alzheimer's disease.
AlzCode is a web resource that developed pipeline to evaluate the association of genes with AD. The association of genes with AD are validated by multiple lines of functional genomic evidence with statistical approaches.
A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer’s Therapeutic Discovery. A Network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development.
AlzScPred - A Package to Predict Alzheimer's Disease Using Single Cell Data
AM-UNet: Automated Mini 3D End-to-End U-NetBased Network For Brain Claustrum Segmentation.
A Comprehensive Database for Association Between Microbiota and Disease.
A machine learning platform for predicting drug-induced phosphol ipidosis.
An R package for Meta-analysis of metabolomics non-integral data.
AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics.
Series of tools written in C++ that allows you to segment your mass spectrometry imaging dataset into regions with similar molecular signatures. The software allows for user input at each step of the process and returns the regions as well as the associated molecular signatures. It is composed of two dynamic libraries and a series of executables using the libraries as a base.
Automated tool for antimicrobial resistance surveillance system (AMASS) was developed as an offline, open-access and easy-to-use application that allows a hospital to perform data analysis independently and generate isolate-based and sample-based surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in R, which is a free software environment.
Adaptive and powerful microbiome multivariate association analysis via feature selection.
Augments the Cytoscape network readers by adding the ability to read in an adjacency matrix.
A web tool to query data for a set of 5k variants that were predicted with high pathogenic probability
An R-package for interactive alteration annotations for molecular tumor boards.
The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
An automated workflow tool for Kepler to perform AMBER GPU molecular dynamics simulations.
A scripting tool for running amber MD in an easy way.
Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.
The Active Modules for Bipartite Networks is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. It does not require predefined pathways and gives highly specific predictions of affected areas of metabolism.
Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation.
Software module for reaction representation, reaction search and structure transformation.
Aquaculture Molecular Breeding Platform (AMBP): a web server and standalone version for genotype imputation and genetic analysis in aquaculture
Accurate mutation clustering from single-cell sequencing data.
Metabolite concentrations in animal tissues and convenient comparison of quantitative metabolomic data.
A versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4.
Automatic Midline Extraction and Background Subtraction of Ratiometric Fluorescence Time-Lapses of Polarized Single Cells. AMEBaS is a new computer program that has been developed to automate the study of cells with polarity and is based in pollen tube growth and ion dynamics data. This program uses a three-step process to analyze fluorescent markers in cells with polarity.
The Annotation, Mapping, Expression and Network (AMEN) software is a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human.
AMEND (Active Module identification using Experimental data and Network Diffusion) is an algorithm designed to find a subset of connected nodes in a molecular interaction network that have large experimental values. It makes use of random walk with restart (RWR) to create node weights, and a heuristic approach for solving the Maximum-weight Connected Subgraph problem using these weights. The resulting subnetwork is then scored based on average experimental values and connectivity, and it is used as input into RWR for the next iteration. This process is performed iteratively until an optimal subnetwork (i.e., module) is found.
AmetaRisk is an online tool for quantitative assessment of CRC metastasis risk based on the local invasion.
AgroMarker Finder (AMF) provides a graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice.
The Automatic Mycorrhiza Finder (AMFinder) allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks.
Web application which provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.
Amica is an interactive and user-friendly web-based platform that accepts proteomic input files from different sources and provides automatically generated quality control, set comparisons, differential expression, biological network and over-representation analysis on the basis of minimal user input.
Gene prediction server that can identify coding sequences in microbes.
Multi-platform (Windows and Linux) toolbox which covers all the steps of the iterative identification procedure: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.
The GO Consortium GO browser and search engine.
AMIGOS III is a plugin to PyMOL for pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.
Analysis of amino acid conservation using conservation index
AMIS (A Mouse Imaging Server) is a still growing webserver providing imaging information about the distribution of certain GPCRs in mice.
a web‐based prognostic model to predict the prognosis of Acute myeloid leukaemia patients. Using log-rank test and univariate COX regression analysis as well as LASSO-COX, AML patients were divided into high-risk and low-risk groups based on AML risk score (AMLRS) which was constituted by 10 survival-related genes.
AMLVaran, the AML Variant Analyzer is a web-based software platform for variant analysis on targeted NGS data, addressing the requirements of a clinical setting.
Adaptive Multilinear Meshes (AMMs) is a new framework to represent piecewise multilinear volumetric data using mixed-precision adaptive meshes.
Tool which helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI.
Automatic Molecular Mechanics Optimization for in silico Screening 2. Efficient computational refinement of protein–small organic molecule complexes. Employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes.
Curated database of Indian anti-tubercular medicinal plants.
It is a new functional genomic databases serving the amoebozoa research communities. It contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. Importantly it utilizes the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility.
Database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space.
AMOS is a Modular, Open-Source whole genome assembler.
A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. This tool aims to search active modules in multi-layer WGCN using a continuous optimization approach.
Prediction of antimicrobial peptide function based on a BERT model.
AMPZero is a predictor designed for predicting the effectiveness of a peptide sequence against various microbial species. The predictor takes the peptide sequence and any N/C-termini modifications together with the genomic sequence of a microbial species to generate targeted predictions.
Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data.
A tool for hemolytic activity prediction of antimicrobial peptides using transfer learning.
Annotated collection of normalized data describing antimicrobial peptides, their sources, their 3D structures, and their target organisms. It enables users to perform quick queries and allows the entire peptide community to contribute to the repository.
AmPEPpy is a Python application that implements a random forest classifier for predicting antimicrobial peptide sequences using the distribution descriptor set from the global protein sequence descriptors. amPEPpy has improved portability, increased accuracy relative to similar methods, and includes utilities for easily training and optimizing random forest classifiers on novel training data.
A computational model to identify antimicrobial peptides and their functions based on sequence-derived information.
The Amphibian Genomics Consortium (AGC) is an international initiative focused on advancing genomic resources for amphibian research and conservation. It brings together researchers to improve understanding of amphibian biology and facilitate genomic studies.
Automated Phylogenomic Inference Pipeline for bacterial sequences. From a given a set of protein sequences, it automatically identifies 31 phylogenetic marker genes. It then generates high-quality multiple sequence alignments for these genes and make tree-based phylotype assignments.
Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data and genomic data.
Visualize outputs generated by the metagenomic and genomic analysis tool AMPHORA2 or its webserver implementation AmphoraNet.
An R package for fast genome-wide prediction of antimicrobial peptides. It is fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.
AMPL is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery. The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools. AMPL is an end-to-end data-driven modeling pipeline to generate machine learning models that can predict key safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters.
A program for Molecular Replacement with search ensembles generated from uncoventional models.
It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
AmpliconDesign is an interactive webserver for the design, documentation and analysis of targeted bisulfite sequencing studies.
a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.
AmpliDiff is a computational tool for finding highly discriminatory genomic regions in viral genomes and designing primers for their amplification. It provides a cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.
AmplificationTimeR is an R package for timing sequential amplification events in genomic regions, enabling the inference of amplification order and providing insight into tumor evolution. It builds upon existing methods and allows for the timing of more copy number states.
AMPlify is an attentive deep learning model for antimicrobial peptide prediction.
Automated methylation analysis of amplicons from bisulfite flowgram sequencing. The Roche 454 GS Junior sequencing platform allows locus-specific DNA methylation analysis using deep bisulfite amplicon sequencing. However, bisulfite-converted DNA reads may contain long T homopolymers, and the main sources of errors on pyrosequencing platforms are homopolymer over- and undercalls. Furthermore, existing tools do not always meet the analysis requirements for complex assay designs with multiple regions of interest (ROIs) from multiple samples. We have developed the amplikyzer software package to address the above challenges. It directly aligns the intensity sequences from standard flowgram files (SFF format) to given amplicon reference sequences, without converting to nucleotide FASTA format first, avoiding information loss by rounding flow intensities, and taking special measures to correctly process long homopolymers
Tool to process and analyze targeted NGS data.
Pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.
The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq.
Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides
Suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. It also implements flexible pattern matching and database scanning options, and includes functions for running randomisations to estimate the significance of sequence similarities.
NMR protein structure refinement. Amber (acronym to Assisted Model Building with Energy Refinement) is a suite of programs 1N3L that allow users to perform molecular dynamics (MD) simulations on biological systems. This web portal makes available the entire functionality of AMBER, in particular (but not only) using NMR-derived information as restraints for MD.
Matlab functions for analysis of patterns in (functions of) parameter values of the Add-my-Pet collection.
ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.
a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data
AMScorer and AMReader are tools designed to streamline the process of recording and analyzing data from arbuscular mycorrhizal colonization assays. AMScorer is an Excel spreadsheet for data recording and processing, while AMReader is an R package for visualization and statistical analysis.
AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms
AMRmap is a interactive web platform for the monitoring of antibiotic resistance in Russia, which contains a set of tools for the analysis and visualization of data on the susceptibility of microorganisms to antimicrobial agents.
AMRViz is a toolkit for analyzing, visualizing, and managing bacterial genomics samples, bundled with a best-practice analysis pipeline. It allows researchers to perform comprehensive analysis of raw sequencing data and provides a web-based visualization dashboard for interactive examination of results.
Predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences.
Animal movement tools (amt) for managing tracking data and conducting habitat selection analyses.
Asymmetric multi-task attention network for prostate bed segmentation in computed tomography images.
Automated multi-peak tracking kymography (AMTraK) is a software tool that uses peak information and distance minimization to track and automatically quantify kymographs.
AMULET: ATAC-seq MULtiplet Estimation Tool which is a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Running AMULET consists of two parts: 1) Identifying all loci with >2 uniquely aligning reads for each cell, and 2) detecting multiplets that have more loci with >2 reads than expected. The bash shell script combines both of these steps, but they can be run independently as well. The latter (multiplet detection) may be useful for running multiplet detection using q-values different from the default.
AMVOC (Analysis of Mouse VOcal Communication) A deep, unsupervised method for rapid detection, analysis, and classification of ultrasonic vocalizations.
AmyloGraph is a database of interactions between amyloid proteins and its functionalities are also accessible in an R package.
Consensus prediction method for identifying possible amyloidogenic regions in protein sequences.
A Consensus Method for Amyloid Propensity Prediction.
An online database dedicated to amyloid precursor families and to their amino acid sequence signatures.
AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning.
Software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others.
An automated pipeline for somatic copy number variation detection and annotation from tumor exome sequencing data.
analogy is a command-line tool and set of rules designed to automate incidence and prevalence analysis in open cohort datasets, improving transparency and reproducibility of analyses. It requires Python 3.9 or later and provides both code-free rules and a CLI implementation.
Analysis and Forecast COVID-19 Patients Worldwide using Regression.
Analysis and Forecast COVID-19 Patients Worldwide
Analysis of the trajectory of close contacts in the spread of new coronary pneumonia( COVID19)
Analysis of the trajectory of COVID19 close contacts
Modular system that enables sharing of customizable R analyses via the web.
This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.
A web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events.
Clustering marker gene data by time-series patterns.
ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to use these GRNs to identify the key transcription factors in cell fate determination.
The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.
Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.
ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository.
ANAT (Advanced Network Analysis Tool) is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart out the molecular pathways that underlie these systems. ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a plug-in for Cytoscape.
Matlab functions for flexible plotting of intracranial or fMRI data on 3D brain models
Anatomical data visualization toolfbox for fMRI ECoG
A medical image segmentation software supporting user interventions and user-defined funtion extention
A python package with modules to measure anharmonicity in the form of higher-order statistics and its variation as a function of time, output a storyboard representation of the simulations to identify key anharmonic conformational events, and identify putative anharmonic conformational substates and visualization of transitions between these substates.
A web server for amino acid networks construction and analysis.
AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.
Software which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known.
AncestralClust is a tool to cluster divergent sequences. A neighbor-joining phylogenetic tree is built from a random number of user-specified initial sequences, the tree is split into initial clusters based on the longest branch lengths, each initial cluster is aligned with a multiple sequence alignment and the ancestral sequence from each cluster is inferred by the root node after being midpoint rooted. The rest of the sequences are assigned to the clusters based on their closest genetic distance to the ancestral sequence (or saved for a future iteration if the distance is greater than the average distance between clusters). The process reiterates until all sequences are assigned to a cluster.
Algorithm that infers the clonal evolution and tumor composition, including mixing fractions of a tumor from multi-sample DNA sequence data.
Ancestry_HMM-S (AHMMS) is a program designed to infer adaptive introgression from population genomic data.
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer.
ANCESTRYMAP finds skews in ancestry that are potentially associated with disease genes in recently mixed populations. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations. It is most advantageous to apply this approach to populations that have descended from a recent mix of two ancestral groups that have been geographically isolated.
Algebraic graph-based method to identify the most significant sub-network underlying ethnic difference in complex diseases risk in a recently admixed population.
Post-processing tools for de novo assemblies.
A python package to find unimodal, bimodal, and multimodal features in any data that is normalized between 0 and 1, for example alternative splicing or other percent-based units.
Prediction of protein binding regions in disordered proteins
Anchored DIALIGN is a WWW server for multiple alignment of protein and nucleic acid sequences using DIALIGN with user-defined anchor points.Alignments can be created either fully automatically or by using a list of user-defined constraints. By specifying such anchor points, the user can force the program to align selected segments of the sequences to each other. The remaining parts of the sequences are then aligned automatically, respecting the constraints imposed by the selected anchor points.
AncientMetagenomeDir is a community curated resource of metadata of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples
ANCOM-BC2 is a Bioconductor package designed for performing multigroup differential abundance analyses of microbiome data, accounting for covariates and repeated measures. It offers a flexible framework to compare multiple groups and provides methods for bias correction.
Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.
Webserver/tool for evaluation coordinate and ordinal correlations between genomic tracks and/or expression or protein binding profiles.
A web-based module of ANDSystem for the search of knowledge in the scientific literature. The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
The fundamental data structure underlying, is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment. They include the root mean square deviation plot and the computation of base conversion frequencies, variation, inter-sample clustering and visualization, threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.
andi estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
Max Planck Institute for Evolutionary Biology
This tool performs k-mer genome-wide association studies (GWAS) to identify markers associated with anthracnose and bean common mosaic virus (BCMV) resistance in the Andean Diversity Panel of common beans. The analysis uses historical data and incorporates insights from genome sequencing and structural variation.
K-mer GWAS for Anthracnose and BCMV Resistance
Web tool that helps to assign structural domains to protein sequences and to classify them according to SCOP.
This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
Tool, developed for the reconstruction of molecular genetic networks. It is based on an automated text- and data- mining techniques.
Anduin is a freely available research tool to segment vertebrae in a CT scan, uploaded as NIFTI data. It allows to calculate trabecular vBMD, download the segmentation as NIFTI, and vertebral centroid coordinates as JSON files.
A Simple Web-Based Platform to Build Stakeholder Understanding of Groundwater Behavior. This package models simple aquifer and well configurations.
This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.
Detection of Cerebral Aneurysm using Modified Hough Circle Transform
anexVis is a transcriptome tool to visualize organ/tissue-specific glycosaminoglycan biosynthetic and catabolic pathways in human health and diseases. anexVis allows one to analyze a large number of genes that are related to biosynthetic and catabolic pathways of all glycosaminoglycans, such as heparan sulfate, chondroitin sulfate, keratan sulfate, and hyaluronic acid, in parallel across various human tissues organs. Such visual analyses have not been accessible to the broad research community despite the accumulation of a large amount of RNA-seq data.
This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.
An open-source computational platform for the analysis of sequencing data for rare genetic diseases. Anfisa is a Variant Analysis and Curation Tool. Its purpose is to bring together Genetic Research and Clinical settings and provide a medical geneticist with access to research Genome.
Database of Streptocarpus rexii transcriptome.
A fully automatic method to segment the vessels would eliminate potential subjectivity and provide a quantitative and systematic measurement of diameter reduction. Here, we have designed a convolutional neural network, AngioNet, for vessel segmentation in X-ray angiography images
Automated image analysis tool for quantification of angiogenesis. It is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. It provides quantitative and repeatable measurements of the lengths and sizes of tubule complexes as well as the numbers of junctions (branching points) in the tubule complexes.
Program for predicting coding sequences from low quality cDNA. To achieve error-tolerant prediction, it uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences.
Method of determining the orientation of an α-helix relative to a defined axis in a rotationally symmetric protein structure such as a membrane protein channel.
Software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
ANGSD-wrapper is a utility developed to aid in the analysis of next generation sequencing data.
Quantification of fibrous spatial point patterns from single-molecule localization microscopy data.
Artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom.
Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3' untranslated regions and thereby influencing a series of biological processes. Recent studies have highlighted the important roles of APA in human. However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human.
A comprehensive animal enhancer RNA database.
The Animal QTLdb and CorrDB are unique resources for livestock animal genetics and genomics research which have been used extensively by the international livestock genome research community.
Comprehensive TF database; identified and classified all the genome-wide TFs in 50 sequenced animal genomes. Also collects transcription co-factors and chromatin remodeling factors of those genomes, which are also essential in the gene transcription regulation.
The AnimalAssociatedMetagenomeDB (AAMDB) provides standardized and manually curated metadata for 10,885 non-human, animal-associated metagenomes collected from public repositories such as SRA and MG-RAST. It allows users to search, filter, visualize, and export metadata through an interactive web application featuring quick and advanced search options, geographic map-based selection, and support for raw data download. The tool facilitates the discovery and reuse of metagenomic data in biodiversity and microbiome studies.
animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework.
Multi-omics data resources for exploring animal microbial genomes and microbiomes.
Transforming and visualizing animal movement data from static stations.
AnimalTraits is a curated database containing body mass, metabolic rate and brain size measurements across a wide range of terrestrial animal taxa.
Anipose is an open-source toolkit for robust, markerless 3D tracking of animal behavior from multiple camera views. It leverages the machine learning toolbox DeepLabCut to track keypoints in 2D, then triangulates across camera views to estimate 3D pose.
The Animal Proteome Database (AniProtDB) is a comprehensive collection of proteomes from 100 species spanning 21 animal phyla. In addition to providing open access to this collection of high-quality metazoan proteomes, information on predicted proteins and protein domains for each taxonomic classification is provided, along with the ability to perform sequence similarity searches against all proteomes in the database.
ANISE (grAphical coNfigurator of TiFoSi In Silico Experiments) is an application that allows you to configure the input file of TiFoSi (Tissues: Forces & Signalling) which is a computational tool to simulate the cellular dynamics of planar epithelia.
Anisotropic diffusion with memory based on speckle statistics for ultrasound images.
Anisotropic Diffusion for Ultrasound Images
Simple NMA tool for analysis of vibrational motions in molecular systems. It uses Elastic Network (EN) methodology and represents the system in the residue level.
ANMDA is an anti-noise based computational model for predicting potential miRNA-disease associations.
A simple ImageJ macro for rapid analysis of neuromuscular junction morphology. Large-scale data analysis of synaptic morphology is becoming increasingly important to the field of neurobiological research (e.g. 'connectomics'). In particular, a detailed knowledge of neuromuscular junction (NMJ) morphology has proven to be important for understanding the form and function of synapses in both health and disease. The recent introduction of a standardized approach to the morphometric analysis of the NMJ-'NMJ-morph'-has provided the first common software platform with which to analyse and integrate NMJ data from different research laboratories. ImageJ macro language was used to encode the complete NMJ-morph workflow into seven navigation windows that generate robust data for 19 individual pre- post-synaptic variables
Functions for handling data from BioConductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.
AnnapuRNA is a knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method.
From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."
RPy2 converter from AnnData to SingleCellExperiment and back.
Anne O’Tate is a value-added PubMed search engine for analysis and text mining.
ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.
Provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.
an R Package to annotate and prioritize putative oncogenic RNA fusions. Filter and prioritize fusion calls. Using annoFuse, users can filter out fusions known to be artifactual and retained high-quality fusion calls using support of at least one junction read and remove false calls if there is disproportionate spanning fragment support of more than 10 reads compared to the junction read count. For prioritization, users can capture known as well as putative driver fusions reported in TCGA, or fusions containing gene partners that are known oncogenes, tumor suppressor genes, or COSMIC genes. Finally, users can also determine recurrent fusions across the cohort and recurrently-fused genes within each histology. By providing a standardized filtering and annotation method from multiple callers (STAR-Fusion and Arriba) users are able to merge, filter and prioritize putative oncogenic fusions across the PBTA
Pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission
AnnoGen is a toolkit for annotating three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy, and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases.
Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.
A web server for systematically annotating novel human lncRNAs.
AnnoLnc2 is a web server for integratively annotating novel human and mouse lncRNAs
AnnoMiner is a web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.
Automatic preparation of annotated DNA sequences for bulk submissions to ENA.
The Annotation Query (AnnoQ) is an integrated functional annotation platform for large-scale genetic variant annotation.
AnnoSINE is a SINE annotation tool for plant genomes. The program is designed to generate high-quality non-redundant SINE libraries for genome annotation. It uses the manually curated SINE library in the Oryza sativa genome to benchmark the annotation performance.
An integrated tool to annotate eukaryotic proteins using multi-omics data.
Annotatability is a framework for analyzing the dynamics of deep neural network training on single-cell and spatial omics data to identify annotation mismatches and characterize biological data structure. It develops a signal-aware graph embedding method for downstream analysis.
annotate_my_genomes is a pipeline that aims to annotate genome-guided transcriptome assemblies from StringTie, coming from long read RNA-Seq alignments in vertebrate genomes (i.e. PacBio technology)
This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution.
Web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations.
This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.
Provides user interface and database connection code for annotation data packages using SQLite data storage.
It provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.
Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.
Functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db).
This package provides a client for the BioConductor corresponding web resource, which provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard BioConductor data structures.
Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).
Annotator-RNAtor is a software pipeline and graphical user interface designed for interspecies transcriptomic analysis and the study of intragenus evolution, particularly in Leptospira species. It facilitates homologous gene inference and highlights differences in gene expression to identify adaptive changes.
An ImageJ plugin to ease hand-annotation of cellular compartments.
Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.
Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.
A tool for finding relevant genetic variants from high-throughput sequencing data based on functional annotation.
Annotate genetic variants detected from diverse genomes.
Annotate genetic variants detected from human genome.
AnnSQL is a Python package that enables SQL-based queries on AnnData objects, leveraging an in-process DuckDB engine for significant performance enhancements in large-scale single-cell genomics analysis.
A Non-Parametric Statistical Test to Compare Clustering Structures.
AnoExpress is a Python package and online interface for exploring insecticide resistance candidate expression in malaria vectors. It integrates RNA-Sequencing, whole-genome sequencing, and microarray data to identify drivers of insecticide resistance.
Server to assess the quality of a three dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.
Bringing anonymity to the Matchmaker Exchange platform for rare disease gene discovery. Advances in genome sequencing and genomics research are bringing us closer to a new era of personalized medicine, where healthcare can be tailored to the individual's genetic makeup and to more effective diagnosis and treatment of rare genetic diseases. Much of this progress depends on collaborations and access to data, thus, a number of initiatives have been introduced to support seamless data sharing.
AnoPrimer is a Python package designed to rapidly design primers and probes in *Anopheles* mosquitoes while accounting for genetic variation and allowing visualisation of primer binding sites. It's an open-access platform hosted on GitHub and designed to avoid amplification problems caused by SNPs.
This package allows for genome wide studies of translational control using partial variances and the random variance model, identifying differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels.
It provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA.
ANOX is an improved machine-learning based prediction tool for identifying the antioxidant proteins.
AnOxPePred predicts the antioxidative (free radical scavenging and ion chelating) properties of peptides using convolutional neural network.
Implementing Automated Nonparametric Statistical Analysis on Functional Analysis Data.
ANSWER can be used by clinical geneticists or pathologists to identify clinically actionable variants from next-generation sequencing data for the purposes of recommending personalized treatment options.
Predict miRNA targets for human and mouse using the two predictive models: a model trained from microarry studies following transfection, and a model trained from PAR-CLIP datasets.
Multi-objective sequence design by inverse folding.
A New Platform for Data-Dependent Acquisition Mode-Based Untargeted Metabolomic Profiling Analysis with Advantage of Recognizing Insource Fragment Ions to Improve Compound Identification.
ANTHEM is an integrated platform for HLA-peptide binding prediction and machine learning models construction.
Interactive program with a graphical user interface that allows handling of protein sequence and data in a very interactive and convenient manner. It provides many methods and tools, which are integrated into a graphical user interface.
Anthrax Knowledge Portal (AnthraxKP) is a multi-module database management system, which allows researchers to query, browse and download anthrax biomedical resources in multiple formats
an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins.
An initiative to predict Ebola virus inhibitors through machine learning.
Machine learning assisted prediction of IC50 activity of chemicals against biofilms of microbes causing antimicrobial resistance and implications in drug repurposing.
A database and server termed ANTIAGE-DB that allows the prediction of the anti-aging potential of target compounds.
User-friendly web server for the prediction of anti-angiogenic peptides.
The Antibody Registry is a public, open database that enables citation of antibodies by providing a persistent record for any antibody-based reagent used in a publication.
Antibp server predicts the antibacterial peptides in a protein sequence.Prediction can be done by using QM,ANN and SVM based methods using binary patterns of peptide sequences and overall accuracy of this server is ~92.11%.This server can help in finding and designing of peptides based antibiotics.
AntiBP2 server predicts the antibacterial peptides in a protein sequence
AntiBP3: A Method for Predicting Antibacterial Peptides against Gram-Positive/Negative/Variable Bacteria
Anticlustering partitions a pool of elements into subsets (i.e., anticlusters) in such a way that the subsets are as similar as possible. This is accomplished by maximizing instead of minimizing a clustering objective function, such as the intra-cluster variance (used in k-means clustering) or the sum of pairwise distances within clusters. Thus, anticlustering creates similar sets of elements by maximizing heterogeneity within anticlusters.
Web based prediction server for anticancer peptides. SVM models developed are based on amino acid composition and binary profile features. Positive dataset consists of 225 antimicrobial peptides with anticancer properties.
AntiCP 2.0 is an updated version of AntiCP, developed to predict and design anticancer peptides with high accuracy
DefenseFinder is a free, open-source tool and web service that detects anti-defense systems within genomic sequences. It facilitates the identification of these systems and contributes to understanding host-pathogen interactions.
The AntiDMPpred tool is a predictor that can be used to foretell if the query peptides might be anti-diabetic bioactive peptides.
Antifp is an in silico method, which is developed to predict and design antifungal peptides. The main dataset used in this method consists of 1459 antifungal peptides.
Contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In it, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. It also provides links to major internal and external databases.
AntiMPmod is an in silico method, which is developed to predict efficient modified antimicrobial peptides (ModAMP).
Implements gene expression anti-profiles.
Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
ANTISOMA is a pipeline for the reduction of the aggregation tendency of mAbs through the decrease in their intrinsic aggregation propensity, based on an automated amino acid substitution approach.
AntiTbPdb is a database of experimentally verified anti-tubercular or anti-mycobacterial peptides
This webserver is designed to predict peptides having effective bactreicidal activity against Mycobacteruium species.
It is a software for constructing genetic linkage maps using an ant colony optimization algorithm. It seeks the linear order of loci that minimizes the sum of adjacent recombination fractions or that maximizes the log likelihood of locus order. Analyses based on simulated data sets indicated that the algorithm displayed a high efficiency level. The high performance of the algorithm enabled to save time and labor, and also to validate an estimated order by bootstrap tests.
AntPack is a software resource developed by the Wang lab at UC San Diego for antibody sequence generative modeling. It includes tools for humanizing sequences, generating new sequences, and scoring sequences for humanness, all while being fast and interpretable.
anTraX is an algorithm and software package for high-throughput video tracking of color-tagged insects. anTraX combines neural network classification of animals with a novel approach for representing tracking data as a graph, enabling individual tracking even in cases where it is difficult to segment animals from one another, or where tags are obscured.
Animal Network Toolkit Software (ANTs) is a free open R package for analysing animal networks.
This tool is provided for marking ant motion trajectories dataset from video. We provide marking software, three data quality analysis scripts, and a tracking performance evaluation tool.
The Advanced Normalizations Tools ecosystem (ANTsX) consists of multiple open-source software libraries which house top-performing algorithms used worldwide by scientific and research communities for processing and analyzing biological and medical imaging data.
ANUBIS is a Python framework to analyze Tn-seq data.
Aggregation Nucleation Prediction in Peptides and Proteins (ANuPP) is a ensemble-classifier developed and trained to identify amyloid-fibril forming peptides and regions in protein sequences.
The NHGRI AnVIL (Genomic Data Science Analysis, Visualization, and Informatics Lab-space) is a project for biomedical researchers to access data, run analysis tools, and collaborate.
AnVILWorkflow is an R package that allows users to execute bioinformatics workflows hosted on the AnVIL cloud computing platform. It simplifies the process of utilizing AnVIL's resources, such as data and computing power, through R functions.
Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. It brings together many aspects of today’s cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
Convert various sequence formats to FASTA
AnyExpress is a software package that combines cross-platform gene expression data using a fast interval-matching algorithm.
Chemo-structural diversity of anti-obesity compound database. AOCD delivers a comprehensive resource on botanicals isolated from plant source(s) and its classification. It also includes compounds derived from Marine seaweeds; Microbial source that are found to have potent source of inhibition targeting obesity.
A comprehensive database for antioxidants including small molecules, peptides and proteins.
This tool was developed to identify antioxidant proteins based on the sequence information.
A web application for DNA/RNA tandem mass spectrometry data interpretation.
Genome mining for anti-CRISPR operons using machine learning.
Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application.
AOP-helpFinder is a web tool for identification and extraction of associations between stressors and biological events at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)). AOP-helpFinder is a hybrid tool, combining text mining and graph theory. Currently, AOP-helpFinder screens all the >30 millions of abstracts available from the PubMed database, to decipher co-mentioned terms (e.g. a stressor and a MIE).
The AOP4EUpest webserver is a resource for annotated pesticides-biological events involved in Adverse Outcome Pathways (AOPs).
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest.
PolyAMiner-Bulk is a deep learning algorithm that decodes alternative polyadenylation (APA) dynamics from bulk RNA-seq data. It resolves overlapping cleavage and polyadenylation sites and generates visualizations to illustrate APA dynamics.
APA-Scan detects the potential Alternative Polyadenylation (APA) events in the downstream 3'-UTR of a gene among two different biological conditions. APA-Scan is a python tool which can be downloaded directly from github. Python (version 3.0 or higher) is required to be installed on users machine to run APA-Scan. It can work on Windows, Linux and Mac platform.
Open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.
Trino is a distributed SQL query engine designed to query large data sets distributed over one or more heterogeneous data sources. Trino is a tool designed to efficiently query vast amounts of data using distributed queries. If you work with terabytes or petabytes of data, you are likely using tools that interact with Hadoop and HDFS. Trino was designed as an alternative to tools that query HDFS using pipelines of MapReduce jobs, such as Hive or Pig, but Trino is not limited to accessing HDFS. Trino can be and has been extended to operate over different kinds of data sources, including traditional relational databases and other data sources such as Cassandra. Trino was designed to handle data warehousing and analytics: data analysis, aggregating large amounts of data and producing reports. These workloads are often classified as Online Analytical Processing (OLAP).
Web-based notebook that enables data-driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more.
Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.
A R bioinformatics package for analysis of alternative polyadenylation isoforms. Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.
Open source software tool for fast and light-weight data analysis and data conversion from platereaders and images to formats of more powerful analysis software such as MATLAB, GraphPad Prism and SBToolbox2 (IQMTools).
A web-based platform for alternative polyadenylation analyses in hematological cancers.
Atom Pair-Based Scoring function (APBScore) is a physical-based scoring function, which includes pairwise van der Waals (VDW), electrostatic interaction, and hydrogen bond energies between the receptor and ligand.
A R package and Shiny app for covariate adjusted principal coordinates analysis.
Functions to estimate a bipartite graph of protein complex membership using AP-MS data.
APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints.
A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly.
Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.
It provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
Aperture is a new alignment-free SV caller designed for cfDNA dataset. Aperture applies a unique strategy of k-mer based searching, fast breakpoint detection using binary labels and candidates clustering to detect SVs and viral integrations in high sensitivity, especially when junctions span repetitive regions, followed by a barcode based filter to ensure specificity. Aperture takes paired-end reads in fastq format as inputs and reports all SVs and viral integrations in VCF 4.2 format.
Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool.
apex is an R package that can be used for phylogenetic studies. It implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data.
R package designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis.
Automated Pipeline for Infants Continuous EEG (APICE) is a fully automated, flexible, and modular. Artifacts are detected using multiple algorithms and adaptive thresholds, making it suitable to different age groups and testing procedures without redefining parameters
APICURON is an open resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data - mainly from literature - requires a huge effort which is difficult to quantify and acknowledge. APICURON collects biocuration events from third party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities.
APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. APID also includes a data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions reliability of the "edges") and a mapping of the functional environment of the proteins (functional annotations of the "nodes").
Antimicrobial peptide identification using multi-scale convolutional network. BACKGROUND:Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem. RESULTS:In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. To further improve the performance, we also incorporated additional information into the designed model and proposed a fusion model
A database of apoptosis-inducing anticancer peptides.
APIR: flexible and powerful FDR-control framework for aggregating peptides identified by multiple database search algorithms from mass spectrometry data.
Collection of wing images for conservation of honey bees (Apis mellifera) biodiversity in Europe. We provide 26,481 forewing images of honey bee workers. They represent 1,725 samples from 13 European countries. The shape of the wings was described using the coordinates for 19 landmarks at wing veins’ intersections. The whole dataset, including the wing images, landmark coordinates, geographic coordinates of sampling locations, and other data, is available on the Zenodo website under a Public Domain licence.
The Association in the Presence of Linkage tool provides a novel test for association in the presence of linkage using general pedigree data.
John P. Hussman Institute for Human Genomics
APL@VORO is a software designed to aid in analyzing membrane simulations made with GROMACS.
The R package apLCMS is designed for the processing of LC/MS based metabolomics data. It starts with a group of LC/MS files in the same folder, and generates a table with features in the rows and intensities in the columns. There are two major routes of data analysis. The first, which we call unsupervised analysis, doesn't use existing knowledge. It detects peaks de novo from the data based on the data itself. The second, which we call hybrid analysis, combines de novo peak detection with existing knowledge. The existing knowledge can come from two sources - known metabolites and historically detected features from the same machinery.
Converts MaxQuant APL (Andromeda peak lists) to MGF.
ApoCanD: Database of Human Apoptotic Proteins in the context of cancer
APOD (Accurate Predictor Of Disordered flexible linkers) is an accurate sequence-based predictor of disordered flexible linkers. It utilizes both local- and protein-level inputs that quantify propensity for disorder, sequence composition, sequence conservation and selected putative structural properties.
Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) is a platform where users can upload and map multiple types of 'omics' data such as genomics, transcriptomics, proteomics, metabolomics, etc. in human cellular interaction networks. User can filter the interactions (protein-protein, gene regulatory, etc.) based on the status of the omics data. This filtered network of interaction can be used to identify topologically important nodes (TINs), namely hubs, central nodes and bottleneck nodes.
Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.
Apollo Genome Annotation and Curation Tool
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size.
Predicting allosteric pockets in protein biological assemblages.
ApoPred is a tool for odentification of apolipoproteins and their subfamilies with multifarious features.
Tool to automate the process of creating standalone, model-exploration apps for SimBiology model
R package for accurate SNP-based parentage analysis in the absence of guiding information.
APPECO (Applying Evidence with Confidence) is a tool that aims to help you find and use the best evidence for the rehabilitation of patients with Multiple Sclerosis.
Web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. It provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients.
Web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences.
An R package for building and computational analysis of protein-protein interaction networks.
Set of tools to analyse promoter sequences on a genome-wide scale.
Scalable Distance-based Phylogenetic Placement with or without Alignments | distance based phylogenetic placement | APPLES stands for Accurate Phylogenetic Placement with LEast Squares and addresses the problem of phylogenetic placement of DNA and protein sequences into an already existing reference tree. APPLES is a command-line tool and it can run on Linux, Mac OSX, and Windows
The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED).
Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.
Computational tool that predicts the interaction of a PPR (pentatricopeptide repeat) with its RNA binding site.
ApproximantCoefficientsSIR is a MATLAB tool that computes the the coefficients of an approximate analytic solution to the SIR epidemic model.
APPTEST is an innovative new method for the automatic prediction of peptide tertiary structures.
Appyters are standalone applications for generating jupyter notebooks, the appyter catalog features many bioinformatics related appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications. Appyters present to users an entry form enabling them to upload their data and set various parameters for a multitude of data analysis workflows.
aPRBind is a convolutional neural network (CNN)-based ab-initio method for RNA-binding residue prediction. aPRBind is trained with sequence features and structural ones (particularly including residue dynamics information and residue-nucleotide propensity developed by us) that are extracted from the predicted structures by I-TASSER
ApreciseKUre is a digital platform designed to facilitate data collection, integration, and analysis for patients affected by Alkaptonuria (AKU). It incorporates genetic, biochemical, histopathological, clinical, and therapeutic resources to support precision medicine approaches.
Integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.
APRICOT (Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools) is an open-source extension to support customised virtual infrastructure deployment and usage from Jupyter notebooks. Scientific publications are meant to exchange knowledge among researchers but the inability to properly reproduce computational experiments limits the quality of scientific research. Furthermore, bibliography shows that irreproducible preclinical research exceeds 50%, which produces a huge waste of resources on nonprofitable research at Life Sciences field. As a consequence, scientific reproducibility is being fostered to promote Open Science through open databases and software tools that are typically deployed on existing computational resources. However, some computational experiments require complex virtual infrastructures, such as elastic clusters of PCs, that can be dynamically provided from multiple clouds
Apscale is a metabarcoding pipeline that handles the most common tasks in metabarcoding pipelines like paired-end merging, primer trimming, quality filtering, otu clustering and denoising as well as an otu filtering step.
This search engine recommends PubMed articles relevant to a given article. It automatically extracts keywords from the title and abstract indexed in PubMed to generate recommendations. The database contains all PubMed records, providing up to 60 recommendations per searched article. Researchers were invited to annotate degrees of relevance for provided recommendations. All evaluations received will be curated into a benchmark dataset to be made available for free download and redistribution.
Article-based PubMed Search Engine (APSE)
This server allow to predict the secondary structure of protein's from their amino acid sequence
APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence.
A tool for designing primers and identifying accurate normalization controls for ATAC-qPCR.
Design RNA complexes that hybridize via sticky bridges.
Allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets.
AptaDB is an online database that integrated comprehensive information on aptamers. It collects thousands of aptamers obtained from SELEX-based screening in the literature and and other databases, which may facilitate biologists to develop novel aptamers and accelerate aptamer-related researches.
AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the comparison of the matrices representing the two secondary structures to analyze, assimilable to dotplots.
Computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information.
Aptardi (Alternative Polyadenylation Trascriptome Analysis from RNA sequencing and DNA sequencing Information) predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.
A method for optimized de novo motif discovery of RNA aptamers via HTS-SELEX.
The Automated Phonetic Transcription (APT) Comparison Tool (APTct) is an online tool that facilitates the comparison of phonetic transcriptions for a variety of clinical and research purposes.
A web server that identifies weak molecular interactions in protein structures.
The AQMM was developed to perform absolute quantification of multiple metagenomes and it's parallel metatranscriptome. In order to use this algorithm, the experiment should be designed with both metagenome and metatranscriptome data. From the initial stage, the molecular experimental data should be recorded to help on estimating the overall DNA or RNA of a unit (ml/gram) of the sample. The AQMM was demonstrated to obtain better results of differential expression genes identification in comparative metatranscriptomic studies.
Suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy.
Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP). Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data. Induced chromatin interactions anchored with protein contacts will be readily differentiated using AQuA-HiChIP, but with normalizing by total interactive paired-end tags (PETs), differential interaction frequencies may produce false positives or false negatives.
AQUA (Advanced QUery Architecture for the SPARC Portal) is an application that aims at improving the search capabilities of the SPARC Portal.
A tool to assist aquaculture production design based on abiotic requirements of animal species.
CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform
Simplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...).
Department for Bioinformatics and Computational Biology, Technische Universität München
Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney
Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney
School of Molecular Bioscience, The University of Sydney
Open-source laboratory software for design, execution and data management. Build reproducible experimental workflows, manage samples, store data, and share know-how.
Expanding our understanding of the trade in aquatic marine wildlife. Marine Aquarium Biodiversity and Trade Flow. Aquariumtradedata.org is a commitment to understanding the diversity and magnitude of the marine aquarium trade by illuminating and evaluating the global shipping pathways of the trade. You will be logged off in seconds due to inactivity. Click here to continue using this web page. Clownfish, or anemonefish (family Pomacentridae), are some of the most iconic fish species on tropical coral reefs, where they live symbiotically with giant sea anemones. Read more about the global trade of clownfish by RET TALBOT
AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.
A spatial omics database and analysis platform.
Novel automatic muscle artifact reduction method for ictal EEG interpretation.
Predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups.
An automatic pipeline for exploration of SRA datasets with sequences as a query
An ""Electronic Fluorescent Pictograph"" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets.
Integrated network of Arabidopsis growth regulators.
Program for assembling data from whole genome shotgun sequencing experiments.
A simulation environment with simple user interface for analyzing neural and neuroglial networks organisation, optimisation and execution.
ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.
ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.
ARADEEPOPSIS is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner.
AraDQ is an automated digital phenotyping software for quantifying disease symptoms in flood-inoculated Arabidopsis seedlings. It utilizes deep neural networks for object detection and segmentation and requires a fixed-size color balance card for accurate and reproducible results.
ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes
arakno is an R package for effective spider nomenclature, distribution and trait data retrieval from online resources. Online open databases are increasing in number, usefulness, and ease of use. There are currently two main global databases exclusive for spiders, the World Spider Catalogue (WSC) and the World Spider Trait (WST) database. Both are regularly used by thousands of researchers. Computational tools that allow effective processing of large data are now part of the workflow of any researcher and R is becoming a de facto standard for data manipulation, analysis, and presentation. Here we present an R package, arakno , that allows interface with the two databases. Implemented tools include checking species names against nomenclature of the WSC, obtaining and mapping data on distribution of species from both WST and the Global Biodiversity Information Facility (GBIF), and downloading trait data from the WST.
ARAMEMNON database of plant membrane proteins
Botanical Institute University of Cologne
Accurate long-Reads Assembly correction Method for Indel errorS (ARAMIS) is a NGS long-reads indels correction pipeline that combines several correction software in just one step using accurate short reads. As a proof OF concept, six organisms were selected based on their different GC content, size and genome complexity, and their PacBio-assembled genomes were corrected thoroughly by this pipeline.
A major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. AraPheno is a public database collection of Arabidopsis thaliana phenotypes.
Resource for Arabidopsis thaliana genomics. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services
AraQTL is the A.thaliana workbench and database for eQTL analysis. It allows easy access to the data of all published Arabidopsis thaliana genetical genomics experiments.
A graph-based modular reasoning tool for translational biomedicine.
The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria
ARBic is an All-Round Biclustering Algorithm for Analyzing Gene Expression Data. Identifying significant biclusters of genes with specific expression patterns is an effective approach to reveal functionally correlated genes in gene expression data. However, existing algorithms are limited to finding either broad or narrow biclusters but both due to failure of balancing between effectiveness and efficiency. ARBic can accurately identify any meaningful biclusters of shape no matter broad or narrow in a large scale gene expression data matrix, even when the values in the biclusters to be identified have the same distribution as that the background data has. ARBic is developed by integrating column-based and row-based strategies into biclustering procedure. The column-based strategy borrowed from ReBic, a recently published biclustering tool, prefers to narrow bicluters.
ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads. It is used for merging and scaffolding an existing genome assembly. It takes a position sorted read alignment file in the bam/sam format with 10X Chromium barcodes in the BX tag, and if additionally provided with the genome fasta file used for mapping, it will sort and merge the provided contigs into scaffolds. A key functionality is the possibility to resolve links between contigs by overlap-layout-consensus (OLC) instead of indiscriminately inserting a gap between them.
Pipeline for automated retrieval of all sequences for a specified gene from GenBank.
efficient and scalable inference of gene regulatory networks. Usage Example — arboreto 0.1.5 documentation. Free document hosting provided by Read the Docs.
Scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories.
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies.
Academic Resources Platform for COVID-19 The Academic Resources for COVID-19 (ARC) is an online platform to match equipment, consumables, reagents and other critical resources needed by Swiss diagnostic laboratories involved in combating the Sars-CoV-2 virus with Swiss academic groups who are able and willing to provide them.
Light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.It is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation. It translates text-based descriptions of biological networks into standardized diagrams. Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations.
Improving the performance of clonal hematopoiesis variant calling and interpretation.
Ab initio predictions of enzyme class (if any) from sequence.
Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.
Tool able to decode protein sequence motifs that have a potential to form amyloids.
Structural classification of loops extracted from known protein structures.
Plant Root System Architecture Analysis Using DART and RSML Files.
This tool detects architectures of all-β and α/β-classes
Architect is a tool for producing high-quality metabolic models through improved enzyme annotation. Architect is a pipeline for automatic metabolic model reconstruction. Given the protein sequences of an organism, enzyme annotation is first performed through ensemble approaches (that is, combining predictions from individual enzyme annotation tools), followed by gap-filling.
This tool performs a structural classification of kinase loops with information of functional residues to find relationships between structure and function of classified kinase-loops.
ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.
ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available. Maybe licensed under GPL>=2.
ArchSchema is a java program that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB.
Scaffolding genome assemblies using 10X Genomics Chromium data or stLFR linked reads
Toolkit of Perl modules aimed at bioinformatics, genomics, and gerontology, partly based on the BioPerl package, which aim is to allow the comparative genomics of aging. It is a collection of data-mining tools, algorithms, parsers, wrappers, spiders and web applications, etc.
ARCTIC-3D is a software for data-mining and clustering of protein interface information. It retrieves existing interface data from the PDBE graph database and groups similar interfaces based on 3D structural information.
Arctos is both a community and an online museum collection management information system; as such Arctos is also a provider of research-grade data. It provides fundamental research infrastructure and is intended for curators, collection managers, investigators, educators, and anyone interested in natural and cultural history.
ARD2 (Alpha-rod Repeat Detector) is an application for the identification of alpha-rod repeats, also defined as alpha-solenoids (HEAT, Armadillo among others) in protein sequences using a neural network.
Analysis of surfaces of protein structures.
AREAdata is a worldwide climate dataset averaged across spatial units at different scales through time. It is a PearseLab data resource where you can download daily estimates of climate/environmental data which have been averaged across different levels of spatial units. Additionally, we include data on population density and estimates from future climate forecasting models at the same spatial levels.
AREM: Aligning Short Reads from ChIP-sequencing by Expectation Maximisation
Arena is a stand-alone program used for the full-atomic reconstruction of RNA structures from coarse-grained models.
visualization of multi-layered networks in 3D
Arena3Dweb is the first, fully interactive and dependency-free, web application which allows the visualization of multi-layered graphs in 3D space. With Arena3Dweb, users can integrate multiple networks in a single view along with their intra- and inter-layer connections. For clearer and more informative views, users can choose between a plethora of layout algorithms and apply them on a set of selected layers either individually or in combination. Users can align networks and highlight node topological features, whereas each layer as well as the whole scene can be translated, rotated and scaled in 3D space. User-selected edge colors can be used to highlight important paths, while node positioning, coloring and resizing can be adjusted on-the-fly. In its current version, Arena3Dweb supports weighted and unweighted undirected graphs, is written in R, Shiny and Javascript.
ARES-GT is a python script that identify CRISPR targets in query sequences (in FASTA format) and can also identify CRISPR targets matching multiple genes. Several online CRISPR tools exists with very good performance, however only a set of availables genomes can be selected (in some cases only a few, though in some tools more than 1500 can be selected) but none of them can identify sequences to be able to target multiple genes. This work usually needs manual (an slow) evaluation of alignments and offtargets.
Online resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3' UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs as well as related publications.
ARETT (Augmented Reality Eye Tracking Toolkit for Head Mounted Displays) is a toolkit for Unity 3D which contains scripts for acquiring eye tracking data on the Microsoft HoloLens 2. An R package also contains analysis scripts for eye tracking data acquired using ARETT and the Microsoft HoloLens 2.
arf is a genetic analysis program for sequencing data.
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functIonal information, and deep convolutional neural network.
Metagenomics pipeline for antibiotic resistance genes.
ARGEOS is a bioinformatic tool for detailed systematics search in GEO and ArrayExpress. ARGEOS will allow you to carry out a systematic search for transcriptomes, collecting all the unique datasets from the most popular databases. With the web tool, you can conveniently select publicly available datasets for data reanalysis! All you need is to compose a query that will be searched. ARGEOS will let you carry out a systematic search for transcriptomes, methylation data, CHIP-seq experiments, and many others. Handy output format minimizes the need for additional information.
ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.
argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database. argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.
Tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.
Argonaut is a web-based utility which facilitates collaborative exploration of Condition/Control-type mass spectrometry experiments. Spreadsheets of quantitative values can be uploaded and organized in a way that best describes your specific experimental setup. Brief statistical analysis is conducted on uploaded data to calculate the significance of molecular perturbations for each condition. These data can then be queried on-the-fly to conduct commonly conducted analyses inside the data portal, including volcano plots, GO enrichment, linear correlations, and others.
Several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.
Annotation Retrieval of Gene Ontology Terms
Pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.
Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats. Antibiotic-resistant genes (ARGs) have emerged as one of the top global concerns in both medical and environmental fields.
Tool for analyzing experimental or simulated particle networks.
Multilevel visualization of non-synonymous single nucleotide variants & advanced pathogenicity score modeling for genetic vulnerability assessment.
It is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in it, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created.
An R Package for Analysis of Illumina Genotyping Arrays.
A software for automated NOE assignment and NMR structure calculation.
Cloud Access management software for projects and facilities, providing access, facility and data management tools.
Ariadne software for absolute and relative quantification of SRM mass spectrometry data
Ariadne is a novel assembly graph-based algorithm, that can be used to deconvolve a large metagenomic linked-read dataset.
ARIAweb is a a server for that implements the ARIA software (Ambiguous Restraints for Iterative Assignment) for automated NMR structure calculation with enhanced analysis and visualization.
Advanced Research Infrastructure for Experimentation in genomicS (ARIES). ARIES is a public Galaxy server. More information can be found in the following links.
Using the Autoregressive Integrated Moving Average (ARIMA) and Generalized Regression Neural Network (GRNN) hybrid model to predict the incidence of infectious diseases.
Set of computer programs that carry out the alignment of short DNA sequences to a comparatively large reference sequence or genome.
High performance, ‘end-to-end’ analysis pipeline for the classification of omics profiles. Incorporating highly parallel architecture and sophisticated database technologies to overcome inherent technology based bottlenecks, currently faced in the Life Science research path. Arion is a scalable platform providing rapid exploratory analysis via machine learning, visualization and statistical modules with topology planned for a future release.
Web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.
Aristotle addresses the two challenges intrinsic to omics data: high dimensionality and hidden stratification. It employs existing biological knowledge and a state-of-the-art patient stratification method to tackle the above challenges and applies a quasi-experimental design method to each stratum to find stratum-specific potential causes.
Desktop application that allows users to draw and align genetic maps.
Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. This project is a new kmer-based (alignment free) implementation of ARCS. It provides improved runtime performance over the original ARCS implementation by removing the requirement to perform alignments with bwa mem.
Large set of basic methods and statistical tests, to extract information on genetic and demographic features of a collection of population samples. The analyses can perform on the data fall into two main categories: intra-population and inter-population methods.
Web server for analyzing antibody mutation probabilities.
Armitage's trend test on genotype distribution of marker(s).
An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research.
An evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.
Computational method for aromatase-related proteins using machine learning approach.
Predicting aromatic stacking energy using an atomic neural network model.
An R package for geometric morphometric methods and virtual anthropology applications.
A program for building macromolecular models from crystallograpgic data. It builds proteins, RNA/DNA, seqondary structure, side chains, loops, solvent and ligands
A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
ARPEGGIO is a snakemake workflow that analyzes whole genome bisulfite sequencing (WGBS) data coming from (allo)polyploid species. The workflow includes all basic steps in WGBS data analysis (trimming, quality check and alignment), a read sorting tool specific for allopolyploids, the most comprehensive statistical tool for Differential Methylation (DM) analysis and a set of downstream analyses to obtain a list of genes showing differential methylation. This folder provides the ARPEGGIO config file and the metadata file used to run the analyses of the Mimulus dataset. In the folder you will find additional information about the datasets used together with the output from the downstream analyses.
ARPEGGIO (Automated Reproducible Polyploid EpiGenetic GuIdance workflOw) is a snakemake workflow that analyzes whole genome bisulfite sequencing (WGBS) data coming from (allo)polyploid species. The workflow includes all basic steps in WGBS data analysis (trimming, quality check and alignment), a read sorting tool specific for allopolyploids, the most comprehensive statistical tool for Differential Methylation (DM) analysis and a set of downstream analyses to obtain a list of genes showing differential methylation.
ARPIR (Automatic RNA-Seq Pipelines with Interactive Report) performs RNA-Seq analysis: quality control, pre-processing, alignment (primary-analysis), transcript quantification and differential expression analysis on BAM files (secondaty-analysis).
Efficacy of the KLab interspecies tiling program which was demonstrated by interrogating the endogenous and human protamine loci in a transgenic mouse line. Species specific probe sets were designed by adapting a previously reported maskless array synthesis strategy.
Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. Array Server is a backend enterprise server for storage and analysis of -OMIC and NextGen sequencing data.
It is one of the significant challenges to find unknown subtypes of several diseases at the molecular levels. This task can be addressed by grouping gene expression patterns of the collected samples on the basis of a large number of genes. Application of commonly used clustering methods to such a dataset however are likely to fail, because the number of samples to be grouped is much smaller than the data dimension. To overcome such difficulty, a novel model-based clustering method is developed.
Public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies.
RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets.
This tool implements a set of five open-source R functions that allow the user to acquire data from public sources such as GEO, train a set of Lasso models on that data, and directly map one microarray platform to another. It significantly predicts expression levels with higher fidelity than technical replicates of the same RNA pool, demonstrating its utility in the integration of data sets from different platforms.
Tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms.
A curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. The arrayMap resource represents the part of the Progenetix project for which direct access to source data (i.e. probe-specific genomic array read-outs) has been available during data curation.
ArrayMiner® is a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. Its unique graphical interface gives you an intimate understanding of the analysis and an easy publishing of its results.
This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.
ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.
Set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.
Functions for performing print-run and array level quality assessment.
This package generates microarray quality metrics reports for data in BioConductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.
An application for gene expression and variant analysis. It enables analyzing a variety of experimental data.
This package is designed to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. It generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.
This tool provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, it is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study.
Wave correction for genotyping and copy number arrays.
Web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.
This tool is designed to enable a deep understanding of antigen receptor sequences with a cascade of algorithms and databases.
ArrestinDb is dedicated to arrestin proteins, which like G proteins, are major GPCR transducers but also have their own highly active research community.
Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.
This software calculates asymptotic and robust regressions corresponding to the constant and linear asymptotic regression models.
Method of calculating side-chain aromatic chemical shifts from protein structures.
ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD
ART-Net (Augmented Reality Tool Network) is a integrated lightweight framework for tool detection, segmentation, and 3D pose estimation from a laparoscopic image.
ARTDeco is a pipeline for analyzing and characterizing transcriptional readthrough. ARTDeco functions to process a set of BAM files such that transcriptional readthrough can be quantified via a variety of measures including read-in levels, readthrough levels, downstream of gene (DoG) transcript detection, and inference of read-in genes. ARTDeco can also correct gene expression values by using read-in levels to deconvolute native gene expression and contribution from upstream readthrough transcription. ARTDeco works on both single-end and paired-end data, stranded and unstranded data, and forward and reverse strand oriented data.
ARTEM is a tool for the superposition of two arbitrary RNA 3D structure fragments. ARTEM doesn’t rely on sequence similarity, annotated interactions, or backbone topology. Instead, ARTEM assumes at least one residue-residue match has a close-to-zero RMSD in the ideal superposition. Then, ARTEM tries all N*M single-residue matches and derives a subset of mutually closest residues as the matches for each of the single-residue-based superpositions. Finally, ARTEM returns the superpositions ordered by their size, letting the user choose the best one based on any specific requirements. ARTEM can read/write both PDB and mmCIF format.
Free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment
The Arthropoda Assembly Assessment Catalogue is a database of metadata and assembly quality metrics for all Arthropod assemblies on the NCBI
Arthropoda Assembly Assessment Catalogue
An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX.
A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
Artifact3-D offers a suite of functions for analysing 3D scans of archaeological artifacts. These functions are repeatable, objective, precise, and customizable.
New Artificial Landscape for Single-Objective Problems
Artistoo (Artificial Tissue Toolbox, formerly called CPMjs) is a framework that lets you build interactive, explorable simulation models of cells and tissues in the web browser.
The Analysis of Replication Timing and Organization tool uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. It takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region).
Adaptive Rank Truncated Product is an R package for analyzing pre-defined genetic pathway based on a genetic association study.
Division of Cancer Epidemiology and Genetics (DCEG), NCI
ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.
ARTS-DB is an online repository of precomputed results of Antibiotic Resistant Target Seeker (ARTS), a rapid genome mining tool for the exploration of antibiotics with interesting and novel targets. ARTS-DB supports two main searching functionalities.
Antibiotic Resistant Target Seeker. Specific and efficient genome mining for antibiotics with interesting and novel targets. Automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. It integrates target directed genome mining methods, antibiotic gene cluster predictions and ‘essential gene screening’ to provide an interactive page for rapid identification of known and putative targets in BGCs.
ARTS is a fully automated biomarker that outputs a score linked to the likelihood a person suffers from arteriolosclerosis based on brain MRI data (3D T1w, T2w FLAIR, DTI data) and basic demographic information (age at MRI, sex). The higher the ARTS score, the higher the likelihood of arteriolosclerosis.
ArVirInd is a knowledge-base of Arbo-Viral proteins from India and its neighbourhood. his is a annotated database, which acts as a repository of Protein sequences for arbo-viruses along with antigenic information. Users can search for protein sequences by virus / protein name or by country of origin (India and countries of the Indian subcontinent: Nepal, Bhutan, Bangladesh, SriLanka, Pakistan) and year of collection (that is, the year of outbreak which defines the origin of the strain).
ARX is a comprehensive open source software for anonymizing sensitive personal data. It supports a wide variety of (1) privacy and risk models, (2) methods for transforming data and (3) methods for analyzing the usefulness of output data. The software has been used in a variety of contexts, including commercial big data analytics platforms, research projects, clinical trial data sharing and for training purposes. ARX is able to handle large datasets on commodity hardware and it features an intuitive cross-platform graphical user interface.
A pan-cancer database of alternative splicing for molecular classification of cancer.
AS-Quant generates the expression level of alternative splicing among two different biological conditions.
This system consists of servers for protein structure analysis and modelling.
Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.
ASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin. These plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.
Galaxy-based framework to analyze microbiota data.
A framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.
ASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments. ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.
Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning (ASAP-SML) is a pipeline to identify distinguishing features in targeting antibody set when compared to a reference non-targeting set. The pipeline first extracts germline, CDR canonical structure, isoelectric point and frequent positional motifs features from sequences and creates an antibody feature fingerprint. Machine-learning and statistical significance testing are applied to antibody sequences and feature fingerprints to identify distinguishing feature values and combinations thereof. When applied to an MMP-targeting set, ASAP identifies salient features and recommends features to use when designing novel MPP-targeting antibody sequences.
Automated Single-cell Analysis Pipeline.
Statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments.
AsaruSim is a workflow for simulating synthetic single-cell long-read Nanopore datasets, designed to mimic real experimental data and facilitate the evaluation of isoform detection methods. The workflow incorporates multiple steps, including count matrix creation, read generation, optional PCR amplification, error introduction, and quality control reporting.
ASAS (Analysis and Simulation of Atomic Spectra) software is a tool to be used in studies involving atomic spectroscopy.
Discriminates aa substitutions with high and low probabilities of occurrence.
Empirical Bayes method to detect differential expression based on sequencing technology.
Asc-Seurat is an Analytical single-cell Seurat-based web application.
A website to calculate advanced structural characteristics of G-quadruplexes.ssr (X3DNA.ORG)
AScall is a web tool providing automatic processing of allele specific real-time PCR experiments: variation conducted real-time whereis each allele is detected by independent reaction separated into individual wells. The positive outcome of the reaction for a particular allele is judged by the increase in the fluorescent signal.
aScan is a software tool for the determination of allele-specific-expression at the single individual level from matched RNA-Seq and genomic data.
A comprehensive knowledgebase of alternative splicing in human cancers.
Positional feature annotation and protein structure-based representation of single amino acid variations.
Tool for accurate dissection of genome-wide allele-specific copy number in tumors. It accounts for normal cell admixture and tumor aneuploidy in the analysis of SNP array data from cancer samples. It allows analysis of Illumina and Affymetrix SNP array data of tumor samples (with or without matching germline samples).
scRNA-seq analysis toolkit (R package) for quality control, normalization, dimensionality reduction, clustering and differential expression.
ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds). A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves.
Automated Selection of Changepoints using Empirical P-values and Trimming (ASCEPT), to select an optimal set of changepoints in mobile health data
ASCoVPred is a machine learning-based platform for quantitative prediction of anti-SARS-CoV-2 activity and human cell toxicity of molecules. ASCoVPred is a collection of compounds descriptors / fingerprints (FPs) calculator tool (PaDEL v2.21) and different machine learning (ML) algorithms (implemented in Weka v3.8.2) that are used to build the ML-based quantitative structure-activity relationship (QSAR) prediction models. These QSAR models can be used for ML-assisted prediction of anti-SARS-CoV-2 activity and human cell toxicity of compounds.
ASCS is a statistical toolbox that analyzes synonymous codon signatures to define codon bias in genomes. Application to *Saccharomyces cerevisiae* revealed relationships between codon usage and gene function, identifying functional gene families.
AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.
Genome-wide scans for selective sweeps using convolutional neural networks.
ASDmiR is a step-wise method to uncover miRNA regulation related to autism spectrum disorder. MiRNAs (miRNAs) are involved in nervous system developmental, and have potential to cause ASD. However, the miRNA regulation mechanism in ASD is largely unclear. In this work, we present a novel framework, ASDmiR, to identify miRNA-target networks and modules, miRNA sponge networks and modules for uncovering the pathogenesis of ASD, as well as conduct enrichment analysis.
Semi-supervised medical image segmentation using adversarial consistency learning and dynamic convolution network.
R package to predict lysine sites that can be acetylated by a specific KAT-family.
Tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.
Rapid Sequence-Based Characterization of African Swine Fever Virus by Use of the Oxford Nanopore MinION Sequence Sensing Device and a Companion Analysis Software Tool. https://www.ncbi.nlm.nih.gov/pubmed/?term=31694969. O'Donnell VK, Grau FR, Mayr GA, Sturgill Samayoa, Dodd KA, Barrette RW., RAPID SEQUENCE-BASED CHARACTERIZATION OF AFRICAN SWINE FEVER VIRUS USING THE OXFORD NANOPORE MINION SEQUENCE SENSING DEVICE AND A COMPANION ANALYSIS SOFTWARE TOOL. J Clin Microbiol. 2019 Nov 6. pii: JCM.01104-19. doi: 10.1128/JCM.01104-19. Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Plum Island Animal Disease Center, New York.
Protein Fold Recognition based on Evolutionary Features with Variable Parameters using Full Connected Neural Network.
A web server for the development of customized scoring functions in the field of protein docking.
The African Swine Fever Virus Database (ASFVdb) is an integrative resource for genomic and proteomic analyses of African swine fever virus.
Using scRNA-seq data, Asgard repurposes drugs and predicts personalized drug combinations to address the cellular heterogeneity of patients.
The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).
A method for allele-specific modeling of diploid Hi-C data (chromatin contacts and structures) using hierarchical Bayesian modeling.
Automated Selection of High quality Libraries for the Extensive analYsis of Strandseq data (ASHLEYS) is an automated quality control for single-cell Strand-seq data.
Server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.
Automatic Statistical Identification in Complex Spectra quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.
Design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.
ASimulatoR is a tool for splice-aware RNA-Seq data simulation.
AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL
A database for alternative splicing atlas in livestock animals. The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa), chickens (Gallus gallus) and horses (Equus Caballus).
Novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants.
ASLPrep is a robust preprocessing pipeline for Arterial Spin Labeling data. ASLPrep is a Arterial Spin Labeling (ASL) data preprocessing and Cerebral Blood FLow (CBF) computation pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
Imaging Clinically Relevant Pain States Using Arterial Spin Labeling | The Center for Functional Neuroimaging at the University of Pennsylvania provides unification for currently distributed medical center efforts in physiological and clinical brain imaging and advance the general interests of the brain imaging community through targeted methods development, symposia and colloquia, handling of regulatory issues, and fund-raising efforts | Updated manual, ASL MoCo code, and asl_perf_subtract.m. Major new features include: | asl_perf_subtract.m has been updated with new parameters (T1b, T2wm, Rwm-blood) from the latest literature. CBF quantification for PASL using voxelwise M0 value has been updated. Please see the document therein for the details | Made a new version for SPM12. Major new features include: | 1) wraper functors for most of the processing steps,
Cconverts the Celera ASM assembly format to the Consed ACE or the CAF file format.
Integrative method for identifying key biomarkers from multi-omics data.
Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and differential DNA methylation in diverse organisms.
Machine learning framework for prediction of abiotic stress-specific miRNAs in plants.
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.
Software for discovery, genotyping and characterization of structural variants.
An ASP-based method for finding attractors in genetic regulatory networks.
Asparaginases are one of the most successful biopharmaceuticals that play a pivotal role in the treatment of acute lymphoblastic leukemia. In order to find new asparaginases with improved properties (stability, substrate affinity, immunogenicity) or to achieve these goals by enzyme engineering, it is essential to collect and accurately classify asparaginases from various sources. The database covers 101 experimentally studied proteins from the literature, a manually curated set of 127 sequences from SwissProt, and more than 100,000 automatically curated enzymes.
A toolkit for constructing statistical models for biological processes. It has been created to make it easy to automate parameter alteration of SBML models.
This package provides functionalities for a systematic and integrative analysis of alternative splicing events and their functional interactions.
ASPEX is a set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits.There are five main analysis programs: sib_ibd, sib_phase, sib_map, sib_tdt, and sib_kin.
The Aspergillus Genome Database is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.
Predicts the gene structure by aligning ESTs against a genomic region.
A lightweight pipeline for gene prediction and alternative isoforms detection.
Database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm and Pintron algorithm, and to the functional annotation of predicted isoforms.
Alternative splicing prediction database (ASPICdb)
An automated pipeline for identification of SARS-Cov2 nucleotidic variants.
Integrative pipeline for the analyisis of alternative splicing using RNAseq.
ASpli2 is a computational suite implemented in R, that allows the identification of changes in both, annotated and novel alternative splicing events, and can deal with complex experimental designs.
ASPRAling builds Algebraic RNA Trees and Structural RNA Trees or calculate ASPRA Distance by aligning Structural RNA Trees of RNA secondary structures with arbitrary pseudoknots.
R package for adaptive sum of powered score test(ASPU) in genetic association studies.
Fits the general linear mixed model and estimates variance components by residual maximum likelihood (REML).
A machine-learning computational model for identifying proteins associated with multiple abiotic stress in plants.
ASSAM tool searches for patterns of amino acid side chains in 3D space within PDB structures. Input must be a 3D amino acid pattern, which will be used in based on distances between the amino acid side chains.
Detecting and removing multiplicative spatial bias in high-throughput screening technologies.
A web application to monitor mutations in COVID-19 diagnostic assays.
Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses.
Assemblage is a microbial genome assembly pipeline that runs various QC, assembly and post-assembly steps on Illumina PE/SE reads. The different steps of the pipeline are - downsample reads using Seqtk/Mash (optional), clean reads with Trimmomatic, assemble clean reads with SPAdes assembler, perform post-assembly correction with PILON and annotates assembled genome using PROKKA.
Design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.
Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry and other data. The protocols is based on our Xlink Analyzer and external software: Integrative Modeling Plafform (IMP), Python Modeling Interface (PMI), UCSF Chimera, and imp-sampcon. Comparing to other methods, Assembline enables efficient sampling of conformational space through a multi-step procedure, provides new modeling restraints, and includes a unique configuration system for setting up the modelling project.
The AssemblX Toolkit for Reliable and User-Friendly Multigene Assemblies.
snakemake-powered cli to download genomes using NCBI datasets
Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.
An Emboss tool that searches for a sequence assembly and returns the data in one of the EMBOSS assembly formats.
Software tool for computing the robotic commands for 2ab assembly. It takes as input a list of composite parts described in terms of their basic part composition.
This series of scripts calculates various metrics on an input FASTA file. Typically this is most useful on either denovo genomic or transcriptomic data.
Software of allele specific study of next generation sequencing data, with emphasis on RNA-seq and ChIP-seq data.
An R package for subset-based analysis of heterogeneous traits and subtypes.
Tool to evaluate the pathway deregulation/activation status in patient samples. It employs a Bayesian factor analysis approach to adapt predetermined pathway signatures derived from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.
Assignment of DNA and RNA conformers A unified dinucleotide alphabet describing both RNA and DNA structures by Černý et al., was published in Nucleic Acids Research, Vol 48, pages 63667-6381 (2020). The DNA-only ~45 conformers and the ways they were identified is described in the paper by Schneider et al., Acta Cryst D, 74, 52-64 (2018). Application of the DNA Structural Alphabet is in Schneider et al., Genes, 8(10), 278, (2017). The web service in version 2 is described in Černý et al., Nucleic Acids Research, 44, W284 (2016).
Tool for the efficient filtering of Illumina Infinium/BeadExpress based SNP markers.
ASSIST is an application for the detection of catalytic sites in unknown function proteins.
ASSIST v1- Active Site Similarity Search Tool
AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs.
Assess Secondary Structure Prediction takes a multiple protein sequence alignment and estimates the range in accuracy that one can expect for a “perfect” secondary structure prediction made using the alignment.
Alternative splicing trascriptional landscape visualization tool retrieves all alternative splicing events from generic transcript annotations.
AStarix is a sequence-to-graph semi-global aligner based on A* shortest path algorithm. It supports general graphs and finds alignments that are optimal according to edit-distance with non-negative weights.
AltSplice and AltExtron provide information on alternative intron/exons, alternative splice events, and isoform splice patterns. AEdb contains: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events).
A package for accurately estimating the number of cell types in single-cell chromatin accessibility data.
Set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.
A Tool for the ExploRation and Integration of omiCS
A new minimum balanced evolution supertree algorithm robust to missing data.
ASTHERISC (Algorithmic Search of THERmodynamic advantages In stoichiometric Single-species Community models). Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
An asthma-environment interaction knowledge graph leveraging public databases and scientific literature.
astir is a tool for automated cell identification from single-cell multiplexed imaging and proteomics. astir is a modelling framework for the assignment of cell type across a range of single-cell technologies such as Imaging Mass Cytometry (IMC). astir is built using pytorch and uses recognition networks for fast minibatch stochastic variational inference.
AStra is a Python-based software AStra for de novo estimation of the genome-wide aneuploidy profile from raw WGS reads. And Aneuploidy Spectrum (Digital Karyotyping) for Rapid Authentication of Cell Lines.
Java program for estimating a species tree given a set of unrooted gene trees.
Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)
Web server for analyzing and visualizing short time-series gene expression data.
Detection of allele-specific RNA secondary structure in structuromic probing data.
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity.
Asymmetron is a toolkit for the identifcation of asymmetry patterns in biological sequences. Asymmetron can identify strand asymmetries within consecutive occurrences of a single genomic element and for pairs of overlapping and non-overlapping genomic elements. It can also measure strand asymmetries of genomic elements relative to transcriptional and replicative orientations. Asymmetron can assign strand orientation to third features such as mutations, by orienting them relative to other genomic elements.
AmbiguityRemover removes ambiguously aligned sites from protein sequence alignments, for input into AsymmetryCounter. AsymmetryCounter counts the number of amino acid substitutions in each direction between pairs of protein sequences. AsymmetryScaler takes the results from AsymmetryCounter and summarizes substitutional asymmetry data in a single scale.
Computational process for comparative mapping between two genome assemblies, or between two different genomes.
Cloud ATAC is an open-source, cloud-based interactive framework designed for the analysis of ATAC-seq data, particularly suited for both pooled-cell and single-cell populations. It offers a streamlined analysis workflow and leverages interactive tutorials and cloud resources to simplify the data processing for non-bioinformatic researchers.
Tool for detecting ecDNA/HSRs from bulk and single-cell ATAC-seq data.
a reference-based annotation tool for single cell ATAC-seq data.\n\nIn the first round gene-level annotation, AtacAnnoR compares gene activity profiles derived from scATAC-seq data with reference gene expression profiles, assigning a subset of query cells with reference cell type labels.
A comprehensive human chromatin accessibility database with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner.
ATACgraph is a simple and effective software for the analysis of ATAC-Seq data. It contains 12 analyses to profile (epi)genome. ATACgraph utilizes peak BED files and BigWig files generated by callPeak module to compute peaks abundances between two samples.
an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq.
aTAP is a comprehensive bioinformatics web-based platform for analyze RNA-Seq data.
A toolkit for measuring and comparing ATAC-seq results.
Computational quantification of gene suppression phenotypes from multisample RNAi screens.
ATAV is a comprehensive platform for population-scale genomic analyses. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases.
The Automated Topology Builder (ATB) and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include the study of biomolecule:ligand complexes, free energy calculations, structure-based drug design and refinement of x-ray crystal complexes.
Global biological materials resource and standards organization whose mission focuses on the acquisition, authentication, production, preservation, development, and distribution of standard reference microorganisms, cell lines, and other materials.
The ATCC Genome Portal provides authenticated microbial reference genomes, offering researchers access to high-quality genomic data traceable to ATCC’s biorepository. The portal includes 3,938 assemblies produced under ISO 9000 quality standards.
Identify coexpressed genes or gene coexpression neighborhoods associated with cis-regulatory motifs or GO categories.
Autophagy and Tumor Database (ATdb) is a database used to compile the published information concerning autophagy and tumor research. Such a database can be used for optaining an in-depth understanding of the complex correlations between autophagy and tumor.
Open-source web-based application which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence.
Integrating Self-Attention Transformer with Triplet Neural Networks for Protein Gene Ontology Prediction.
Sequence-based prediction of autophagy proteins with feature representation learning.
AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
ATHENA is an open-source computational framework written in Python that facilitates the visualization, processing and analysis of (spatial) heterogeneity from spatial omics data.
athisomiRDB is a database providing a comprehensive collection of isomiRs derived from Arabidopsis thaliana miRNAs. It houses over 20,764 isomiRs and offers insights into their expression patterns, variant information, and interactions.
AthRiboNC is a database that identifies ncRNAs with coding potential in Arabidopsis thaliana using Ribo-seq data and provides analysis of their expression, co-expression networks, and module enrichment.
ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of the reference vaccine strains to predict influenza A/H3N2 antigenic drift.
Proteome activity landscapes of tumor cell lines determine drug responses. Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms of drug action.
Collection of software tools to facilitate the assembly of large genomes from whole genome shotgun reads, or a combination of whole genome shotgun reads and BAC or other localized reads.
A Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data | A global overview of pleiotropy and genetic architecture in complex traits | ATLAS - Three commands to start analysing your metagenome data | Genome wide association study ATLAS | Welcome to the Atlas of GWAS Summary Statistics | This atlas is a database of publicly available GWAS summary statistics | All databases and dependencies are installed on the fly in the directory db-dir | Free document hosting provided by Read the Docs
Atlas is a Python software that converts genome graphs and gene regulatory, interaction, and metabolic networks into dynamic models using rule-based languages.
ATLAS is a free, publicly available, web-based tool developed by the OHDSI community that facilitates the design and execution of analyses on standardized, patient-level, observational data in the CDM format.
SNP detection tool developed for next generation sequencing platforms.
Next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data.
Automated template-derived brain extraction in animal MRI | atlasBREX: Automated averaged template-derived brain extraction in animal MRI | Copy all gzipped (.nii.gz) NIFTI volumes and atlasBREX.sh into a common folder. There should be no directory or file containing 'orig', 'temp' or '_.nii.gz' in this folder
ATLAS gathers standardized molecular dynamics simulations of protein structures accompanied by their analysis in the form of interactive diagrams and trajectory visualisation.
Deals with the repetitive gap assembly problem by using the unique gap-flanking sequences to group reads and convert the problem to a local assembly task. Localizing the assembly reduces the numbers of repeats in the assembly, allows more data to be incorporated, and allows for gaps to be filled.
Suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application.
Construction of a rat spinal cord atlas of axon morphometry | Scripts to generate a microstructure atlas of the rat spinal cord | Pipeline for generating spinal cord atlas from electron microscopy | This pipeline is designed to generate an atlas of the spinal cord based on electron microscopy images. The output is a 4D nifti volume containing metrics obtained from scanning electron microscopy | One slice corresponds to one spinal level: C1, C2, ... C8, T1, ...T13, L1, ... L6, S1, ... S4
The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography.
A software facilitating the high throughput analysis of the human protein atlas online database.
Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.
ATLASx is a computational map for the exploration of biochemical space ATLASx databases explore potential biochemical reactions within different chemical scopes: bioDB, bioATLAS, and chemATLAS.
Web platform for visualizing and sharing spatial epigenome data.
Analysis and design of protein-protein or protein-peptide interactions based on atlas database.
a public repository for large-scale measurements of genome, transcriptome, methylome, pathway and phenotype associations in Arabidopsis, designed for facilitating identification of eQTL, emQTL, pathway-mQTL, pathway-phenotype, GWAS, TWAS and EWAS. AtMAD identifies candidate variants/methylations/genes for specific phenotypes or biological processes,and provides many associations that were previously unknown in exploring biological mechanisms.
ATOLL (Aligned Transmembrane dOmain Layout fLattening) is a program for visualizing 3D structures of the transmembrane helix bundle of membrane proteins.
Automated analysis of atomic resolution images using two-dimensional Gaussian fitting.
Atomic Charge Calculator II (ACC II) is a web application for fast calculation of partial atomic charges.
A web application for the calculation and analysis of atomic charges in both large biomolecular complexes and small drug-like molecules.
Masaryk University, Brno, Czech Republic
A Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats.
Template-based method for ATP-specific protein-ligand docking.
ATPGCN: Adversarially-Trained Persistent Homology-Based Graph Convolutional Network for Disease Identification Using Brain Connectivity.
Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.
ATPint:is a web based tool for prediction of ATP binding residue in protein sequence
Performs targeted de novo assembly of loci from paired-end Illumina runs.
Software that finds and displays approximate tandem repeats (ATR) in DNA sequences. An approximate tandem repeat (ATR) in a genomic sequence is a string of nucleotides repeated consecutively at least twice with some small differences between the repeated copies.
An ultra-fast and accurate adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
AtrialJSQnet is a modified U-Net consisting of two decoders for LA segmentation and scar quantification, respectively.
Atri-U is a tool for assisted image analysis in routine cardiovascular magnetic resonance volumetry of the left atrium. Atri-U is an automated data analysis pipeline for long-axis cardiac cine images, computes the atrial volume by: (i) detecting the end-systolic frame, (ii) outlining the endocardial borders of the LA, (iii) localizing the mitral annular hinge points and constructing the longitudinal atrial diameters, equivalent to the usual workup done by clinicians.
A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients.
ATSE is a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism.
Affinity Test for regulatory SNP detection package is a bioinformatics tool for computing and testing large-scale motif-SNP interactions.
AtSRGA is a user-friendly application enabling users to retrieve stress-responsive genes in Arabidopsis thaliana. AtSRGA presents stress-responsive genes in a heatmap format based on a stress responsiveness measure (SRscore, see section 2-3 of tutorial). It facilitates the comparative analysis of individual stress responses and groups of genes responsive to multiple stress conditions. Researchers can identify groups of genes with similar patterns by examining the SRscore pattern of a gene of interest across 11 stress conditions. AtSRGA will enhance the screening of biologically significant stress-responsive genes in Arabidopsis in functional genomics research.
AtSRGA (Arabidopsis thaliana Stress Rsponsive Genes Atlas)
A highly accurate subcellular localization prediction tool for annotating the Arabidopsis thaliana proteome.
ATTED-II is a gene coexpression database for nine plant species based on publicly available RNAseq and microarray data.
AttnSleep an attention-based deep learning approach for sleep stage classification with single-channel EEG.
This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.
Attune offers a versatile framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data.
Calculates the Area Under the ROC curve, and plots the ROC curve. Completely vectorized, very fast.
Fast AUC calculator and ROC curve plotter
Compares two AUCs derived from same cases
Analysis of 'gene set' activity in single-cell RNA-seq data allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell.
Inferring and comparing metabolisms across heterogeneous sets of annotated genomes.
AUCpreD is a method that predicts intrinsically disordered regions (IDR). AUCpreD works well without sequence profile, comparing favorably to or even outperforming many methods using sequence profile.
An Automatically Unsupervised Clustering Toolbox for 3D-Segmentation of High-Grade Gliomas in Multi-Parametric MR Images.
audiomath is a package for Python programmers who want to record, manipulate, visualize or play sound waveforms.
A GUI for AutoDock Vina, it helps in virtual screening of huge number of ligands continuously. Helps in resumption of work in accidental shutdowns. This program can help you in docking several ligands automatically in to a prescribed protein receptor site.
Python package for inferring Gene Regulatory Networks (GRNs) and Boolean Networks (BNs) by processing high-throughput gene expression data (RNA-Seq).
AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.
Open-source software system for accurate and user-friendly identification of relative expression molecular signatures.
A unified workspace built around a Python package PADMet (Python library for hAndling metaData of METabolism), to house the reconstruction of genome-scale metabolic models.
Proteomic signature library of Staphylococcus aureus Pathophysiology for inter-experimental expression data analyses.
Compute AUROC (Area under Receiver Operating Characteristic) from frequency weighted instances of predictions and ratio of positive instances
AUROC - Area under Receiver Operating Characteristic
Receiver Operating Characteristic curve with convex hull, plus areas under ROC and ROCCH.
AUSPP is a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read mapping, and normalized wiggle file creation.
A Federated Model for Integrating Genomics into Healthcare. Preparing Australia for the integration of genomics into healthcare. COVID-19: Information for our research network and participants here. National diagnostic & research network. Driving a coordinated & sustainable system for genomic healthcare. See a sample consent form for an Australian Genomics flagship study.
spatial modelling, visualisation, and reporting of estimates. An interactive, online atlas designed to show how the burden of cancer varies across small geographical areas for the whole country, using the latest available data.
라스인증,라스인증작업,라스인증판매,파일화 국내 최저가판매 텔레그램:@choinongsim t.me/choinongsim The world's first data computing platform designed to serve as the foundation for AI-automated discovery.
AuthentiCT is a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded libraries. It estimates contamination using an ancient DNA damage model and assumes that the contaminant is not deaminated.
Autism_genepheno is an automatic text mining pipeline to identify sentence-level mentions of autism-associated genes and phenotypes in literature through natural language processing methods.
An evidence-based knowledgebase of autism genetics.
Auto-CORPus (Automated and Consistent Outputs from Research Publications) is a automated pipeline that cleans HTML files from biomedical literature. The output is a single JSON file that contains the text for each section, table data in machine-readable format and lists of phenotypes and abbreviations found in the article.
The Rosetta-based "auto-DRRAFTER" method builds RNA models into moderate-resolution RNA cryo-EM density as part of the Ribosolve pipeline.
Auto-HMM-LMF is a feature selection-based method to accurately predict cell line-drug associations and response using autoencoder and Hidden Markov Model.
Auto-phylo v2 is a software resource for building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels, and identification of positively selected amino acid sites. It includes a graphical user interface and supports various data types and workflows.
auto-phylo is a software resource for building advanced phylogenetic inference pipelines, estimating variability levels, and identifying positively selected amino acid sites. It provides a GUI application for pipeline creation and execution.
XGBoost-based automatic classification of sequence types for prostate mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This was applied to all data on ProCAncer-I to derive initial results for sequence types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.
AutoProSeq - automatic classification of sequence types for prostate mpMRI
Auto-qPCR is a Python web application and command line tool designed to process raw data files from thermal cycler machines.
Automated crystal structure determination platform
Auto3D is a Python package for generating low-energy conformers from SMILES. It automatizes the stereoisomer enumeration and duplicate filtering process, 3D building process, fast geometry optimization and ranking process using ANI and AIMNet neural network atomistic potentials.
A comprehensive automatic data analysis strategy for gas chromatography-mass spectrometry based untargeted metabolomics. Home >> Software >> autoGCMSDataAnal
A software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.
Using this software, complete backbone resonance assignments are now routinely made within hours of completing the final data acquisition.
Computational design (fully automated) of regulatory circuits in E. coli able to provide the nucleotide sequence.
A Deep Learning Tool for the Classification of Biological Sequences
AutoBridge is an automation framework to boost the FPGA design frequency.
Automated cancer-associated TCRs discovery from TCR-seq data.
Automated Collision Cross Section calculation software for ion mobility-mass spectrometry
AutoClass is a deep learning tool for scRNA-Seq data cleaning and denoising. AutoClass integrates two deep neural network components, an autoencoder and a classifier, as to maximize both noise removal and signal retention.
Unsupervised Bayesian classification system. It provides a web interface for this clustering algorithm.
A web app to run AutoClass C Bayesian clustering
AutoClassWrapper: a Python wrapper for AutoClass C classification. AutoClass is an unsupervised Bayesian classification system and AutoClass C is its implementation in C made by the NASA. AutoClassWrapper is a Python wrapper to ease the use of Autoclass C.
AutoCloner is a custom pipeline that designs homeologue-specific primers for polyploids. It achieves this by extracting SNP locations unique to your gene of interest, and placing the 3` ends of primers at these SNPs.
AutoCNV is a semiautomatic CNV interpretation system for clinical interpretation of copy number loss or gain based on the 2019 ACMG/ClinGen Technical Standards for CNVs. It is a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs.
AutoCoEv is a high-throughput in silico pipeline for predicting novel protein-protein interactions. It is a user-friendly computational pipeline for the search of coevolution between hundreds and even thousands of proteins.
AutoCoV, a deep learning method with multiple loss object, that can track the early spread of COVID-19 in terms of spatial and temporal patterns until the disease is fully spread over the world in July 2020.
AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity.
A tailored AutoML for disease classification from gene expression data
autodE is a Python module designed for the automated calculation of reaction profiles from just SMILES strings of reactant(s) and product(s).
A GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting.
A web-based communication tool for visualizing biomolecular structures. It enables to prepare, explore, and share interactive 3D and immersive VR structural walkthroughs directly in a web browser
AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). AutoDimer was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.
Suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
AutoEpiCollect is a GUI software utilizing machine learning to generate safe and immunogenic epitopes from missense mutations in oncogenes, streamlining preclinical vaccine design. The software incorporates a probabilistic logistic regression model trained on experimental T-cell assay data and has been applied to design a pan-cancer vaccine targeting PIK3CA mutations.
A web tool for automatic editing sequence design for genetic manipulation of microorganisms.
AutoFAIR is portal for automating FAIR assessments for bioinformatics resources. AutoFAIR a semi-automated tool to assess a resource according to the Findability, Accessibility, Interoperability and Reusability (FAIR) criteria. The aim is to create a portal that presents the assessment score together with a report that researchers can use to gauge a resource.
An R Package for Automatic Item Pairing in Forced-Choice Test Construction.
AutoGeneS is a Python package that automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples. AutoGeneS requires no prior knowledge about marker genes and selects genes by simultaneously optimizing multiple criteria: minimizing the correlation and maximizing the distance between cell types. It can be applied to reference profiles from various sources like single-cell experiments or sorted cell populations.
Integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.
AutoGraph performs autonomous graph based clustering on metabolite conformers to reduce redundancy from configuration space. AutoGraph prioritizes autonomation, simplicity, and practicality.
AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.
A dockerized workflow integrating clin var and inter var germline sequence variant classification.
Analysis of H/D-exchange data using isotopic distributions.
AutoIdeogram displays autozygous regions, identified in Affymetrix microarray SNP chip genotype data, against an ideogram of the human autosomal genome
Scientific software for analyzing 6xxx Al-Mg-Si-(Cu) precipitates in atomic resolution HAADF-STEM images.
A function to automate bacterial colony counting in images of plated agar in a Petri dish.
Automated Counting of Bacterial Colonies
This program reads in ultrasound videos and automates the process of measuring muscle architecture.
Automated Measurement of Muscle Architecture from Ultrasound Images
Automated detection and segmentation of non-small cell lung cancer computed tomography images
UM - Automated detection and segmentation NSCLC
Automatic objective neuronal spike detection for electrophys. measurements.
Automatic objective neuronal spike detection
Tool that automatically detects the histological type of a tumor region of interest from Whole Slide Imaging technique
Matlab script that will calculate an instantaneous rate matrix (and its eigen value decompostion for use in phylip programs) from a series of substitution count matrices calculated for different levels of sequence identity/similarity.
AutoMeKin is an automated reaction discovery tool. Web server allows you to unravel the reaction mechanisms (with intermediates and transition states) of your system, just providing an equilibrium structure (reactant)
Automated Retinal Vascular Morphology Quantification via a Deep Learning Pipeline.
An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning.
Automated ion mobility metabolomic fingerprinting.
Mathematica package for analyzing time-series of oscillatory signals, particularly those originating from biological/chemical systems.
The paper-based microfluidic device design software.
High-resolution data source for the analysis of autophagy and its regulation.
An automatic pipeline for phylogenetic analysis.
XGBoost-based automatic classification of sequence types for prostate mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv//Excel/parquet datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This was applied to all data on ProCAncer-I to derive initial results for sequence types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.
Autoprot is a Python module designed to simplify the analysis of quantitative mass spectrometry-based proteomics data, particularly when processed with MaxQuant. It integrates Python and R algorithms, offering interactive visualizations for data exploration and streamlined analysis pipelines.
Framework for simple experimentation with radiomics features. Includes an experimental desktop app.
AutoRELACS is a Python script for automated generation and analysis of ultra-parallel ChIP-seq.
Open-source software employing a novel image analysis approach to support fully-automated plant phenotyping.
A web application for constructing cancer staging models by recursive partitioning analysis.
It creates data files, uses MAKEPED, DOWNFREQ, and PEDCHECK programs and finally starts statistical analyses via the ANALYZE package that performs parametric linkage analysis, nonparametric affected sib-pair analysis, family-based association analysis, and homogeneity testing. Input files are the pedigree,the disease model, the number of loci, and the ANALYZE input file. It allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.
A suite of ImageJ and Micro-Manager scripts to perform intelligent imaging.
AutoScore is a machine learning-based automatic clinical score generator consisting of 6 modules for developing interpretable point-based scores. Future users can employ the AutoScore framework to create clinical scores effortlessly in various clinical applications.
Given a new dataset with time-to-event outcomes and baseline covariates, the AutoScore-Survival package provides a pipeline of functions to split data and implement the six modules to generate the final scores that require minimal manipulation from users.
AutoScore-Ordinal is a novel machine learning framework to automate the development of interpretable clinical scoring models for ordinal outcomes, which expands the original AutoScore framework for binary outcomes.
Batch Assembly of Contigs for Sanger Sequences.
AutoSequin is designed to speed up the process of submitting HIV sequences to GenBank via NCBI’s Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI’s tbl2asn program to generate .sqn file for submission to GenBank.
Computational method for identifying and characterizing small molecules binding sites for receptors of known three-dimensional structure. Binding sites are identified using energetic aspects to select high affinity points in space around the receptor, and a clustering technique for segregating these points into clusters called fills and corresponding to potential binding pockets.
A software to aid the identification of regions of Identity By Descent (IBD) in inbred families, by visually presenting colour-coded SNP genotype data ordered by physical or genetic distance.
Combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.
Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules
AutoSpill is a method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data.
AutoTune is a methof which finds the optimal number of layers to be fine-tuned automatically for a target dataset for improved transfer learning.
An open-source deep learning network for arterial-venous area segmentation in OCT angiography.
Here we present the AntiViral Antibody Response Deconvolution Algorithm (AVARDA), a multi-module software package for analyzing VirScan datasets
Avatar is a standalone software for analysis and visualisation of alteration data. Avatar features interactively customizable alteration plots, extensive data import capabilities and a multi-objective optimization algorithm to find alteration patterns, e.g. gene sets with mutually exclusive alterations or small gene sets with high sample coverage. License: EPL-2.0 (https://spdx.org/licenses/EPL-2.0.html)
AVATREE is an open-source computational modelling framework modelling Anatomically Valid Airway TREE conformations and provides capabilities for simulation of broncho-constriction apparent in obstructive pulmonary conditions. Additional functionalities of AVATREE include visualization of spatial probability maps for the airway generations projected on the CT imaging data, and visualization of the airway tree based on local structure properties.
An R function for assessing genetic distinctness and genetic redundancy.
averageRegions is a tool that generates average spectra in for the regions defined in a Bruker SCiLS Lab dataset and exports these in the Bruker .xy format.
Web based annotation and visualization workflow that allow users with variation data to easily get more information about their specific mutations without having to search multiple websites or databases.
Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.
Aviator is a web-server monitoring the availability of other published web-servers. It allows researchers to monitor their own tools or to asses if a tool they would like to access is temporarily or permanently offline.
Avida is a software platform that mirrors key aspects of biological evolution, making it a useful twin for evolutionary studies.
AViS is an Analysis and Visualization Software for Molecular Dynamics Simulations
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
A software package for automatic phylogenetic detection of candidate horizontal gene transfers.
Anti Viral Peptide Database. Experimentally verified AVPs targeting over 60 medically important viruses including Influenza, HCV, HSV, RSV, HBV, DENV, SARS, etc.
ANPpred webserver is an antiviral peptide prediction server. It contains 1245 peptides which have been experimentally validated for antiviral activity against human viruses.
aWCluster is a network-based integration method of multiomics data as well as a clustering technique founded on the Wasserstein (Earth Mover's) distance from the theory of optimal mass transport.
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications | fast computing for adaptively weighted fisher's method | Github repository for adaptively weighted fisher's method (AW-Fisher)
A protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.
An auto-weighted supervision attention network for myocardial scar and edema segmentation in multi-sequence cardiac magnetic resonance images.
Asymmetric Winsorization per Sample Transformation (AWST) is data normalisation method for RNA-seq data. It is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering.
Combined assessment of MHC binding and antigen expression improves T cell epitope predictions. Antigen eXpression based Epitope Likelihood-Function (AXEL-F)
Axes of Biology is a software resource that uses a novel axes-based network embedding paradigm to decipher the functional mechanisms of cells. It shifts functional exploration from gene embedding vectors to the axes of the embedding space, uncovering new data-driven functional interactions.
Converts imaging data from the Axima formats to the Analyze format used in BioMap.
Automation, eXtension, and Integration Of Microbial Ecology is a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.
Script to analyse axonal aggregates based on fluorescence variation. Use together with script baseline analysis.
Simulator of White Matter Axons Arrangement.
AxonSeg is a GUI that performs axon and myelin segmentation on histology images.
A free, open source visualization tool for researchers in biochemistry, molecular dynamics, and protein folding.
PyMOL plugin for construction, visualization and analysis of glycan molecules.
Collection of NMR programs for interactive display and processing of NMR data.
The AstraZeneca PheWAS Portal is a public repository of gene-phenotype associations. These data were generated using exome sequencing and phenotype data from the UK Biobank accessed as part of application 26041. The AstraZeneca PheWAS Portal uses reference genome GRCh38.
B-AMP is an Antimicrobial Peptide (AMP) repository for biofilms, consisting of a vast library of 5544 structural AMP models, AMPs annotated to relevant biofilm literature, and protein-peptide interaction models with potential biofilm targets.
B-COSFIRE filters detect line at different orientations by combining the responses of DoG filters.
Trainable COSFIRE filters for curvilinear structure delineation in images
B-DeepNoise is a Bayesian deep noise neural network designed for density regression and uncertainty quantification. It extends standard Bayesian DNNs by incorporating random noise variables in hidden layers and provides a closed-form Gibbs sampling algorithm for efficient posterior computation.
Bayesian ridge regression-based method (B-GEX) is a method to infer gene expression profiles of multiple tissues from blood gene expression profile.
An online tool for prediction and classification of β-lactamase class, subclass, and family.
The software combines the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks.
The Bird 10,000 Genomes (B10K) Project is an initiative to generate representative draft genome sequences from all extant bird species. The project aims to reconstruct the tree of life with full genome data, reveal the genomic basis of global bird diversity, and assess the impact of environmental change on diversity.
The bio2byte tools server (b2btools) offers the following single protein sequence based predictions: - Backbone and sidechain dynamics (DynaMine) - Helix, sheet, coil and polyproline-II propensity - Early folding propensity (EFoldMine) - Disorder (DisoMine) - Beta-sheet aggregation (Agmata) In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA
Blood-Brain Barrier Database (B3DB) is a curated diverse molecular database of blood-brain barrier permeability with chemical descriptors.
B3Pdb: a database of blood-brain barrier-penetrating peptides.
In silico tool for predicting and designing Blood-Brain Barrier Penetrating Peptides.
A tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families.
A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software | Structural learning of Bayesian networks (BNs) from observational data has gained increasing applied use and attention from various scientific and industrial areas. The mathematical theory of BNs and their optimization is well developed. Although there are several open-source BN learners in the public domain, none of them are able to handle both small and large feature space data and recover network structures with acceptable accuracy. bAIcis® is a novel BN learning and simulation software from BERG. It was developed with the goal of learning BNs from "Big Data" in health care, often exceeding hundreds of thousands features when research is conducted in genomics or multi-omics. This article provides a comprehensive performance evaluation of bAIcis and its comparison with the open-source BN learners
Tool for the prediction of promoters in cyanobacteria and Escherichia coli.
An R package that enables users to efficient fit and cross-validate Bayesian and likelihood whole-genome regression methods.
A web tool for generating Bland-Altman plots and constructing limits of agreement.
This package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele-specific events. It is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.
An open-source application for prospective modeling of transcranial focused ultrasound for neuromodulation applications.
Integrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling. It integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods.
Computational Genomics Department. Prince Felipe Research Center (CIPF)
This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.
R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service.
BacAnt is a consolidation tool for finding the Resistance genes, Insertion elements and Transposon regions from genome sequences. It provide curated database for transfer elements search and annotation.
Modeling framework for cellular communities in their environments. Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.
A Comprehensive and Interactive Web-Resource to Discern Antibiotic Resistance Gene Diversity in –Omics Datasets.
An online platform for clinical back-averaging. The back-average technique is very useful to study the relation between the activity in the cortex and the muscles.
BacDive (The Bacterial Diversity Database) is the worldwide largest database for standardized bacterial and archaeal strain-level information. Its mission is to mobilize and integrate research data on strain level from diverse sources and make it freely accessible. BacDive is a comprehensive resource containing diverse data on bacterial and archaeal strains, including taxonomy, morphology, physiology, sampling and environmental data and sequence information.
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
The API for retrieving BacDive data in machine-readable JSON format. BacDive is the Bacterial Diversity Database and provides strain-linked information about bacterial and archaeal biodiversity. The API offers several possibilities to query detailed strain information.
The DSMZ's Bacterial Diversity Metadatabase (BacDive) focuses on providing organism-linked information covering the multifarious aspects of bacterial biodiversity: taxonomic classification, morphology, physiology, cultivation, origin natural habitat and more, both for bacterial and archaeal strains. BacDiveR helps you investigate this data offline, and semi-automatically in R.
BacDiveR: A Programmatic Interface For BacDive
BacEffluxPred is a SVM based 2-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins and their sub-families.
Predictor for the subcellular localization of proteins in eukaryotes.
This server allows to use the BACHSCORE tool with the aim of discriminating the best model of a protein (the native state or a structure very similar to it) among a large set of alternative conformations.
BACH Bayesian Analysis Conformation Hunt
AciDB is a database of about 600 manually curated acidophilic organisms, their genomic information and associated metadata.
Tool to identify the presence of common RNA background in a PAR-CLIP dataset.
Back-translate a protein sequence to ambiguous nucleotide sequence.
Back-translate a protein sequence to ambiguous nucleotide sequence. It reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.
Back-translate a protein sequence to a nucleotide sequence.
Back-translate a protein sequence to a nucleotide sequence, using codon frequency.It reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from.
A user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.
An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.
A set of tools used in production and exploration of bacterial artificial chromosome restriction maps based on the information on the cloneDB server.
Bacnet is a Java based platform for fast development of ‘personalized’ multiomics website. Bacnet is easy to import, modify and deploy on web server.
BAse COmposition CAlculator is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions.
Bayesian Analysis of COpy number Mixtures is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR.
This tool can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies by constructing an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.
The BACPHLIP software is designed to test whether a given phage genome is likely to be either temperate (lysogenic) or virulent (lytic). The software makes this determination by searching for a particular set of what are hypothesized to be "temperate-specific" protein domains.
A bi-directional attention neural network for compound-protein interaction and binding affinity prediction.
BacPipe is a rapid, user-friendly whole genome sequencing pipeline for clinical diagnostic bacteriology and outbreak detection.
A web-based tool for Gram-negative bacterial promoter prediction.
Automated pipeline for whole-genome sequence analysis of bacterial genomes.
A GUI for bacterial identification base on PNN and MDS.
Script package for quantifying bacterial load within cells using images from Olympus IX81/Slidebook
R-Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data.
This tool analyses bacterial sequences and detects genes.
Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences. Like Bioclipse, Bacting is written in the Java language, making use in Java-derived languages like Groovy easy, but also accessible to Python. Deposition of the Bacting package on Maven Central allows it to be easily used in Groovy scripts with @Grab instructions.
Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
BacVacDB is a manually curated comprehensive database containing information of the vaccines for human bacterial diseases
BacWGSTdb is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections.
BADASS is a software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data.
For RNA sequencing count data, this tool fits a Bayesian hierarchical model. Its algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.
Program for the differential analysis of gene expression microarray experiments.
BadgerFilm is a tool which can calculate thickness(es) and composition(s) of thin films as well as composition of the substrate.
Library and command-line tool for generating realistic-looking synthetic Electronic Health Records (EHR) data for testing purposes; optional plugin BadMedicine.Dicom for extending this to generating DICOM files.
Applying deep learning to integrate deleteriousness prediction scores for whole-exome SNV studies. Our services require cookies to keep track of your submissions and find your results. Submissions expire after 24 hours.
This package identifies regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.
BEAST2 package to infer who infected whom using within- and between-sample genetic variation data and epidemiological data.
An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data | Detection and Analyis of Expressed Intergenic Elements in Bacterial RNA-seq Data | The baerhunter package comprises a set of tools for the prediction, annotation and filtering of bacterial intergenic expressed regions from RNA-seq data. In addition, it supports further stages of bacterial RNA-seq data analysis, such as transcript abundance quantification and differential gene expression testing. It also offers additional options for the selection of genomic features by their expression strength and editing of the annotation file
BAFinder is a program developed for the unknown bile acid identification from LC-MS/MS data in both positive and negative modes.
Software that detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.
BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.
BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.
The Bayesian Analysis of Gene Essentiality 2 (BAGEL2) is a robust gene essentiality identifier from CRISPR-cas9 genome wide pooled library screen data.
Automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases. Input is single or multiple FASTA formatted files.
Mine bacterial (meta-)genomic DNA for bacteriocins and RiPPs. Additionally it provides databases and a BLAST against the core peptide databases.
BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction of specific gene and protein sequences from completely determined prokaryotic genomes. Query results can be exported as a rich text format file for printing, archival or further analysis.
Bagheera is a web server of prediction of genes in yeast species by providing the correct CUG decoding scheme , that allows determining the most probable CUG codon translation for a given transcriptome or genome assembly based on extensive reference data.
Bagphenotypeis a softwaree of Mapping QTLs in populations descended from known founders
Bagpipe is a program for performing genomewide linkage disequilibrium mapping of quantitative trait loci in populations whose genome structure can be accommodated in the happy framework. This includes most diploid crosses where the founders of the individuals have known genotypes.
R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.
BAGS is an automated barcode, audit and grade system for DNA barcode reference libraries.
Bayesian Hierarchical Analyses of MedDRA-coded Adverse Events (BAHAMA): A Bayesian hierarchical model for the detection of MedDRA coded adverse events in RCTs.
Open source code for calculating bioaeosol deposition in lungs
BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.
A fully Bayesian approach to estimate selection coefficients from Evolve-and-Resequence time series data.
Bakdrive provides a novel approach for driver species from real metagenomic data and simulate fecal microbial transplantation FMT process.
Tool for uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
BAlaS is an interactive web application for performing CASM via BudeAlaScan and visualizing its results. BAlaS is interactive and intuitive to use. Results are displayed directly in the browser for the structure being interrogated enabling their rapid inspection. BAlaS has broad applications in areas, such as drug discovery and protein-interface design.
A system for solving protein structures using x-ray crystallographic data.
An ORF (Open Reading Frame) annotation approach, in which classifiers are constructed from the class specific expression patterns discovered by bicluster analysis. Firstly a set of bicluster classifiers is build using a labelled training set from the annotated ORFs in the expression data. These biclusters are then used to classify an unlabelled ORF set i.e. the unannotated ORFs from the expression dataset.
BALD is the R package BALD implements/combines functions for Genome-Wide Association Studies including simulation of SNPs data, constrained hierarchical clustering using Linkage Disequilibrium (LD) measures, the Gap statistic to find the optimal number of clusters, and statistical regression models for SNP selection (Univariate, Lasso, Group Lasso, Elastic-Net).
BALDR is an automated pipeline for biomarker comparison and prioritization in the context of diabetes. BALDR includes protein, gene and disease data from major public repositories, text-mining data and human and mouse experimental data from the IMI2 RHAPSODY consortium. These data are provided as easy-to-read figures and tables enabling direct comparison of up to 20 biomarker candidates for diabetes.
Pipeline for reconstructing human or rhesus macaque immunoglobulin(Ig)/B cell receptor(BCR) sequences from single cell RNA-Seq data generated by Illumina sequencing
Markov chain Monte Carlo software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). It handles generic Bayesian modeling via probabilistic programming.
Software tool based on the Biochemical Algorithms Library (BALL). It enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions.
Galaxy-based workflow toolkit for structural bioinformatics.
BAllCools is a software toolkit designed for efficient parsing, indexing, and querying of single-cell DNA methylation data stored in the BAllC format, addressing the challenges of storage and processing associated with large methylation datasets.
Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
Balrog is a prokaryotic gene finder based on a Temporal Convolutional Network.
Extract and plot Lorenz and Coverage stats directly derived from bam files
The purpose of this program is to generate metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls. Help is currently available on the commandline if you do not supply the program any arguments.
Extract reads from a bam file and write them in fastq format.
Calculate coverage from a BAM alignment file.
Converts a list of BAM format files to SAM format.
Variant detector and graphical alignment viewer for SAM/BAM format data.
An algorithm for scaffolding genome assemblies. It enables the use of linking data and allows the user to control the scaffolding parameters.
Bayesian metabolic flux analysis reveals intracellular flux couplings | Bayesian metabolic flux analysis | Bayesian Metabolic Flux Analysis MATLAB package by Markus Heinonen, Maria Osmala, Henrik Mannerström, Juho Rousu, Samuel Kaski and Harri Lähdesmäki from the CSB research group of Aalto University
Checksum program for verifying the integrity of sequence data.
Bamkit is a collection of tools for common BAM file manipulations
de-novo motif discovery and regulatory sequence analysis. Discovery of regulatory motifs with higher-order Bayesian Markov Models (BaMMs)
Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.
BaMORC (Bayesian Model Optimized Reference Correction) is designed to facilitate protein NMR research with an easy-to-use tool that detects and corrects 13C referencing errors before and after the protein resonance assignment step.
Proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens.
BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
Large file viewer for BAM and SAM alignment files.
The BAM Search Infrastructure - is a tool for extracting data from the 1000 Genomes phase 3 set of mapped reads (BAM files). It is a filtering tool - subsets of the ~60TB data can be specied and downloaded via the browser, with no need to download the entire data set.
This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.
Extract reads from byte ranges of an unaligned BAM file and convert to interleaved FASTQ format for parallel processing. Only decompresses the relevant range.
BamSnap is a lightweight command-based visualization tool for sequencing reads in BAM files.
Generate mapping statistics from the bam file.
Tools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.
BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.
Bamutil provides a serie of programs to work on SAM/BAM files.
Interactive Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequence
Plot bending and curvature data for B-DNA.
Dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone.
GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.
bandbox is a Python package that assesses the organization of bioimaging data and flags potential issues before archival, offering recommendations for improvement as detailed in a peer-reviewed publication. The tool facilitates data curation and archival for bioimaging datasets.
BANΔIT (B’‐factor analysis and ΔB’ interpretation toolkit) is web application that provides a graphical user interface for the normalization and analysis of B’‐factor profiles. The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐based drug design since protein mobility changes have been associated with the quality of protein‐ligand interactions.
Web-based submission of one or a few sequences to GenBank.
A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation.
Biologically Annotated Neural Networks (BANNs), a novel probabilistic framework that makes machine learning fully amenable for GWA applications. BANNs are feedforward models with partially connected architectures that are based on biological annotations.
It is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.
An R and Stata package for visualizing and analyzing age-period-cohort data.
Predicting bacteriocins using an optimal set of features.
It is for the annotation of protein sequences relying on a comparative large-scale analysis on the entire UniProt. With BAR 3.0 and a sequence you can annotate when possible: function, structure, protein domains. Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM that allows you to directly compute your 3D model. Cluster HMMs are available for downloading.
BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB. This is a legacy version, please refer to https://bio.tools/bar for the latest release.
The BAR-Seq web application, an online, freely available and easy-to-use software that allows performing clonal tracking analyses on raw sequencing data without any computational resources or advanced bioinformatic skills. BAR-Seq pipeline is a strategy for clonal tracking of cells harboring homology-directed targeted integration of a barcoding cassette.BAR-Seq can be applied to most editing strategies.
A freely available catalogue describing expertise and molecular analysis resources available at centers and companies in Sweden for analysis of biobanked samples.
Encodes a multiple alignment according to the method developed by Véronique Barriel (C.R.Acad.Sci.III 317(7):693-701).From a an existing alignment (which will not be changed) BARCOD builds a character matrix suitable for use in phylogeny recontstruction programs. The method allows to encode each insertion/deletion event as one single event (whatever the number of nucleotides involved), while retaining any indel common to two or more taxa as a possibly shared character.
The program generates barcodes for sequences suitable for Illumina sequencing.
A command line interface for data retrieval from the barcode of life data system.
An interactive gateway designed for the tracking and dissemination of DNA barcode reference data. The most commonly used marker is a region of the cytochrome c oxidase I (COI) gene found in mitochondria but multiple other are used for plants and fungi. Supported markers: COI, ITS, rbcL, matK and 18S.
A tool to generate unique, orthogonal genetic tags for qPCR detection. barCoder is a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes and appropriate spacer sequences.
barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data from cellular barcoding experiments.
It is a web tool for selecting an optimal set of barcode sequences. User must provide a set of candidate barcodes from which the defined number of barcodes is selected.
Design of barcoded primers, for multiplexed high-throughput sequencing.
The bardensr (barcode dexmixing through non-negative spatial regression) package is a collection of tools for modeling linearly multiplexed observations. There is some true signal we are interested in, but our observations are some noisy linear mixture of those signals.
Robust peak calling for RNA-DNA interaction data.
BAREB, a BAyesian REpulsive Biclustering model, that can simultaneously cluster the Periodontal diseases (PD) patients and their tooth sites after taking the patient- and site-level covariates into consideration. BAREB uses the determinantal point process (DPP) prior to induce diversity among different biclusters to facilitate parsimony and interpretability.
The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.
Integrative gene expression database for barley.
BarleyNet is a co-functional gene network with a companion web server for network-assisted systems genetics analysis of cultivated barley. It is a Bayesian statistics-based combination of a wide range of biological data, including the genomic information of the latest IBSC_v2 genome and barley-specific gene expression profiles. It is able to prioritize novel genes for biological trait of interest or infer functions of unannotated barley genes by combining prior knowledge from forward- or reverse-genetics studies of user with the information included in BarleyNet via three in silico gene/function prioritization algorithms implemented in BarleyNet web server.
BarleyVarDB is a comprehensive genomic variation database for Barley.
Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
Barracuda is a high-speed sequence aligner based on BWA and uses the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers.
Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
BARS is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines.
Transcription factor prediction tool with query gene sets or epigenomic profiles.
BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analysis for Regulation of Transcription) to make the prediction.
BART3D is a computational method for inferring transcriptional regulators (TRs) associated with genome-wide differential chromatin interactions (DCIs) detected by comparing two Hi-C maps. And Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.
Fast and accurate clustering algorithm to count barcode reads.
BARtab and bartools are a suite of tools designed for the analysis of cellular barcoding datasets from population-level, single-cell, and spatial transcriptomics experiments. The tools streamline data extraction, quality control, analysis, and visualization, offering a comprehensive workflow for lineage tracing.
This web server is to perform Binding Analysis for Regulation of Transcription (BART) is a bioinformatics tool for predicting functional factors (including transcription factors and chromatin regulators) that bind at cis-regulatory regions to regulate gene expression in human or mouse, taking a query gene list or a ChIP-seq dataset as input.
A software tools for barcoded single-cell genomics
Breast Aesthetic Scale Calculator (BAS-Calc) is a platform for calculating Breast Aesthetic Scale (BAS) score, which is a quick and simple objective assessment of results in cosmetic breast surgery
BaSDAS (Barcode-Seq Data Analysis System) is a GUI-based pooled knockout screening data analysis system to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information
A comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.
An easy-to-use software for complete data analysis in single cell immunoglobulin cloning.
BASE is a workflow to integrate non-ubiquitous genes in comparative genomics analyses for selection. It is used to built to ease the inference and interpretation of selection regimes in the context of comparative genomics. While the majority of these analyses are restricted to ortholog groups of ubiquitous genes - i.e. genes which are present in all the species considered - BASE allows to integrate ortholog groups of non-ubiquitous genes - i.e. genes which are not present in all the species considered.
Base Pad is a windows based base sequence editor. Search, complement, XNA to amino acid,amino acid to XNA,3 to1 & 1to 3 letter code, invert, find ORF,statistics of bps,2bp palindromes
This package provides tools to work with Illumina bcl2Fastq software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command.
Lightweight detection of sequences in raw MinION data. BaseLess reduces your MinION sequencing device to a simple species detector. As a trade-off, it runs on inexpensive computational hardware like single-board computers. The neural network it uses is a composite of many smaller networks, each detecting a different k-mer, thus reconfiguration of baseLess to detect a different sequence amounts to combining different smaller networks.
High performance of a GPU-accelerated variant calling tool in genome data analysis
A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.
A new machine learning-derived questionnaire for screening obstructive sleep apnea.
Background and shading correction of optical microscopy images.
A basic mzML visualization software for plotting single scans, total- and extracted ion chromatograms.
R/BioConductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.
Semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.
BASICO, a simplified Python interface to COPASI. It provides a set of functions that allow to create, edit, simulate and analyze models in an automated way
Bayesian Analysis of Single-Cell Sequencing data is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments. It could perform built-in data normalisation and technical noise quantification. BASiCS provides an intuitive detection criterion for highly variable genes within a single group of cells. Also, it can compare gene expression patterns between two or more pre-specified groups of cells.
Basicsynbio is an open-source Python package to help facilitate BASIC DNA Assembly workflows.
Probabilistic model of the conformational space of amino acid side chains in proteins. It models the chi angles in continuous space, including the influence of the protein's backbone.
Bioinformatics approach for accurate prediction of type VI secreted effectors.
BastionHub is a universal platform to integrate and analyze the five major types of substrates (i.e. from types I-IV and VI secretion systems) secreted by Gram-negative bacteria Secretion systems are one of the key “weapons” used by bacteria to unleash a repertoire of virulence factors into eukaryotic host cells or into neighboring bacterial cells to disrupt their normal cellular processes.
BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.
Bisulfite Analysis Toolkit. It facilitates the analysis of bisulfite sequencing data. It covers the essential analysis steps of read alignment, quality control, extraction of methylation information, and calling of differentially methylated regions, as well as biologically relevant downstream analyses, such as data integration with gene expression, histone modification data, or transcription factor binding site annotation.
Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity, especially for echolocating bat species. This tool helps better assess bat population trends accurately and allow the detection and classification of bat calls in large collections of audio recordings.
Calling somatic mutations with a tumor- and site-specific prior. Implements BATCAVE: Bayesian Analysis Tools for Context-Aware Variant Evaluation. This package is an implementation of the BATCAVE algorithm described in Mannakee et al. .... The algorithm is a post-variant-calling filter for variants that incorporates a tumor-and-site-specific prior probability of mutation
This file batch download files from NCBI GEO according to a list of URLs.
Batch-Mask is an automated mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis. Batch-Mask utilizes a customized region-based convolutional neural network (R-CNN) model to generate masks of snakes in photographs.
BatchBench is a Nextflow workflow for running the following scRNA-Seq data batch effect correction methods. The pieline is run through the bash script. Here the profiles, data directory and output directory are specified. Nextflow can generate an execution report, a timeline and a flowchart which output directory is specified here. Additionally, the -resume command line option allows for the continuation of a workflow execution.
BatchEval is a workflow designed to evaluate batch effects during joint analysis of multiple transcriptomics datasets, generating comprehensive reports to guide batch effect removal.
Parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species.
Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This can produce technical biases that can lead to incorrect results. This is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. Its diagnostics help determine if batch adjustment is needed, and how correction should be applied.
BatchServer is a web application for batch effect evaluation, visualization and correction.
A software program to count moving animals.
The aim of BATEx is the establishment of a data warehouse for array-based gene expression data of plants to enable experiment-spanning expression data analyses. Therefore, data is integrated from various data sources, such as BarleyBase, AtGenExpress, AFGC, TIGR SGED and IPK’s operational system FLAREX.
BATH is a tool for sensitive annotation of protein-coding DNA based on direct alignment to protein sequences or profile hidden Markov models, incorporating frameshift-aware algorithms to detect insertions and deletions.
Bayesian annotations for targeted lipidomics (BATL) is a bioinformatic tools capable of annotating, rapidly and reproducibly, large targeted lipidomic datasets are limited. Specifically, few programs enable high-throughput peak assessment of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) data acquired in either selected or multiple reaction monitoring (SRM and MRM) modes. It is a Gaussian naïve Bayes classifier for targeted lipidomics, that annotates peak identities according to eight features related to retention time, intensity, and peak shape. Lipid identification is achieved by modelling distributions of these eight input features across biological conditions and maximizing the joint posterior probabilities of all peak identities at a given transition.
BATMAN is a novel tool for batch effect correction (integration) of single-cell RNA-Seq datasets.
Google-based, open source, automatic search tool for training materials.
An algorithm that integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes to improve unique mapping rate, speed and precision.
It consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.
Boston ASL Template and Simulator (BATS) offers high-quality, high-resolution perfusion-weighted and quantitative perfusion templates accompanied by ATT and different anatomical contrasts readily available in the Montreal Neurological Institute space.
Streamlining Bayesian Calibration With Artificial Neural Network Metamodeling.
Bayesian analysis of allele-specific expression (BayesASE) is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating Allelic imbalance (AI) and formally comparing levels of AI between conditions.
Program that estimates recent migration rates between populations using MCMC.
BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.
An R Package for Bayesian Trial Design Using Historical Control Data.
Bayesian method for doing transcriptome assembly from RNA-seq data.
This software tool is used for accessing the performance of different epidemiological models (including both growth and compartmental models) in a Bayesian framework.
We develop this web app to help local people assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. This has been done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at an early stage.
Implementing Bayesian second-level fMRI analysis with multiple comparison correction and Bayesian meta-analysis of fMRI images with multiprocessing.
Algorithm for realistic modeling of morphological tree clones. Here the morphological clones are defined as trees similar (and not the same) at the tree-level structure with varying fine-scale structural detail.
Bayesian estimation of the coancestry coefficient FST
BayeshERG : A Bayesian Graph Neural Network for predicting hERG blockers.
3D reconstruction algorithm for electron cryo-microscopy.
A Bayesian Adaptive Basis Algorithm for Single Particle Reconstruction
BayesKAT methodology to detect the presence of any genetic association between a trait and a group of preassigned genetic features. BayesKAT can implement a kernel-based association test that automatically selects the optimum kernel using the Bayesian approach and returns an interpretable result by incorporating prior knowledge based on biological experiments or known biological mechanisms.
A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.
Flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. It can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.
R package for Mendelian risk prediction. It includes R implementation of the BRCAPRO and CRCAPRO models, as well as functionality to adapt BRCAPRO and CRCAPRO to specific population and to develop new Mendelian risk prediction models for other syndromes.
BayesMix is a piece of computer software, a suite of R functions and C routines with a graphical user interface, which can be used as a tool for performing model-based inference for differential gene expression, using a non-parametric Bayesian mixture probability model for the distribution of gene intensities under different conditions.
BayesMotif is a de novo identification algorithm for finding a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions.
BayesNF is a statistical model and open-source software package for scalable spatiotemporal prediction, utilizing a deep neural network architecture and hierarchical Bayesian inference. It's designed for data-analysis tasks like forecasting and interpolation and can be run on GPU and TPU accelerators.
This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.
BayesPI is a biophysical model for studying protein-DNA interaction. Using Bayesian model regularization with biophysical modeling to study protein-DNA interaction.
BayesRCO is a software for complex trait prediction with Bayesian hierarchical models using genome-wide genetic variation grouped into potentially overlapping annotation categories based on prior biological information
Modification of SIMCOAL 1.0. It is powerful because it allows flexible coalescent modelling from a variety of different priors. The enables parameter estimation, likelihood calculations, and Bayesian inference.
A computationally efficient Bayesian seemingly unrelated regressions model for high-dimensional quantitative trait loci discovery.
Predicting effects of mutations on protein stability with uncertainty quantification.
Perform genotyping of all types of variation (including SNPs, indels and complex structural variants) based on an input set of variants and read k-mer counts.
bayesynergy is an R package for Bayesian semi-parametric modelling of in-vitro drug combination experiments.
Analysis of zero inflated dichotomous variables from a Bayesian perspective.
Bayesian demultiplexing is a fast and accurate tool for demultiplexing reads generated by Illumina sequencers.
R package and web application for the calculation of Bayes factors for superiority, equivalence, and non-inferiority designs.
Method for global scaling normalisation, imputation and true count recovery of gene expression measurements from scRNA-seq data.
This package is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).
BayPR (Empirical Bayes Inference for Prevalence Ratios) is an R package that estimates the prevalence ratio of an exposure in a population of cases and a reference population using samples from each population.
Bayesian sampling of HIV-1 integration dates by root-to-tip regression.
This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.
BaySiCle is a bayesian Inference joint kNN method for imputation of single-cell RNA-sequencing data making use of local effect.
Semiparametric Bayesian inference for the transmission dynamics of COVID-19 with a state-space model.
Bayz is a statistical analysis software using Bayesian models. Bayz is a command-line tool that shares similarities with other statistical analysis software such as SAS, R, or Genstat: the general set-up is to import/describe the contents of data files, and then to specify the analysis model to be built in terms of the response variable(s), possible link function and factors or covariates to be fitted.
This package visualizes the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.
bbeaR is an R package and framework for epitope-specific antibody profiling for the data obtained with the Bead-Based Epitope Assay (BBEA).
Batch effect removal tool for single cell RNA-Seq data that can be directly used in the scanpy workflow.
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.
Database of collections of biomaterial and associated data subsumed under the umbrella of BBMRI-EU.
Database of collections of biomaterial and associated data subsumed under the umbrella of BBMRI-NL.
A reference for scientists seeking information about biological samples and data suitable for their research.
BBPpred is a web application used to identify Blood-brain barrier peptides (BBPs) using a logistic regression classifier based on feature representation learning scheme. BBPs can cross the blood-brain barrier based on various mechanisms and have a variety of biomedical applications.
The BBPpredict tool is a predictor that can be used to foretell if your peptides might be blood-brain barrier penetrating peptide.
BBrowser allows biologists to handle scRNA-seq data without programming knowledge. Intuitive operation. Functions are updated. It has a new CITE-seq dashboard, a complete package for interactively exploring single-cell gene expression data in parallel with surface protein information.
bbsBayes is a R package to perform hierarchical Bayesian analysis of North American Breeding Bird Survey (BBS) data. 'bbsBayes' will run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for JAGS, or modelled.
An R package for analyzing RNA-Seq transcriptional count data.
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version 7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. BBTools is open source and free for unlimited use, and is used regularly by DOE JGI and other institutions around the world.
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data.
Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA-seq). It offers the possibility to explore gene-expression of genes of interest in breast cancer.
A program for analyzing and selecting sets of barcodes for mgi-sequencing. The application allows analyzing the compatibility of barcodes on a single lane of a flow cell in a set in the case of equal and arbitrary fractions.
BC_subtyping allows the stratification of breast cancer (BC) expression profiles from RNA-seq data into intrinsic molecular subtypes using improved versions of the dataset-level PAM50 test or single-sample machine learning-based classifiers.
Database platform for managing molecular data (sequence variants and DNA array) with associated phenotypes and analyzing the data for QTL mapping.
Python scripts and modules for automated next gen sequencing analysis. These provide a fully automated pipeline for taking sequencing results from an Illumina sequencer, converting them to standard Fastq format, aligning to a reference genome, doing SNP calling, and producing a summary PDF of results.
Automated and scalable RNA-seq methods for identifying gene abundance counts.
Aims to provide the scientific community with the several tools to indirectly assess brain disconnections.
The Reference DB Creator (BCdatabaser) is a pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data. It can optionally be used to trim and orient the sequences and train taxonomic classifiers.
Bioactive Conformational Ensemble (BCE) is a platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug Discovery.
The BcePred server predicts B cell epitope based on physio-chemical properties of amino acids.
This tool allows the user to index sorted BCF for random access.
Find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold.
BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms includes a grammar for describing forms of macromolecular complexes composed of DNA, RNA, protein, and small molecular subunits and crosslinks between the subunits. The DNA, RNA, and protein subunits can be described using BpForms and the small molecule subunits can be described using SMILES. BcForms also includes four software tools for verifying descriptions of complexes and calculating physical properties of complexes such as their molecular structure, formula, molecular weight, and charge: a web application, a JSON REST API, a command line interface, and a Python API.
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer
Austrian GEN-AU projects "bioinformatics integration network III"
Wrapper tool for rnpB gene prediction by combining speed of rnabob descriptor model and sensitivity of infernal covariance model.
BCINFO: A COMPLETE GUIDE TO B-CELL EPITOPE PREDICTION
A database of b cell epitopes. The prime/boost vaccine strategy has suggested that only immunodominant epitopes, rather than a large collection of defined epitopes with varying immunogenicity should be selected for vaccines.
Bio Chemical Library is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data.
BCL::Conf is a web application for generating conformational ensembles of small molecules.
Comprehensive database of LncRNAs associated with breast cancer.
Toolkit for Bayesian analysis of Computational Models using samplers.
Includes reverse complement, 6-frame translation, RepeatMasker, ReadSeq format conversion.
The BCO App is a Shiny app to create, validate, and browse BioCompute Objects. It is a tool for generating BioCompute Objects from next-generation sequencing workflows and computations.
Stand-alone software application which allows calculation of disability-adjusted life years (DALYs) for a selection of 32 communicable diseases and six healthcare-associated infections.
Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search.
BCR evaluator is used to evaluate bisulfite conversion ratio in whole genome shotgun bisulfite sequencing (WGSBS) experiment. BCReval is a small python script to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control.
BCRgt is a Bayesian Cluster Regression based genotyping approach to genotype samples with Copy Number Alterations (CNAs). This is motivated by the facts that cancer tissues often have large regions of genetic structural alterations such as CNAs, and that researchers have been interested in genotyping SNPs from such samples.
Correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests.
The Beacon Calculus is a process algebra designed to make modelling biological systems fast, intuitive, and accessible.
A database of biomarkers of cancer stem cells.
Fast sequence mapping in high-throughput shRNA and CRISPR screens.
Tool for quantifying gene expression from single cell RNA-seq.
BCseq (bias-corrected sequencing analysis)
R package that can be used to detect differentially methylated CG sites and differentially methylated regions using a Bayesian smoothing curve method.
BCyto is an open-source project that provides an user-friendly, high-performance interface for Flow Cytometry analysis in R.
Bases-dependent rapid phylogenetic clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.
Graphical user interface that allows you to create high quality sequence datasets using the tools included. Using these tools you can perform several common tasks such as doing BLAST alignments, getting the open reading frames of the sequences in a Fasta file or changing the format of a Fasta file. All these task make use of several known tools such as EMBOSS, bedtools, and NCBI's BLAST, Splign and Compart.
BDdb is a comprehensive database associated with birth-defect-related diseases. It consists of multi-omics datasets involving tens of common birth-defect diseases, and BDdb supplements more than 2000 biomarkers belonging to 22 types of birth defects.
A MATLAB Package for Boolean Delay Equation Modeling.
An assessment metric for protein complex structure models based on distance difference matrix.
BDOCK is a novel enzyme-inhibitor docking algorithm based on the degree of burial and conservation of surface residues
Estimator of epidemiological parameters under the Birth-Death with Contact Tracing (BD-CT) model from phylogenetic trees and a non-parametric CT detection test.
It provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.
BE-dataHIVE is a MySQL database containing over 460,000 base editing gRNA target combinations. It provides an API and Python library for practitioners and researchers to analyze base editing data and predict outcomes.
BE-FF (Base Editors Functional Finder) is a pythonic tool that identifies suitable base editors to repair a given single nucleotide variation (SNV). The web tool does not require any registration, installation or additional plugins. By inserting the reference and variation nucleotides, BE-FF attempts to find base editors that provide precise correction.
Single-cell analysis tool for mouse cortex.
Automated tool for Bacterial GEnome Annotation ComparisON.
Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.
Software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences
This forward looking GA4GH Beacon interface implements Beacon Project roadmap features beyond in close coordination with the official API. The use of the Beacon protocol is demonstrated on to of the Progenetix cancer genome data collection. While not primarily documented for independent deployment, the Beacon+ code base can be coopted for developing genomic information resources in biomedical settings.
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Importing data from Illumina SNP experiments and performing copy number calculations and reports.
Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.
Monte-Carlo simulation to calculate position of micronsized particles in optical trap
BeadNet is a U-Net-based software for the detection and counting of small poorly-resolved objects in images
ChIP-seq data normalization for Illumina
Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
Analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance.
BEAP uses a short starting DNA fragment, often a EST or partial gene segment, as “primer”, to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the “primer” therefore help to “extend” the length of the original sequence for constructing a “full length” sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis.
The Batch Electroencephalography Automated Processing Platform (BEAPP). The Boston EEG Automated Processing Pipeline (BEAPP) is a modular, Matlab-based software designed to facilitate automated, flexible batch processing of baseline and event-related EEG files in datasets with mixed acquisition formats.
RNA secondary structure analysis, comparison and classification, motif finding and phylogeny.
Takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3' terminus to look for the patterns.
Bayesian ERCC Assesstment of Robustness of Single Cell Clusters is a noise estimation and injection tool that is designed to assess putative single-cell RNA-seq clusters in the context of experimental noise estimated by ERCC spike-in controls.
The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. It uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.
Beastiary is designed for visualising and analysing MCMC trace files generated from Bayesian phylogenetic analyses. Beastiary works in real-time and on remote servers (e.g. a HPC). Its goal is to be a beautiful and simple yet powerful tool for Bayesian phylogenetic inference.
Open source software tool designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform.
Model-based analysis of single-cell methylation data.
This program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence.
Software to understand the molecular mechanisms of infectious disease and to identify therapeutic and diagnostic targets via NGS data.
Beav is a command-line tool that automates bacterial genome annotation, focusing on mobile genetic elements, gene clusters, and regulatory features. It combines existing tools with custom models and databases to improve annotation accuracy, particularly for plant-associated microbes, and is available on Bioconda.
A browser-based tool for the exploration and visualization of RNA-seq data. BEAVR is a graphical tool to automate analysis and exploration of small and large RNAseq datasets using DESeq2.
BEBE is a benchmark for computational analysis of animal behavior using bio-logger data, providing datasets, modeling tasks, and evaluation metrics to facilitate machine learning-based analysis of animal behavior.
Web application, API and widget for biomedical concept identification. It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts.
This tool provides some functions to detect and correct for batch effects in DNA methylation data. Its core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.
Interpreting DNA methylation findings from blood in the context of brain.
Biological Entity Dictionary. Get and explore mapping between identifiers of biological entities. It provides a way to connect to a BED Neo4j database in which the relationships between the identifiers from different sources are recorded.
Detection and comparison of epialleles within multiple tumour regions enables phylogenetic analyses, identification of differentially expressed epialleles, and provides a measure of epigenetic heterogeneity.
Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP).
BEDOPS is an open-source command-line toolkit that performs efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets
Bedshift is a tool for randomly perturbing BED file regions. The perturbations supported on regions are shift, drop, add, cut, and merge. This tool is particularly useful for creating test datasets for various tasks, since there often is no ground truth dataset to compare to. By perturbing a file, a pipeline or analysis can be run on both the perturbed file and the original file, then be compared.
Bedtk is a set of simple tools to process BED files. It so far implements intersection, subtraction, sorting, merging and computing the breadth of coverage.
Convert a bed file to a genePred file. If BED has at least 12 columns, then a genePred with blocks is created. Otherwise single-exon genePreds are created.
BEDTools is an extensive suite of utilities for comparing genomic features in BED format.
Convert a BAM file to a BED file. The end coordinate is computed by inspecting the CIGAR string. The QNAME for the alignment is used as the BED name field and, by default, the MAPQ is used as the BED score.
Count the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target).
Calculate a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
Report overlaps between two feature files.
Create a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file. Example usage would be to cull a BAM file from an exome capture experiment to include on the "on-target" alignments.
Merge multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
Identify common intervals among multiple, sorted BED files.
BedtoolsR is an R package that provides a convenient wrapper for bedtools functions allowing for the documentation and use of them from within the R programming environment, using standard R data types. It uses the version of bedtools installed on your system, rather than its own version, such that you should be able to use it interchangeably from the command line or within R. It also includes additional functionality including the ability to provide either file paths or R objects as inputs and outputs. Bedtoolsr automatically detects the format of the input/output and handles it accordingly.
Suite of software tools for working with next-generation sequencing datasets.
Biomedical Entity Exploration (BEE) is a tool comparing key bioinformatical categories to each other based on diverse databases.
BeeDeeM is a general-purpose Bioinformatics Databank Manager. It is capable of installing sequence databanks, such as: Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta and Silva, as well as any files using these formats. In addition, BeeDeeM can install major biological classifications (ontologies), such as NCBI Taxonomy, Gene Ontology, Enzyme and Intepro. BeeDeeM can be used from the command-line or from a graphical user interface. It is cluster ready: use of a job scheduler (e.g. PBS, SLURM), smooth use of cluster structures (e.g. data downloading from Internet-connected nodes vs. data processing on network-isolated nodes). Finally, the software comes with utility tools such as databank filtering and querying, and BLAST/DIAMOND/PLAST annotator tools; banks installed by BeeDeeM being indexed, they can be used to collect features data (including ontologies) and add all that information within results of above mentioned sequence comparison tools.
Fast and faithful conversion of mmCIF format structure files to PDB format.
BEEM-Static is an R package for learning directed microbial interactions from cross-sectional microbiome profiling data based on the generalized Lotka-Volterra model (gLVM).
Web server is an online resource to help in protein structure prediction. It ranks submitted structural models of a protein using evolutionary information.
BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more.
R Shiny app for automated high-throughput explorative analysis of multivariate behavioural data. The app is designed to provide an easy access to fundamental analysis techniques such as clustering, boxplot visualization and pairwise comparisons, heatmaps, principal component analysis (PCA), correlation matrices and pairwise correlations.
BEERS2 is a software tool for RNA-Seq simulation that combines a flexible design with detailed modeling of the library preparation and sequencing pipeline. It allows for the generation of realistic RNA-Seq reads, facilitating the assessment and benchmarking of bioinformatics tools.
Tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.
Suite of applications for building and manipulating the Burrows-Wheeler Transform (BWT) of collections of DNA sequences. The algorithms employed are intended to scale to collections of sequences containing one billion entries or more.
The database contains genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules, it has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum.
Database collects results of highly accurate QM calculations of molecular structures, energies and properties.
A two-photon imaging analysis pipeline for astrocytic Ca2+ signals
Automated behavior classification and analysis in rodents.
Agent-based simulation of static models in Biological Expression Language.
bleg is a R-package that contains functions to calculate relative and absolute Boltzmann entropy using the hierarchy-based and the aggregation-based methods. Boltzmann entropy (also called configurational entropy) has been recently adopted to analyze entropy of landscape gradients . The goal of belg is to provide an efficient C++ implementation of this method in R.
BELIEF (Biological Expression Language Information Extraction WorkFlow) is a semi-automated workflow for BEL network creation. It embeds an information extraction workflow with state-of-the-art named entity recognition (NER) and relation extraction (RE) methods.
BELT (Bin-based Enrichment Level Threshold) is a ChIP-seq peak calling tool. This is the engine used in our published web application W-ChIPeaks, meant to be used as a command-line application. Although it does not include all of the features of W-ChIPeaks (such as archive support and target FDR) as some of these are implemented by the Web-based framework, it is nonetheless a full-fledged standalone peakcalling utility.
Calculate trees from multiple alignments.
Boolean matrix factorization (BMF) via expectation maximization (EM). BEM is more aligned with the molecular mechanism of transcriptomic coregulation and can scale to matrix with over 100 million data points.
BEMM-GEN is a toolkit for generating biomolecular environment-mimicking models for molecular dynamics simulations. It allows users to create spherical and cylindrical models with varied chemical properties and integrate arbitrary protein conformations.
Benchmark of differential abundance methods on microbiome data.
This tool contains scripts used to perform analyses in the paper "Towards a Standardized Framework for Pangenome Graph Evaluation: Assessing Crop Plant Pangenome Variation Graph Construction from Multiple Assemblies
Pipeline to compare the performance of different tools for the non-coding variant scoring.
BenchmarkST is a resource for evaluating spatial transcriptomics clustering, alignment, and integration methods. It provides a suite of tools and datasets for benchmarking these algorithms and provides recommendations based on quantitative and qualitative metrics.
BenchStab is a command-line tool and Python package for querying and benchmarking web-based protein stability predictors. It includes a dataset for independent evaluation of these predictors, intended to be excluded from future training and validation.
BenMAP is an open-source computer program that calculates the number and economic value of air pollution-related deaths and illnesses. The software incorporates a database that includes many of the concentration-response relationships, population files, and health and economic data needed to quantify these impacts.
BENTO is a workflow management platform with a graphic user interface (GUI) that is built on top of CodaLab, to facilitate the process of building clinical NLP pipelines. BENTO comes with a number of clinical NLP tools that have been pre-trained using medical notes and expert annotations and can be readily used for various clinical NLP tasks. It also allows researchers and developers to create their custom tools and use them in a controlled and reproducible way.
Bento is a Python toolkit for performing subcellular analysis of spatial transcriptomics data. The package is part of the Scverse ecosystem. Check out the documentation for installation instructions, tutorials, and API.
BENviewer is a brand-new online gene interaction network visualization server based on graph embedding models.
The Bologna ENZyme Web Server (BENZ WS) annotates the Enzyme Commission numbers (EC numbers) of enzymes. BENZ WS is based on HMMs and PFAMs and returns a four-level EC number for a target which is retained by the system.
Prediction of the location of linear B-cell epitopes.
BEReX is a new biomedical knowledge integration, search and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD and MSigDB) and delineates an integrated network by combining the information available from these databases.
The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference.
Trim, circularise, orient and filter long read bacterial genome assemblies
Bidirectional Encoder Representations from Transformers with Graph Transformer (BERT-GT) is a tool for cross-sentence n-ary relation extraction.
BERT-Kcr is a tool for prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models.
An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection.
BERT4Bitter is a bidirectional encoder representations from transformers (BERT)-based web application for improving the prediction of bitter peptides.
A Python script to predict peptide MHC binding and presentation with BERT model. Improves MHC-peptide class II interaction prediction with transformer and multiple instance learning.
TCR binding prediction using bidirectional encoder representations from transformers augmented with random TCR pairing.
The Batch Effect Signature Correction (BESC) algorithm that uses the batch effect signatures calculated on the reference set to efficiently predict and remove Microarray batch effect, which has been the primary bottleneck for large-scale integration of data from multiple experiments.
The BESCA (BEyond Single Cell Analysis) package contains many useful python functions to use for your single-cell analysis.
This tool is a scaffolder. The input is a contig file and a set of BAM files from mapping paired-ends and/or mate-pair reads to the contigs, and the output are scaffolds, i.e., the contigs linked and oriented. It is both fast and accurate. Careful estimation of the gaps between contigs, many other scaffolders have seriously biased estimation. Novel treatment of paired-end contamination in mate-pair libraries, which identifies that some links in the MP data are better treated as PE.
Program for optimal planning of X-ray data collection from protein crystals
A web server for brain expression Spatio-temporal pattern analysis.
This code Find out the best infocus image from a image stack using Tamura coefficient.
Bam Error Stats Tool (best): analysis of error types in aligned reads. best is used to assess the quality of reads after aligning them to a reference assembly.
Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature.
A web-based application automatically combines various tools to precisely predict differentially expressed genes (DEGs) from RNA-Seq data.
Beta Structure Selection. Novel method for the secondary structure determination and fold recognition from protein circular dichroism spectra.
A new method called Beta-PSMC, which introduces the probability density function of a beta distribution with a broad variety of shapes into the Pairwise Sequentially Markovian Coalescent (PSMC) model to refine the population history in each discretized time interval in place of the assumption that the population size is unchanged.
This software computes molecular voids and channels with guaranteed mathematical correctness and computational efficiency and also computes their geometrical properties.
BetaScan2 is a statistics suite. BetaScan2 can calculate βstd on a predefined window of interest, instead of requiring the use of a sliding window across the genome. This locus-based calculation is made possible by standardization allowing comparison of scores across different window sizes, and enables the use of β on species for which only a small fraction of the genome is available.
Powerful method to control Type-I error inflation in partially sequenced data for rare variant association testing. It is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. It can work with any existing rare variant association methods that use genotypes or imputed genotypes as input.
The server is developed for predicting ß-turns in a protein from the amino acid sequence. It allows the user * to predict turns in a protein using existing statistical algorithms. * to predict the type of ß-turn such as Type I, I', II, II', VI, VIII and non-specific i.e., advanced prediction. * to predict the consensus ß-turn in a protein.
The aim of this server is to predict beta turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For beta turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.
This software predicts the beta turns and their types in a protein from its amino acid sequence.
A deep learning framework based on the variational autoencoder (VAE) to impute missing values in transcriptome and methylome data analysis.
This software recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area.
A software package for the analysis of TransMembrane β-barrel proteins.
BetAware-Deep is web server for predicting the topology of TransMembrane Beta-Barrel (TMBB) proteins in Gram-negative bacteria.
Bootstrap Elastic net regression from Time Series (BETS) is a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets.
An easy to use tool designed primarily to augment Agilent’s transcriptome-wide rabbit, Oryctolagus cuniculus, gene expression microarray.
BetweenNet is a computational approach that integrates genomic data with a protein-protein interaction network to identify cancer driver genes. BetweenNet utilizes a measure based on betweenness centrality on patient specific networks to identify the so-called outlier genes that correspond to dysregulated genes for each patient. Setting up the relationship between the mutated genes and the outliers through a bipartite graph, it employs a random-walk process on the graph, which provides the final prioritization of the mutated genes.
Novel software workbench for the operation and analysis of Biofilms experimental data.
Measuring the degree of the skewness of the X chromosome inactivation by the Bayesian method, the penalized Fieller's method and the Fieller's method.
BEXIS2 is an open-source community-driven research data management system to support research data management needs of mid to large-scale research projects with multiple sub-projects and up to several hundred researchers. It is a modular and extensible system providing a range of functions to realise the complete data lifecycle from data structure design to data collection, data discovery, dissemination, integration, quality assurance and research planning. Also, it’s an extensible and customisable system that allows for the development of new functions and customisation of its various components from database schemas to the user interface layout, elements and look and feel. BEXIS2 support making research data compatible with Findable, Accessible, Interoperable and Reusable (FAIR) data principles. The software is developed based on requirements of the biodiversity and ecology domain that mostly deal with tabular data but is generic enough to serve other domains and data types as well.
A machine-guided pipeline for cryptic pocket discovery in undruggable cancer targets. Combines long MD (100–200 ns), metastable state modeling (MSM), hydration thermodynamics, and PLIP-based interaction analysis to identify mutant-specific pockets absent in wild-type. Validated on TP53, KRAS G12D, MYC mutants, and fusion oncoproteins
Beyond Venetoclax Cryptic Pocket Pipeline
Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.
Standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
BFCounter is a program for counting k-mers in DNA sequence data.
Binding free energy estimator 2 (BFEE2) is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.
A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer disease.
Bfimpute is a powerful imputation tool for scRNA-seq data that recovers the dropout event by factorizing the count matrix into the product of gene-specific and cell-specific feature matrices.
A tool to analyse videos of BFP experiments.
Software for Bayesian Factor Regression Models – modelling and analysis of sparse latent factor models use in applications in pathway analysis and predictive modelling with large-scale gene expression data sets, with links to studies in gene expression analysis.
A method to identify specifity determining residues in protein families using Between Group Analysis.
Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data.
The Bovine Genome Database includes mechanisms to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. It includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages.
A database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.
Automatic RNA-Seq present/absent gene expression calls generation
A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program.
An integrated multi-omics database of barley gene families.
Big data-guided LOINC code mapper (BGLM), which leverages the large amount of patient data stored in EHR systems to perform LOINC coding mapping
The BGLR-R package implements various types of single-trait shrinkage variable selection Bayesian regressions.
Fully Bayesian mixture models for differential gene expression.
Documents variations in genes that encode antigens for human blood groups. It is a locus-specific mutation database (LSDB) that covers multiple genes.
Classification of benign and malignant tumors with MRI multi-plane attention learning.
Fits a Bayesian group-sparse multi-task regression model using Gibbs sampling. The hierarchical prior encourages shrinkage of the estimated regression coefficients at both the gene and SNP level. The model has been applied successfully to imaging phenotypes of dimension up to 100; it can be used more generally for multivariate (non-imaging) phenotypes.
Compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples.
BGvaris a comprehensive database for blood group immunogenetics. It contians human blood group alleles belonging to International Society of Blood Transfusion (ISBT) approved human blood group systems. The resource integrates relevant data from a range of public sources.
an R package to perform Bayesian genome wide association studies.
BGWR-Clustering implements a Bayesian geographically weighted regression (BGWR) approach with covariate effect clustering. It integrates a Bayesian geographically weighted regression with post-processing steps using Gaussian mixture models and the Dirichlet process mixture model, designed for analyzing spatial heterogeneous data.
Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
Energy based, for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises 8 different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of helices and strands with known tertiary structures.
A R-page for estimating the burden of healthcare-associated infections.
Tool for predicting beta-hairpins in protein sequences using a support vector machine.
This method performs bottom-up hierarchical clustering using a Dirichlet Process to model uncertainty in the data and a Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data.
R package that provides functions for setting up and fitting Bayesian hierarchical GLMs, for numerically and graphically displaying the results, and for genetic association studies and QTL mapping. The Bayesian hierarchical GLMs include many models as special cases, e.g., classical GLMs, ridge regression, Bayesian lasso, and various adaptive lasso.
BHi-Cect aims to find preferentially self-interacting chromosome clusters using Hi-C data. It only assumes that chromosome architecture consists of a nested hierarchy where we expect to find smaller-sized clusters nested within larger-sized clusters.
Bayesian High-order Interaction Toolkit, a novel Bayesian partition computational method for detecting SNP interactions (epistasis).
Hierarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation.
R software package for a Bayesian hierarchical regression model.
Novel way of modeling the problem as combinatorial optimization problem on graphs: Weighted Bi-Cluster Editing. It is a very flexible model that can handle arbitrary kinds of multi-condition data sets (not limited to gene expression).
A Database for Benzylisoquinoline Alkaloids is an attempt to gather the scattered information related to the BIA's.
BIAFLOWS is a collaborative framework to reproducibly deploy and benchmark bioimage analysis workflows. BIAFLOWS is a web platform centralizing Bio Image Analysis (BIA) workflows to automatically extract biological objects annotations from microscopy images.
This is the web server for BIANA (Biological Interactions And Network Analysis). Here, you can run BIANA by specifying your desired seed bioentities (e.g. proteins), setting the parameters (e.g. depth of network) and choosing which commands to run (e.g. print network in Cytoscape format).
BIANCA (Brain Intensity AbNormality Classification Algorithm) is a fully automated, supervised method for white matter hyperintensities detection, based on the k-nearest neighbour (k-NN) algorithm.
BIAPSS is a tool for bioinformatic analysis of liquid-liquid phase-separating protein sequences.
BIAS-2015 is an open-source algorithm that categorizes germline genomic variants according to the ACMG classification system. It evaluates ACMG criteria and leverages the ClinGen Evidence Repository for evaluation.
BiasAway is a command-line and web server to generate nucleotide composition-matched DNA background sequences. The BiasAway tool provides users with six approaches to generate synthetic or genomic background sequences matching mono- and Dinucleotide composition of user-provided foreground sequences.
The biased signaling atlas provides comprehensive information as well as analysis and visualization functions to study biased signaling.
The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of this database is to provide a searchable structured resource listing variant-containing references.
The Bibliometrix Package is a tool for performing bibliometric analysis, as demonstrated by its use in the recent study of ankylosing spondylitis clinical trials. It facilitates data retrieval, visualization, and quantification of research trends.
This software enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra.
A database for the transcriptional landscape of bacteria in cancer.
Biclustering Analysis and Results Exploration.
An R package for maximal biclique enumeration in bipartite graphs. A tool for enumerating maximal complete bipartite graphs. The input should be a edge list file or a binary matrix file. The output are maximal complete bipartite graphs.
Bi-clustering software for solving the weighted/unweighted bi-cluster editing problem. It provides exact as well as heuristic algorithms.
Bicluster is a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner.
Biclustering constrained by networks (BiCoN) is a powerful new systems medicine tool to stratify patients while elucidating disease mechanisms. BiCoN is a network-constrained biclustering approach which restricts biclusters to functionally related genes connected in molecular interaction networks and maximizes the expression difference between two groups of patients. To alleviate this, we developed the network-constrained biclustering approach BiCoN which (i) restricts biclusters to functionally related genes connected in molecular interaction networks and (ii) maximizes the expression difference between two subgroups of patients.
BICORN (Bayesian Inference of Cooperative Regulatory Network) builds a hierarchical Bayesian model and infers context-specific cis-regulatory modules based on transcription factor-gene binding events and gene expression data for a particular cell type. BICORN automatically searches for a list of candidate CRMs based on the input transcription factor bindings at regulatory regions associated with genes of interest. Applying Gibbs sampling, BICORN iteratively estimates model parameters of CRMs, transcription factor activities, and corresponding regulation on gene transcription, which it models as a sparse network of functional cis-regulatory modules regulating target genes.
Framework to support visual analysis of gene expression by means of biclustering.
Powerful and flexible tool for the exploratory and unsupervised analysis of tabular and network data.
Bioinformatics Unit. CNIO: Spanish National Cancer Research Centre
SING Research Group. Informatics Department. University of Vigo
bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH).
bicycle: bisulfite-based methylcytosine caller
Web-server that can massively generate Monte Carlo simulated sequences and numerical feature data sets.
Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data.
Software for quantifying and Removing Biases in ChIP-Seq Signals.
Online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.
A framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data.
BIDSonym is a BIDSapp for the pseudo-anonymization of neuroimaging datasets.
Web-based interactive framework to assist in the prioritization of disease candidate genes in whole exome sequencing studies.
Base de Datos para la Investigación Farmacoepidemiológica en Atención Primaria (BIFAP) is a population based database administered by the AEMPS (Spanish Agency for Medicines) of longitudinal electronic medical records (EMR) of patients attended in primary care. Its main purpose is to serve as source of information for independent studies on drug safety and support of medicines regulation activities.
Bias-free Footprint Enrichment Test identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions.
Webserver for high throughput analysis of pair-wise epistasis in GWAS of quantitative and disease traits.
Bifrost is a command-line tool for sequencing that features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in.
BiG-FAM is a database containing biosynthetic gene clusters (BGC) capturing the global diversity of BGC predicted from publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results.
The Biosynthetic Gene cluster Meta’omics abundance Profiler (BiG-MAP). A command-line tool that it is able to profile the abundance and expression of a collection of gene clusters across metagenomic and metatranscriptomic data from any kind of biome, including human, plant, animal, marine, and soil microbiomes.
BiG-MEx is a tool for the mining of Biosynthetic Gene Cluster (BGC) domains and classes in metagenomic data.
Visualization methods for differential expression analysis | Methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. Includes examples for visualizing RNA-sequencing datasets and differentially expressed genes | Big multivariate data plotted interactively | bigPint: Make BIG data pint-sized | Welcome to the bigPint package website! If you are a new user, please begin by reading from the Get Started tab at the top of this website. There are ten short vignette articles in that tab, and we recommend reading them in order. These short vignette articles consist of reproducible code that provide: | Alternatives to data metrics object | Clustering, DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, Software, Transcription, Visualization
BiG-SLiCE is a Python-based tool to perform a large-scale (>> 1 million) clustering analysis of Biosynthetic Gene Cluster data.
BiGAN-lncRNA-disease-associations-prediction based on bidirectional generative adversarial network.
Toolbox for integration of BigBrain 3D histology with multimodal neuroimaging.
Tool to run the Burrows-Wheeler Aligner-BWA on a Hadoop cluster. It supports the algorithms BWA-MEM, BWA-ALN, and BWA-SW, working with paired and single reads. It implies an important reduction in the computational time when running in a Hadoop cluster, adding scalability and fault-tolerancy.
BigDataProcessor2 (BDP2) is a Fiji plugin for interactive processing of TB-sized image data. BDP2 uses BigDataViewer for rendering and the ImgLib2 library for image processing.
This package provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.
R package of performing biobank-scale gene-based association test via knockoffs.
BIGL R-package which allows for a quick screening of drug combinations. Combination therapies are increasingly adopted as the standard of care for various diseases to improve treatment response, minimise the development of resistance and or minimise adverse events. Therefore, synergistic combinations are screened early in the drug discovery process, in which their potential is evaluated by comparing the observed combination effect to that expected under a null model.
Haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs.
Methods for working with Illumina arrays using gdsfmt.
This package defines a "BigMatrix" ReferenceClass which adds safety and convenience to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames.
BigMPI4py is a Python module that wraps mpi4py, supporting object sizes beyond this boundary. BigMPI4py automatically determines the optimal object distribution strategy, and uses vectorized methods, achieving higher parallelization efficiency. BigMPI4py facilitates the implementation of Python for Big Data applications in multicore workstations and High Performance Computer systems. We use BigMPI4py to speed-up the search for germ line specific de novo DNA methylated unmethylated motifs from the 59 whole genome bisulfite sequencing DNA methylation samples from 27 human tissues of the ENCODE project.
Comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations.
Institute of Research In Biomedicine - Barcelona
A public health decision support system for measuring obesogenic behaviors of children in relation to their local environment. Inferring the Spatial Distribution of Physical Activity in Children Population from Characteristics of the Environment. Children and adolescents with obesity have a higher risk of developing various diseases later on, compared to children without obesity. The reasons why some children become obese are complex, and behaviour, the living environment, and public health policies all play a role. BigO collects and analyses anonymous data on children's behavioural patterns and their living environment. With advanced analytics BigO extracts data-driven evidence on which local factors are involved, and how these factors influence childhood obesity in Europe.
Quality assessment package for next-genomics sequencing data.
NRG Lab, Washington University School of Medicine
Imaging platform based on the open source XNAT software. It is used for sharing de-identified medical imaging data, and for data exchange in collaborative research projects. The data is served in a standardized way, with proper access control.
The Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.
Fast statistical analysis of large-scale data encoded as matrices.
Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.
BigTop is a 3D reality tool for GWAS visualization. It demonstrates some of the potential of virtual reality for scientific visualization by providing an easy way for scientists and science enthusiasts to become immersed in their data. This provides several key advantages over more traditional 2D visualization methods.
A GWAS Association Testing Pipeline for big data
BIGwas GWAS Association Testing Pipeline
A GWAS Quality Control Pipeline for big data
BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on biigle.de is free for non-commercial use.
The BIJ Database is a resource for Brassica juncea seed omics data, providing genomic data on seed development across contrasting genotypes. It leverages computational analysis of transcriptome data to identify and characterize long non-coding RNAs (lncRNAs) and related regulatory networks.
BIKE is a Bayesian dietary exposure assessment model for microbiological and chemical hazards.
Mapping/alignment customized for mate-pair library next generation sequencing.
BIMAM (Bayesian IMputation and Analysis Model) is a tool for imputing variables missing across datasets using a Bayesian imputation and analysis model. The BIMAM tool is a user-friendly, freely available tool that does not require knowledge of Bayesian methods. The combination of multiple datasets is routine in modern epidemiology, but different studies may have measured different sets of variables; this is often inefficiently dealt with by excluding studies or dropping variables. Multilevel multiple imputation methods to impute these “systematically” missing data (as opposed to “sporadically” missing data within a study) are available, but problems may arise when many random effects are needed in the analysis and imputation models to allow for heterogeneity across studies. BIMAM implements a Bayesian method that works well in this situation.
Baysian Imputation Based Association Mapping. Genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests.
Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements.
A novel Bioinformatic Inference and Multiscale Modeling (BIMM) method that can discovers hub genes of TGFβ, MYC, and SMAD3 varied underlie DEX treatment
The Breeding Information Management System (BIMS). BIMS is a free, open-source, secure and online breeding management system which allows breeders to store, manage, archive and analyze their private breeding program data.
Join subcellular Visium HD bins into cells.
Extracts metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
Mapping quantitative trait loci using binned genotypes | Precise mapping of quantitative trait loci (QTLs) is critical for assessing genetic effects and identifying candidate genes for quantitative traits. Interval and composite interval mappings have been the methods of choice for several decades, which have provided tools for identifying genomic regions harboring causal genes for quantitative traits. Historically, the concept was developed on the basis of sparse marker maps where genotypes of loci within intervals could not be observed. Currently, genomes of many organisms have been saturated with markers due to the new sequencing technologies. Genotyping by sequencing usually generates hundreds of thousands of single nucleotide polymorphisms (SNPs), which often include the causal polymorphisms
BINding ANAlyzer is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions.
Interactive platform for human-guided exploration and binning of metagenomes.
Creates a set of binary volumes from a volume of labels (integers value)
Get binary volumes from a volume of labels integers
Perform network analysis and discover the most significant nodes and structures in a network.
Chemical class enrichment analysis based on the ChEBI ontology.
Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
BIND: The Biomolecular Interaction Network Db
This package implements functions for multi-class discriminant analysis using binary predictors, for corresponding variable selection, and for dichotomizing continuous data.
BindCompare is a user-friendly tool designed to analyze protein-nucleic acid binding datasets and identify combinatorial associations between transcription factors and RNA binding proteins. It is available as an open-source package on PyPI and GitHub, with comprehensive documentation.
Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
BindingDB database of measured binding affinities
Skaggs School of Pharmacy and Pharmaceutical Sciences
BindingSiteFinder is an R/Bioconductor package used to extract reproducible binding sites from iCLIP data, specifically designed for plant iCLIP2 workflows. It provides functions for binding site definition and result visualization.
BINDKIN (effect of point mutations on the BINDing affinity of protein KINase:ligand complexes) benchmark, contains a of available wild type and mutant kinase:ligand complexes.
Takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).
bindSC (Bi-order INtegration of multi-omics Data from Single Cell sequencing technologies) is an R package for single cell multi-omic integration analysis. bindSC is developed to address the challenge of single-cell multi-omic data integration that consists of unpaired cells measured with unmatched features across modalities. Previous methods such as Seurat, Liger, Harmony did not work on this case unless match feature empricallcy. For example, integration of scRNA-seq and scATAC-seq data requires to calculate the gene/promoter activity by counting peaks in gene body, which always loses information. This strategy also did not work on integrating scRNA-seq and cytof data becasue gene expression and protein abundance level is not always correlated due to sparsity of scRNA-seq data or post translational modification.
A database of curated biomolecular interactions.
Automatic server to predict DNA and RNA binding proteins given the three dimensional structure of the protein.
A web server for ligand binding residue and pocket prediction from protein structures.
Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
BingleSeq is a user-friendly R package for Bulk and Single-cell RNA-Seq data analyses. To begin DE analysis of Bulk RNA-Seq data, first a count table with a specific format (shown above) must be loaded. BingleSeq allows some flexibility in terms of the ‘separator’ used. Once a count table is loaded, it is displayed to allow the user to check whether it was loaded appropriately. A metadata table is also required in a specific format (shown above).
A tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.
BinMat offers users of fragment analysis methods an efficient and easy-to-use platform to process their binary data matrices, by means of either a graphical user interface or an R package.
Binnacle estimates coverage for graph scaffolds and integrates with existing metagenome binning tools. Binnacle accurately computes coverage of graph scaffolds and seamlessly integrates with leading binning methods such as MetaBAT2, MaxBin 2.0, and CONCOCT. Using graph scaffolds, as opposed to contigs (most common approach) for binning improves the contiguity and quality of metagenomic bins and can captures a broader set of the accessory elements of the reconstructed genomes.
Analysis of interval-grouped data in weed science. Nonparametric Estimation for Interval-Grouped Data. Kernel density and distribution estimation for interval-grouped data (Reyes, Francisco-Fernandez and Cao 2016, 2017) <doi:10.1080/10485252.2016.1163348>, <doi:10.1007/s11749-017-0523-9>, (Gonzalez-Andujar, Francisco-Fernandez, Cao, Reyes, Urbano, Forcella and Bastida 2016) <doi:10.1111/wre.12216> and nonparametric estimation of seedling emergence indices (Cao, Francisco-Fernandez, Anand, Bastida and Gonzalez-Andujar 2011) <doi:10.1017/S002185961100030X>
A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data.
Scripts required to calculate tetramer frequencies and create input files for ESOM
Improving genome bins through the combination of different binning programs
BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector.
Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. It provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.
The binomialRF package is an R package that provides a feature selection algorithm to be used in randomForest classifiers. Treating each tree as a quasi binomial stochastic process in a random forest, binomialRF determines a feature’s importance by how often they are selected in practice vs. as expected by random chance. Given that trees are co-dependent as they subsample the same data, a theoretical adjustment is made using a generalization of the binomial distribution that adds a parameter to model correlation/association between trials.
An R workflow for detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP. Accurate drug resistance detection is key for guiding effective tuberculosis treatment. While genotypic resistance can be rapidly detected by molecular methods, their application is challenged by mixed mycobacterial populations comprising both susceptible and resistant cells (heteroresistance). For this, next-generation sequencing (NGS) based approaches promise the determination of variants even at low frequencies. However, accurate methods for a valid detection of low-frequency variants in NGS data are currently lacking. To tackle this problem, we developed the variant detection tool binoSNP which allows the determination of low-frequency single nucleotide polymorphisms (SNPs) in NGS datasets from Mycobacterium tuberculosis complex (MTBC) strains.
Novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems.
Peak detection method for ChIP-sequencing data with biological replicates.
Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation
A system to find answers to questions from biomedical texts. The system is configured by a configuration file.
Parse CIGAR strings and translate coordinates to/from reference/query.
Virtualization containers for single-step execution of NGS pipelines.
Large-Scale Application of Named Entity Recognition to Biomedicine and Epidemiology.
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information).
Biophysical approach for GPCRs Automated Template Selection (Bio-GATS) is a tool for automated GPCR template selection through a biophysical approach for homology modeling.
Service platform for interdisciplinary work on biological application domains. It uses the jETI (Java Electronic Tool Integration Platform) service integration technology for remote tool integration and the jABC framework as a graphical workflow modeling tool.
BIO-LGCA is a cellular automaton modelling class for analyzing collective cell migration. To overcome drawbacks of classical on-lattice models, we introduce a novel on-lattice, agent-based modelling class for collective cell migration, which we call biological lattice-gas cellular automaton (BIO-LGCA). The BIO-LGCA is characterised by synchronous time updates and the explicit consideration of individual cell velocities.
BIO-MATE is an R package that reformats biological ocean data from various published datasets to create a standardized, interoperable data product for easy access and use. It aims to address the gap in subsurface bio-physical data aggregates.
The first tool for integrating methodologically diverse OD (Ortholog detection) methods.
Latent feature extraction with a Prior-based self-Attention framework for Spatial Transcriptomics.
A Ruby binding to the SAMtools library.Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format.
Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …).
Bio-SODA is a question answering system over domain knowledge graphs, such as scientific datasets, where training data (in the form of questions and corresponding SPARQL queries) is rare or unavailable.
This software contains a set of tools to analyse the output from Transposon Directed Insertion Sequencing (TraDIS) analyses.
Bio2Byte Tools is a Python package and Galaxy tool suite for predicting various protein biophysical properties, including dynamics, folding, and phase separation. It is freely available online and through package managers like pip and conda, providing a unified platform for computational and experimental researchers.
Bio2Midi converts the text of a DNA or protein sequence to a MIDI file, which you may immediately audition, or import into any MIDI sequencer for further compositional processing.
Bio2Rxn is as a web-based tool to provide putative enzymatic reaction predictions for uncharacterized protein sequences. Bio2Rxn adopts a consensus strategy by incorporating six types of enzyme prediction tools.
Converts bioinformatics formats to Zarr.
Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data.
Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. This application facilitates the identification of protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations, and the quantitative comparison of their predicted structural dynamics.
From command-line bioinformatics to bioGUI. bioGUI provides install modules for bioinformatic software for users and allows developers to script a GUI for their applications. bioGUI: a universal GUI for CLI applications. Tools for bioGUI (e.g. CWL Parser/argparse2biogui/...). With bioGUI developers can easily build a graphical-user-interface (GUI) for their command-line only application. Such a GUI then enables many more people to use their software. Especially in biology, the domain experts are often computer novices and have difficulties using tools written for them by bioinformaticiens/computer scientists. bioGUI documentation — bioGUI documentation. An python argparse-extension which first supplies two useful argparse-type extensions and second provides means to convert the python argparse parser into a bioGUI template. Free document hosting provided by Read the Docs
Bio C# contains classes for handling fasta IO, Blast-search (using an own algorithm), local and global alignments, quality sequence IO, statistics (Mann-Whitney, Poisson Distribution), distribution of features along chromosomes, SNP-identification, gene expression statistics, 454-sequence handling, microsatellite search and basic sequence statistics
Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data
The MOSAIC bioacc application is a turn-key web tool providing bioaccumulation metrics (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances.
Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them.
BioAFMviewer is an interactive interface for simulated atomic force microscopy scanning of biomolecular structures and dynamics
A toolkit for quantification of biological age from blood-chemistry and organ-function-test data.
Bioinformatics Aider (BioAider) is a visualization analysis tool for efficient and convenient in gene annotation and mutation screening on multiple genome-sequencing data.
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT.
Bioinformatics file javascript-based reformatter. Something like awk for VCF, BAM, SAM, FASTQ or FASTA.
User-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) reseacher in mind, but a couple of them can be useful to the wider research community.
Computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
Automated feature engineering and metalearning to predict noncoding RNAs in bacteria.
Meta’omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures.
Tools for early stage NGS alignment file processing including fast sorting and duplicate marking.
Functions that are needed by many other packages or which replace R functions.
Server for feature extraction and Bayesian network modeling of biological sequence data.
Biobb (BioExcel building blocks) are Python building blocks wrapping popular computational biomolecular tools.
BioExcel Center of Excellence for Computational Biomolecular Research
BioExcel Building Blocks Workflows (BioBB-Wfs) is a integrated web-based platform for biomolecular simulations.
Multiplexed wave-optical simulations of light-sheet microscopy.
Web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. It is composed of three components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Users may also invent their own tools.
Standalone command line application and collapsing method that uses prior biological knowledge from a prebuilt database. While it was specifically developed to investigate rare variant burden in traditional genetic trait studies, it can be used to apply multiple levels of burden testing and is useful for exploring the natural distribution of rare variants in ancestral populations.
Open source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.
Biobox provides a collection of data structures and methods for loading, manipulating and analyzing atomistic and pseudoatomistic structures.
This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in BioConductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.
Biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework.
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. Mayo's Data for the bioCADDIE 2016 Dataset Retrieval Challenge
Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.
Python library for genomic feature arithmetic in arbitrarily related coordinate systems.
Search engine for exploratory searches in heterogeneous biological databases.
Information about gene function, proteomic pathways, and reagent exchange; very clear pathway diagrams; can search for pathways by title or browse an organized list.
Automatic Disease Outbreaks Detection from Global News Media.
BioCAT is a tool which is designed for searching potential producers of a given non-ribosomal peptide.
A universal catalogue of web services for the life sciences. BioCatalogue provides a common interface for registering, browsing and annotating web services to the life science community.
A registry of Web Services for the Life Sciences, with a REST API that allows you to browse, search, filter and view details of the services in the registry, together with all the metadata and monitoring information about these service.
Software and data to support the case studies.
Executes BioConductor-specific package checks.
Agent-PDE (Partial Differential Equation) based simulation framework, designed for solving general models of multicellular biological systems.
This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.
S4 generic functions needed by many BioConductor packages.
This package provides examples and code that make use of the different graph related packages produced by BioConductor.
Generative AI models have shown tremendous usefulness in increasing accessibility and automation of a wide range of tasks. Yet, their application to the biomedical domain is still limited, in part due to the lack of a common framework for deploying, testing, and evaluating the diverse models and auxiliary technologies that are needed. The biochatter Python package is a generic backend library for the connection of biomedical applications to conversational AI. It includes connectivity to knowledge representations generated through the BioCypher knowledge graph package.
BioChemDDI web server is constructed to predict drug-drug interactions, which is compatible with most major browsers, and the parallel speed-up is implemented.
Biomedical Confident Itemsets Explanation (BioCIE) is a tool aiming at post-hoc explanation of black-box machine learning models for biomedical text classification. Using sources of domain knowledge and a confident itemset mining method, BioCIE discretizes the decision space of a black-box into smaller subspaces and extracts semantic relationships between the input text and class labels in different subspaces.
This package is used to install and update BioConductor, CRAN, and (some) github packages.
Free and open source workbench for the life sciences.
Integration of the R statistical language in Bioclipse.
Functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.
Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.
BioCommons is a Java library with classes, data structures and embedded static knowledge useful in structural bioinformatics.
BioConceptVec is a collection of concept embeddings on primary biological concepts mentioned in the biomedical literature.
Provide a central interface to various tools for genome-scale analysis of cancer studies.
Sustainable and comprehensive software distribution for the life sciences.
Open development software project, based on the R programming language, providing tools for the analysis of high-throughput genomic data. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software.
Open-source and community-driven framework for software standardization.
Text mining system for extracting information about molecular processes in biomedical articles.Using the data extracted by the software, it is possible to get an overview of a range of biomolecular processes relating to a particular gene or anatomical location.
The BioContextAI Registry is a community-driven catalog of Model Context Protocol (MCP) servers for agentic AI-supported biomedical research. It enables researchers and developers to discover, access, and contribute specialized tools and databases through a standardized protocol.
Collaborative project to facilitate the interconversion of life science data from one format to another.
Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...
This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with BioConductor objects.
This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.
Provides standard formatting styles for BioConductor PDF and HTML documents. Package vignettes illustrate use and functionality.
Structures for vocabularies and narratives of views.
Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.
BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)
Knowledge graphs (KGs) are an approach to knowledge representation that uses graph structure to facilitate exploration and analysis of complex data, often leveraging semantic information. They are popular in many research areas, including the life sciences, due to their versatile use, for instance in data storage, integration, reasoning, and more recently in artificial intelligence. The creation of KGs is a complex task; BioCypher helps you in creating and maintaining your own KG.
A database of uniformly preprocessed and disease annotated omics data. We followed the same preprocessing pipeline for each biological mart to produce ready for downstream analysis and meta-analysis datasets and automatically annotate them with Disease-Ontology terms. We also designate datasets that share common samples. It includes ~2000 datasets, ~200000 samples spanning ~300 diseases. All datasets are publicly available for querying, browsing and downloading via BioDataome web application.
BioDB-Loader toolkit loads several bioinformatics databases into Lisp for facile processin. BioDB-Loader contains utilities for loading flatfiles from the Swiss-Prot, Prosite, Enzyme, EcoCyc, and MetaCyc databases.
The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network.
The Biodepot Launcher is a desktop application that facilitates installation, management and deployment of containerized bioinformatics workflows. This application provides an interactive and easy-to-use interface to launch containerized analytical workflows that can be used to process biomedical data.
A computational environment for Independent Component Analysis of omics data.
A collection of software tools for calculating distance measures.
Resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets are originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, created for this. This makes the resource highly valuable in drug discovery.
Multilevel Modeling of Dendroclimatical Fluctuations.
As research projects require multiple data sources, mapping between these sources becomes necessary. Utilized workflow systems and integration tools therefore need to process large amounts of heterogeneous data formats, check for data source updates, and find suitable mapping methods to cross-reference entities from different databases. BioDWH2 is an open-source, graph-based data warehouse and mapping tool, capable of helping researchers with these issues. A workspace centered approach allows project-specific data source selections and Neo4j or GraphQL server tools enable quick access to the database for analysis. The BioDWH2 tools are available to the scientific community at https://github.com/BioDWH2.
BioDynaMo is an agent-based simulation platform for scalable computational biology research and biology dynamics modeller.
An ad hoc search engine to help biologists to isolate EST clusters corresponding to their research target, based on cross references between TIGR and Unigene.
Bioentity2vec is a method for representing bioentities, which integrates information about the attributes and behaviors of a bioentity.
BioERP: a biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions.
BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations, and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, eluding the need of tools installation.
BioExcel Building Blocks REST API (BioBB-API)
This BioExcel Building Blocks library (BioBB) workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.
BioExcel Building Blocks tutorials: ABC MD Setup
This tutorial aims to illustrate the process of setting up a simulation system to run constant pH Molecular Dynamics simulations with AMBER, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein (PDB code 6PTI).
BioExcel Building Blocks tutorials: AMBER Constant pH MD setup
This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid.
BioExcel Building Blocks tutorials: Automatic Ligand parameterization
This tutorial aims to illustrate the process of building up a command-line workflow using the BioExcel Building Blocks library (biobb). The tutorial is based on the Protein Gromacs MD Setup Jupyter Notebook tutorial.
BioExcel Building Blocks tutorials: Command-line workflows
This tutorial aims to illustrate the process of building up a CWL workflow using the BioExcel Building Blocks library (biobb). The tutorial is based on the Protein Gromacs MD Setup Jupyter Notebook tutorial.
BioExcel Building Blocks tutorials: Common Workflow Language with biobb
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures using Coarse-Grained tools from the FlexServ server and analysing its molecular flexibility
BioExcel Building Blocks tutorials: Macromolecular Coarse-Grained Flexibility
This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures step by step, using the BioExcel Building Blocks library (biobb)
BioExcel Building Blocks tutorials: Molecular Interaction Potentials
This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation, step by step, using the BioExcel Building Blocks (biobb).
BioExcel Building Blocks tutorials: Molecular Structure Checking
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.
BioExcel Building Blocks tutorials: Mutation Free Energy Calculations
This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).
BioExcel Building Blocks tutorials: Protein-Ligand Complex MD Setup (Gromacs Version)
This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the T4 lysozyme protein (PDB code 3HTB) with two residue modifications L99A/M102Q complexed with the small ligand 2-propylphenol (3-letter code JZ4).
BioExcel Building Blocks tutorials: Protein-Ligand Complex MD Setup (Amber Version)
This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).
BioExcel Building Blocks tutorials: Protein-ligand Docking
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb).
BioExcel Building Blocks tutorials: Protein Conformational Transitions
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version)
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the Lysozyme protein (PDB code 1AKI).
BioExcel Building Blocks tutorials: Protein MD Setup (Amber Version)
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).
BioExcel Building Blocks tutorials: Protein MD Setup tutorial through REST API
This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Drew Dickerson Dodecamer sequence -CGCGAATTCGCG- (PDB code 1BNA). The trajectory used is a 500ns-long MD simulation taken from the BigNASim database (NAFlex_DDD_II entry).
BioExcel Building Blocks tutorials: Structural DNA helical parameters from MD trajectory
BioBB Wfs extends and complements the BioBB library offering web-based access to a collection of predefined biomolecular simulation workflows built using the BioExcel Building Blocks library. Molecular Dynamics setup, docking, ligand parameterization, and flexibility analyses are examples of workflows included in the website.
BioExcel Building Blocks Workflows (BioBB-Wfs)
Workflow to perform high throughput Next Generation Sequencing (NGS) sequencing quality control stages
BioExcel genome sequence quality control workflow
The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.
A simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.
Tool for the quantification of biofilm-embedded cells sub-populations from fluorescent microscopic images.
BioFlow-Insight is a Python command-line tool that analyzes Nextflow workflow code to generate visual graphs and a RO-Crate JSON-LD file describing the workflow’s structure. It facilitates workflow inspection and reuse by providing insights into the workflow's components and dependencies.
Bio-Formats image file format to raw format converter
Biofouling is a MATLAB function will output the typical required values for mussel growth on structures.
Bioframe is a Python library designed to provide efficient operations on genomic interval dataframes. It extends the Python data science stack by building upon NumPy and Pandas, enabling flexible and performant data analysis in computational genome biology.
BIOFunctional is a Shiny application for interpreting and visualizing functional analysis of KEGG pathways and Gene Ontologies. It allows users to explore biological processes, create interactive networks, and trace ancestral information for hierarchical classifications, aiding in data analysis and understanding.
Open source diffusive transport solver for biological problems. It can solve for the diffusion of tens or hundreds of substrates on large 3-D domains.
Biogeography-Based Optimizer (BBO) is employed as a trainer for Multi-Layer Perceptron (MLP) training dataset.
An R package for simulating and fitting natural shapes.
biogitflow is development workflow protocols for bioinformatics pipelines with git and GitLab.
Public database that archives and disseminates genetic and protein interaction data from model organisms and humans. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana).
BioGridRunner is a distributed computing application for bioinformatics, incorporating directory services (data and software), grid computing methods (security, authentication, data transport and remote jobs), and gene sequence and genomic data processing methods.
BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.
BioHEL is an evolutionary learning system designed to handle with large-scale bioinformatic datasets.
BioIDMapper is a Cross-referencing and Managing Platform for Biological IDs in R.
Bio Image Operation or 'BIO', is a next generation Image processing tool focusing on biological applications, balancing ease of use with desired flexibility required for research
BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively.
This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.
Bioinspire-Explore is a tool for navigating biodiversity data, specifically designed for bioinspired innovation. It allows users to search for biological models by taxa and provides information on their position in the tree of life, distribution, appearance, and connections to relevant literature.
Open access database dedicated to the study of biological macromolecules by small angle X-ray scattering (SAXS).
BioJava is an open-source project providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. "
Identification of protein modifications in 3D structures from the Protein Data Bank.
Tool for evolving and designing biochemical reaction networks using genetic algorithm (GA).
Open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers.
Object and function to deal with a sequence region (reg:start-end).
Parses newick and extended newick strings(nhx) into JSON.
SAM format parser, with the ability to retrieve regions from a ws.
Rest (Representational State Transfer) API for Ensembl database. This tool enables easier programmatic access to Ensembl database.
A module to analyze multiple seqs (information content, frequency, ...).
Component to represent a chromosome with its bands.
A component for visualising disease information from UniProt data.
Retrieve most relevant GO terms from g:Profiler and render these as a string cloud.
A BioJS component for human genetic variation viewer(protein variants).
Component to represent one summary feature. Originally design to display protein expression information from the Human Protein Atlas (HPA).
Represent a network of protein interactions.
BioJS component to visualize KEGG pathways and to allow their visual integration with functional data.
A BioJS 2.0 component to view protein structures.
Europe PMC citations viewer. It retrieves and displays the principal data (such as authors list, title, journal and source) either of a single citation or of the citations list that matches the query specified in the Europe PMC.
Curated and integrated biomarker knowledgebase for animals. BioKA houses 16296 biomarkers associated with 951 diseases/traits from a comprehensive compilation of 4747 literature references across 31 species, including 9 model animals, 16 domestic animals, 5 other animals and human.
BioKC platform is in constant development and its roadmap foresees support for defining and annotation of complexes, and handling of SBML extensions such as the Multistate and Multicomponent species package.
BioKIT is a versatile toolkit for processing and analyzing diverse types of sequence data. BioKIT is a UNIX shell toolkit for processing molecular sequence data.
Extract UMLS concepts from Biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be use to automatically curate and annotate BioMedical Literature.
Research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires.
BioLearn is an open-source library for the curation, harmonization, and systematic evaluation of aging biomarkers. It provides tools to load data from public sources and run common aging clocks with a few lines of code.
BioLegato is a generic graphical user interface (GUI), in essence, a program that runs other programs. Data are displayed and selected in a canvas. A program is chosen from dropdown menus, parameters are set in a pop up menu, and the program launched by issuing a shell command to the system. Thus, any program, from a simple shell script to a complex analytical pipeline, can be launched from BioLegato.
BioLib is a tool for building webservers. The platform allows developers to create webservers without having to build front-end or setting up and maintaining server infrastructure.
The Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) is a data repository with the aim of sharing data from observational and interventional studies supported by the National Heart, Lung, and Blood Institute.
BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions. The structure data are collected primarily from the Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. BioLiP aims to construct the most comprehensive and accurate database for serving the needs of ligand-protein docking, virtual ligand screening and protein function annotation. Questions about the BioLiP Database can be posted at the Service System Discussion Board.
Web sever resource that integrates scientific publications with existing biological databases. To perform this link, it searches the full text of the article for metadata such as database identifiers and ontology terms.
Biologer is an open platform for collecting biodiversity data.
The tool is designed to perform normalization at the image-level. This normalization method aims to reduce the variability in the intensity values of the Magnetic Resonance (MR) prostate images due to different scanners, acquisition protocols and conditions, based on the intensity values of specific tissues. This tool implements three biologically-motivated intensity normalization techniques: (1) The fat-based normalization method, (2) The muscle-based normalization method, and (3) The single tissue (fat or muscle) piece-wise normalization method.
Biologically motivated normalization techniques
Allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. It queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.
A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
BioMAJ is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.
BIoMap is a powerful image processing and display software that now supports a wide range of imaging techniques such as MRI, optical imaging, PET, CT, NIRF and MSI. It provides a unified visualization and storage platform and supports the reconstruction of multidimensional data and the display of ROIs.
Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.
Biomarker uses graph Laplacian regularized logistic regression to integrate biological networks into disease classification and pathway association problems
Provides an interface to a growing collection of databases implementing the BioMart software suite, that is a database portal formed by dozens of biological databases spanning genomics, protemics, model organisms, cancer data, ontology information and more. The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries.
This tool is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-database searches that might otherwise require several complicated steps.
Web service provides unified access to several databases housed at EBI/Sanger such as Ensembl Vertebrates, Ensembl Bacteria, Ensembl Protists, Ensembl Metazoa, Ensembl Variation, Ensembl Vega, Uniprot, PRIDE, HGNC & EU Rat Mart.
Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases.
A bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow.
BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills.
BioMaS (Bioinformatic analysis of Metagenomic amplicons)
BioMaster is an integrated database and analytic platform to provide comprehensive information about BioBrick parts.
Biologically Relevant Metals (BioMe) is a web based platform for calculation of various statistical properties of metal binding sites including distribution of coordinate geometry and other descriptive statistics for a metal ion. The underlying database contains for each metal ion: PDB code, structure determination method, types of metal binding chains and names and coordinates of bound ligands, among other details.
Biomedisa is a free and easy-to-use open-source online platform for segmenting large volumetric images.
This package provides a toolset for visualizing longitudinal microbiome data with a horizon plot. A horizon plot provides a compact method to display change in the distribution of microbial taxa over time.
BIOMERO is a tool connecting OMERO, FAIR workflows, and HPC environments for scalable image analysis. It simplifies image processing for microscopy users by integrating data management with advanced analysis and supports collaboration through FAIR workflows.
BioMet Toolbox 2.0 is a web server for genome-wide analysis of metabolism and omics data. BioMet Toolbox exploits the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, and gene set analysis and basic microarray analysis, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.
BioMetAll is a command line application to allow the identification of metal-binding sites in proteins from backbone preorganization.
an interactive workflow for (single cell) omics data interpretation and visualization. BIOMEX BIOMEX is a data analysis platform to facilitate the Biological Interpretation Of Multi-omics EXperiments. BIOMEX is a data analysis platform to facilitate the Biological Interpretation Of Multi-omics EXperiments. The software aims to maximize the value of (single cell) -omics data by removing key bottlenecks in the processing, analysis and interpretation workflow. BIOMEX is free for everyone.
This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
A multi-omics visual analytics workflow for biomolecular insight generation.
BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.
Database of annotated published models is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in this database are annotated and linked to relevant data resources, such as publications, databases of compounds and controlled vocabularies, and this modelling formats can be converted, with some of them being available online to be used directly.
BioModels Parameters is a resource that facilitates easy search and retrieval of parameter values used in the SBML models stored in the BioModels repository.
Set of converters between various modelling formats, there are also some available online to be used directly.
BioModME is an R/Shiny-based web application package for building and simulating dynamic computational models of complex biological systems, offering an intuitive graphical user interface for model development, visualization, and analysis.
BioMThermDB is a collection of thermodynamic and dynamic properties of various proteins and their (aqueous) solutions, extracted from the vast and mostly scattered scientific literature.
Creates classes used in model-view-controller (MVC) design.
In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.
This web server addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult to predict.
The BION-2 web server predicts non-specifically surface-bound ions. Ions are essential component of the cell and frequently are found bound to various macromolecules, in particular to proteins. A binding of an ion to a protein greatly affects proteins biophysical characteristics and needs to be taken into account in any modeling approach.
GUI to assess the genome assembly quality using BioNano data.
Ruhr-Universitaet Bochum, Medizinisches Proteom-Center (MPC)
The BIONDA biomarker database provides structured information on all biomarker candidates published in PubMed articles. There is no limitation to any kind of diseases. To this end, PubMed article abstracts and renowned databases such as UniProt and Human Disease Ontology are used as sources for BIONDA’s database entries. These are acquired automatically and updated regularly using text mining methods. BIONDA is available freely via a user-friendly web interface. As a specific characteristic, BIONDA’s database entries are rated by a scoring approach estimating biomarker reliability.
Multitask learning for biomedical named entity recognition with cross-sharing structure | This repository is a Biomedical Named Entity Recognition model. The code is based on XuezheMax/NeuroNLP2 | Python 3+, PyTorch < 1.0, Gensim >= 0.12.0 | In the root of the repository, first make the tmp directory:
BioNERO is an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction. BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations.
This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
CellDesigner plug-in, is a computer assisted design tool for synthetic biology.
BioNetComp is a Python package for biological network development and comparison. BioNetComp compares two biologial networks from a list of genes/proteins. It provides both an easy-to-use object-oriented Python API and a command-line interface (CLI) for network comparison and post-analysis.
General-purpose fitting program for rule-based models that is compatible with BioNetGen and NFsim.
Software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. It is a software for generating mathematical/computational models that account comprehensively and precisely for the full spectrum of molecular species implied by user-specified activities, potential modifications and interactions of the domains of signaling molecules.
Estimating parameters of a Bio Net Gen Model from time-stamped snapshots of single cells.
Biological Network Analysis is a package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view.
Methods, Applications, and Evaluations. Graph Embedding Evaluation / Code and Datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations". BioNEV (Biomedical Network Embedding Evaluation). This repository contains source code and datasets for paper "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations" (accepted by Bioinformatics). This work aims to systematically evaluate recent advanced graph embedding techniques on biomedical tasks. We compile 5 benchmark datasets for 4 biomedical prediction tasks (see paper for details) and use them to evaluate 11 representative graph embedding methods selected from different categories:. 5 matrix factorization-based: Laplacian Eigenmap, SVD, Graph Factorization, HOPE, GraRep.
BIONIC (Biological Network Integration using Convolutions) is a deep-learning based biological network integration algorithm that incorporates graph convolutional networks (GCNs) to learn integrated features for genes or proteins across input networks.
Cloud environment accessing, managing and analyzing large genomics and phenotypic datasets.
This software is well suited for distances estimated from DNA or protein sequences. It has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages.
A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.
Highly reusable code and tools for bioinformatics by leveraging the Node.JS ecosystem.
A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).
NCBI database tool to search, download and compare databases from NCBI.
Template module to use as base for quickly creating bionode modules.
BionoiNet is ligand-binding site classification with off-the-shelf deep neural network.
Model biological networks and simulate their discrete-time dynamics. It includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions.
BiOnt performs relation extraction using a deep learning system. It employs four types of biomedical ontologies, namely, the Gene Ontology, the Human Phenotype Ontology, the Human Disease Ontology, and the Chemical Entities of Biological Interest, regarding gene-products, phenotypes, diseases, and chemical compounds, respectively.
Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.
Analysis of all major applications in bioinformatics: 1D electrophoresis gels, all kinds of chromatographic and spectrometric profiles, phenotype characters, microarrays, and sequences.
BioPAN is a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS. BioPAN for Bioinformatics Methodology For Pathway Analysis is a tool that allows users to upload their own mammalian lipidomics dataset and perform a pathway analysis.
Software system for estimating the rupture potential index for abdominal aortic aneurysms.
Perl program for parsing sequence similarity analysis reports.
Biological Parts Search Portal and Updates to the ICE Parts Registry Software Platform. Capturing, storing, and sharing biological DNA parts data are integral parts of synthetic biology research.
Web design tool for the design of biological parts for combinatorial assembly. The software is designed to assist synthetic biologists in retrieving biological sequences, design and optimize biological parts for Golden-Gate.
Open-source, modular tool for DNA synthesis workflow and parts registration, ready to be used in most scenarios, such as molecular biology laboratories or iGem teams.
BioPAX is a standard language for representing biological pathway data, enabling integration, exchange, and analysis across databases. It provides a common format to reduce complexity in pathway data interchange.
BioPAX-Explorer is a Python framework designed to facilitate the use of BioPAX data by providing an object-oriented data model and expressive query capabilities, shielding users from the underlying BioPAX complexity.
BioPAX Parser is graphical tool to perform pathway enrichment analysis using BioPAX files. In addition BiP enable user to extract and save pathway information in a tabular format.
An open source and extensible framework for defining and searching graph patterns in BioPAX models.
A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.
BioPETsurv is a web application to evaluate biomarkers for prognostic enrichment of time-to-event clinical trials. BioPETsurv is a suite of methods for estimating these elements to evaluate a prognostic enrichment biomarker and or plan a prognostically enriched clinical trial with a time-to-event primary endpoint. BioPETsurv allows investigators to analyze data on a candidate biomarker and potentially censored survival times
BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.
A wiki-like service that gathers tools written in PHP and edited by registered users to be used for solving biological problems or tasks.
Collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. It works on a data stream in such a way that the data stream can be passed through several different tasks: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.
Framework for genomic data analysis using Apache Pig and Hadoop.
Pipeline for taxonomic classification of microbiome profiles and subsequent diversity analysis, suitable for both WGS and RNA-Seq. Bash and R scripts.
Biomarkers Platform, a user-friendly open-source bioinformatic resource, which provides a set of analytic tools for the discovery and in silico evaluation of novel prognostic and predictive cancer biomarkers based on integration and re-use of gene expression signature in the context of follow-up data.
A repository of protein interaction data from mass spectrometry experiments.
The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R
The BioplexPy package provides access to PPI data from Gygi lab. It fetches protein interaction data and offers a simple and intuitive API for Analysis.
Library of C routines for general programming and handling protein structure
BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.
Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.
Suite of benchmark problems for dynamic modelling in systems biology.
Collection of biological data related to a single initiative, originating from a single organization or from a consortium. A record provides users a single place to find links to the diverse data types generated for that project.
Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.
BioProtIS is a pipeline for streamlining protein-ligand interaction analysis, integrating molecular dynamics and docking to automate workflows at genomic and transcriptomic scales. It leverages open-source tools to facilitate docking and incorporates modular design for user customization.
Bioptim is a Python framework for musculoskeletal optimal control in biomechanics.
An open-source and easy-to-use Python platform for offline neurophysiological signals processing and classification.
Framework for developing an online genomics application.
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
Quality control of high-throughput expression data based on tissue gene signatures.
Biological Repository is a toolkit and set of catalogs to retrieve genomic annotation for variants, genes, diseases, conditions, genetic tests, and drugs.
The design for a novel, open source, low-cost bioreactor for load-controlled cyclic loading of tendon explants.
a biomedical relation extraction dataset (BioRED) with multiple entity types (e.g. gene/protein, disease, chemical) and relation pairs (e.g. gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts.
An open source, community curated registry, meta-registry, and compact identifier resolver
A set of tools that allow for data integration while protecting patient privacy. This modular approach allows data and specimens to be associated with a biorepository subject at any time point asynchronously.
An R Package for Analyses of Bioassays and Probit Graphs.
A bioinformatics software for the Ruby programming language. The toolkit contains a set of free development tools and libraries for bioinformatics and biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.
Bios2cor is an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins.
This database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.
BioSANS is a free software for systems biology which is currently being developed in Academia Sinica Institute of Chemistry.
Biosaur is an open‐source Python software for liquid chromatography–mass spectrometry peptide feature detection with ion mobility support.
OmicsSuite (https://omicssuite.github.io, https://github.com/OmicsSuite/), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multi-omics (transcriptomics, genomics, protein omics, metabolomics, single cell), microbiology, clinical, etc.
This service provides operations to (i) obtain synonyms for protein names from a number of sources (ii) provide uniprot identifiers for the input.
an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches | BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches | : Home : Server : Tutorial : Document : Download : Citation : Contact us : | Established in 2017, the platform BioSeq-Analysis (1) is for the first time proposed to analyze various biological sequences at sequence-level based on machine learning approaches, which can do the following main steps automatically: feature extraction, predictor construction, and performance evaluation. BioSeq-Analysis has been increasingly and extensively applied in many areas of computational biology
Platform for analyzing DNA, RNA and protein sequences based on biological language models.
Biological sequence similarity analysis using Diabolo.
Extracting Features from Biological Sequences and Building Classification Model.
BioSequenceAssembler is intended for use by biologist and laboratory technicians who are responsible for managing next-generation genomic sequencing data for alignment, assembly, and/or BLAST identification.
BioSeqZip is a tool for performing exact collapsing of Second-Generation Sequencing datasets.
BioServices is a Python package that provides programmatic access to many Bioinformatics Web Services (e.g., UniProt, EUtils, ENA, UniChem, etc) and a framework to easily implement new Web Service wrappers (based on WSDL/SOAP or REST protocols).
BioShell is a suite of command line tools and a library for structural bioinformatics.
Webserver for protein homology detection. Homology detection is based on sequence profiles and secondary structure profiles.
Small collection of functions that I developed for processing and analysis of biological signals.
This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.
BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.
Cheminformatics tool that uses known mammalian biochemical compounds (scaffolds) and graph matching methods to identify biochemical structures in chemical structure space.
An Open source library that enables to build bioinformatics scripts and applications using Smalltalk programming environment, which is designed for users with little or no experience in programming.
BIOSMILE is a web-based NCBI PubMed search tool. Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts.
BiDesigned and developed as an enhancement to BioSM. It is, on average, 8 times faster than BioSM without compromising the quality of the predictions made. This software will be an extremely useful tool in the timely identification of unknown biochemical structures in metabolomics.
BioSounds is a web application for ecoacoustics that archives and organises soundscape collections, hosts reference recording collections, generates navigable sound spectrograms, and allows annotation of animal vocalisations or other sounds.
Comparison of mass spectrometry spectra.
Palacký University Olomouc, Czech Republic
Biospytial is a modular open source knowledge engine designed to import, organise, analyse and visualise big spatial ecological datasets using the power of graph theory. It handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. The engine uses a hybrid graph-relational approach to store and access information. The data are linked with relationships that are stored in a graph database, while tabular and geospatial (vector and raster) data are stored in a relational database management system (RDBMS). The graph data structure provides a scalable design that eases the problem of merging datasets from different sources. The linkage relationships use semantic structures (objects and predicates) to answer scientific questions represented as complex data structures stored in the graph database.
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
A basic matlab toolkit for analysis protein structure
The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
Management of patients information and the analysis of peptide profiles from mass spectrometry.
A web tool for the superimposition of biomolecules and assemblies with rotational symmetry.
BioSurfDB is a online database for biodegradation and biosurfactants.
Contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures.
BioSWITCH iis a command-line program using the BioPAX standardised language to “switch on” static regulatory networks so that they can be executed in GINML to predict cellular behaviour. Using a previously published haematopoiesis gene network, we show that BioSWITCH successfully and faithfully automates the network de-coding and re-coding into an executable logical network. BioSWITCH also supports the integration of a BioPAX model into an existing GINML graph.
Syntax highlighting for computational biology to bring you intuitively close to your data. BioSyntax supports .sam, .flagstat, .vcf, .fasta, .fastq, .faidx, .clustal, .pdb, .gtf, .bed files & more.
biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads
Database that centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other type.
BioTAGME framework which combinesTAGME annotation framework based on Wikipedia corpus, with DT-Hybrid methodology.
Interactive tool for building, visualizing, and simulating genetic regulatory networks. It is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time.
A user friendly tool to perform transcript expression analysis
Interactive guide of commercial lectins for glycobiology and biomedical research applications.
The biotext library offers resources to support text mining strategy using bioinformatics tool.
Implements an enhanced version of the TextQuest algorithm, providing a user friendly web-based interface. BTQ collects abstracts from Medline literature and OMIM databases matching a user query. Identification of relevant terms enables the representation of text records in a Vector Space Model and the calculation of pairwise document similarities. Employing suitable clustering algorithms, results are transformed into clusters of records along with their corresponding terms.
BioTherapi : Bioinformatics for Therapeutic Peptides and Proteins. This include all the relevant information about the use of Peptides/Proteins in drug and synthesis of new peptides. It also cover problems, in their formulation, synthesis and delivery process.
BioThings is a toolkit for building high-performance data APIs in biomedical research. BioThings SDK provides a Python-based toolkit to build high-performance data APIs (or web services) from a single data source or multiple data sources. It has the particular focus on building data APIs for biomedical-related entities, a.k.a "BioThings" (such as genes, genetic variants, drugs, chemicals, diseases, etc.)..
Query engine for a federated knowledge graph of biomedical APIs.
Pipeline for taxonomic classification outperforming standard Kraken2 application, including control of false-positive detection of microbial taxa
BioTIP: an R-package for Characterization of Biological Tipping Points.
A comprehensive library for computational molecular biology
This package facilitates the discovery of biomarkers from biological sequencing data based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of parameters defined via causal inference whose estimators admit asymptotically linear representations.
A rule-based checker for the bio.tools database.
BioTracs is a transversal framework for computational workflow standardization and traceability. The BioTracs project aims at providing an open community-driven analytics platform. It is an effort for standardizing the implementation and traceability of analytics workflows in bioinformatics.
The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.
Biotrainer is an open-source tool to simplify the training process of machine-learning models for biological applications.
BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.
BioTranslator performs semantic interpretation of genomic data, using pathway analysis and gene prioritization approaches The tool is available at: http://www.biotranslator.gr:8080/ http://motherbox.chemeng.ntua.gr/anastasia_dev/
BiotXplorer is a service dedicated to highlight biotic interactions between species in literature.
Open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data.
BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs.
JSON payloads and ontologies become widely adopted in the life science community, validation of ontologies described in JSON documents becomes ever more important. ELIXIR biovalidator is a custom extension to existing JSON Schema syntax to include ontology validation and an implementation based on the Ajv javascript library
BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.biovenn.nl.
System that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications.
BioViz Connect is a web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser.
BioViz Connect, a middleware Web application that links CyVerse science gateway resources to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the user’s personal computer.
This package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization, saving development effort and encouraging consistency.
A system to analyze multi-omics cancer tissue intratumor heterogeneity and connect to cancer cell lines on user's Amazon cloud computing environment.
Biological visible neural network (BioVNN) is a tool to predict cancer dependencies using pathway knowledge.
Powerful biological sequence editor operating in the most convenient of places: inside your usual word-processor (Microsoft Word 2007 and 2010). Easy to install and embedded into a Microsoft Office Ribbon, BioWord allows instant access to most sequence manipulation and editing needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery.
Search engine for popular or influential open access papers in Life Sciences that supports visualization of publication analytics.
Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces.
A web interface to predict sequence elements embedded within unaligned sequences. Either a bipartite model, consisting of a pair of one-block position weight matrices with a gap distribution, or a single PWM matrix for contiguous single block motifs may be produced. It performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy.
BiPOm is a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.
Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.
The web server where you can predict putative interactions between proteins based on homologs found in Protein-Protein interaction databases. It relies on data integrated in BIANA. You just need to insert your sequences of interest or list of protein identifiers, and the tool will infer interactions based on homology. Predicted partners can be restricted to proteins added in your list or to the complete BIANA database.
BIPS (Build Phage ImmunoPrecipitation Sequencing library) is a software that converts a list of proteins into a custom DNA oligonucleotide library for the PhIP-Seq system. The tool creates constant-length oligonucleotides with internal barcodes, while maintaining the original length of the peptide.
BIPSPI (xgBoost Interface Prediction of Specific Partner Interactions) is a partner specific binding site predictor that employs the XGBoost algorithm
BiQ Analyzer is a software tool for visualization and quality control of DNA methylation data from bisulfite sequencing.
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives
BiQ Analyzer HT is an enhanced version of BiQ Analyzer that supports locus-specific analysis and visualization of high-throughput bisulfite sequencing data.
Bi-channel image registration and deep-learning segmentation (BIRDS) is a tool for efficient, versatile 3D mapping of mouse brain. It is an open source automation pipeline suitable for brain data from different microscopy platforms.
Comprehensive life histories for all bird species and families.
Fast functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.
A computational method BiRGRN to infer GRNs from time-series scRNA-seq data.
Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. The tool uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.
This tool uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.
A package based on the Genome Analysis Toolkit map-reduce framework for genotyping in bisulfite treated massively parallel sequencing on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously.
Analysis of co-evolving amino-acid pairs in protein alignments, especially designed for vertebrate and viral protein families, which typically display a small number of highly similar sequences. It is based on BIS2, a re-implemented fast version of the co-evolution analysis tool Blocks in Sequences (BIS).
Binding sites analyser is a database driven software and stores all of its data in a relational database management system (RDBMS) such as SQL Server in Windows or PostgreSQL on Linux.
Bisbee is a pipeline that perfoms differential splicing analysis, splicing outlier analysis, and splice isoform protein sequence prediction. Each of these analysis steps may be run independently or may be combined into a pipeline using the workflows below. Bisbee also provides utility scripts for extracting data, annotating, filtering and summarizing results. Bisbee has been developed and tested using splice variant detection data from SplAdder.
Protein-protein interaction (PPI) database linking up structural biology and functional genomics researchers. It offers users (i) a structural perspective and related information about binary subcomplexes that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.
BISCAP (Biofilm Imaging and Structure Classification Automatic Processor) a high-fidelity strategy for the automatic processing of 2D OCT biofilm.
Script for determining homozygous and heterozygous positions from an alignment using binomial probabilities from a predicted error rate (BiSCaP) and a method to benchmark the accuracy of this and other alignment/SNP-calling methods (cFDR).
BiSCoT (Bionano Scaffolding Correction Tool) is a tool that aims to improve the contiguity of scaffolds and contigs generated after a Bionano scaffolding. It looks for enzymatic labelling sites on contigs. If two distinct contigs share labels, BiSCoT merges them at the last shared site.
An efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.
Suite of tools for generating equations and associated computer programs for simulating biochemical systems.
This package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
BISG (BIclustering based Survival-related Gene sets detection) is a method for detecting cancer survival related gene markers based on rectified gactor network.
The BiSim Tool is a user-friendly simulation tool designed to aid in the design and development of ligand-binding assays (LBAs). It facilitates exploring parameter combinations and understanding the dynamic equilibrium of free and bound fractions, ultimately saving time and resources during assay development.
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2.
The Biological Sequence Exchange is a bioinformatics tool enabling locus and variant-specific conversion among human gene, transcript, and protein identifiers from several popular databases.
BiSSAP is a computer program designed to facilitate the creation of sequence listings for patent applications containing biological sequences (see Rule 30 EPC, Rule 5.2 PCT, and the Decision of the President and Notice from the EPO dated 28 April 2011 (OJ EPO 6/2011, 372 ff.)).
Software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data. Compared with other published tools, it provides greater sensitivity for mCs with fewer false positives, more precise estimates of mC levels, more exact locations of DMRs, and better agreement of DMRs with differentially expressed genes. The superior accuracy is maintained under various sequencing depths and tissue types.
Bit-Table Based Biclustering and Frequent Closed Itemset Mining in High-Dimensional Binary Data. Method to find both frequent closed itemsets and biclusters in high-dimensional binary data.
Bit-Table Based Biclustering and Frequent Closed Itemset Mining in High-Dimensional Binary Data
BiteNet is a computational approach for the large-scale detection of protein binding sites that considers protein conformations as the 3D-images, binding sites as the objects on these images to detect, and conformational ensembles of proteins as the 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding sites in G protein-coupled receptors.
BITES: Balanced Individual Treatment Effect for Survival data is a package for counterfactual survival analysis with the aim to predict the individual treatment effect of patients based on right-censored data.
Efficient reads mappers for short reads of equal length. It is designed to output all mapping locations for each reads.
BitMapperBS is an ultra-fast and memory-efficient aligner that is designed for WGBS reads from directional protocol.
A bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. This method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights.
A Graph-Based Approach to the Quality Threshold Clustering of Molecular Dynamics.
A CNN-Transformer combined model, called BiTr-Unet, with specific modifications for brain tumor segmentation on multi-modal MRI scans
Bayesian inference of Tumor clonal Tree by joint analysis of Single-Cell SNV and CNA data
This package is targeted for transcript expression analysis and DE analysis of RNA-seq data in a two-stage process. In the first stage it uses Bayesian methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage embraces the DE analysis of transcript expression by providing expression estimates from replicates of multiple conditions.
The aim of BitterDB database is to gather information about bitter-tasting natural and synthetic compounds, and their cognate bitter taste receptors (T2Rs or TAS2Rs).
Classifier which predicts whether a compound is bitter or not, based on its chemical structure.
Bivartect is a simple yet versatile variant caller based on direct comparison of short sequence reads between normal and mutated samples. Bivartect can detect not only single nucleotide variants but also insertions/deletions, inversions and their complexes.
An R package for the nonparametric and semiparametric analysis of bivariate alternating recurrent events.
Optimal gap-affine alignment in O(s) space.
BKMS-react is an integrated and non-redundant biochemical reaction database containing known enzyme-catalyzed and spontaneous reactions. Biochemical reactions collected from BRENDA, KEGG, MetaCyc and SABIO-RK were matched and integrated by aligning substrates and products.
Utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).
BlaCaSurv is a web application for predicting the suvival probability.
BLAS Accelerated Motif Matching or blamm is a tool to find Position Weight Matrix (PWM) occurrences in DNA sequences.
Blannotator is a rapid tool for functional prediction of gene or proteins sequences. The tool accepts DNA or protein sequences, given in FASTA-format, and performs a Blast homology search against UniProtKB databases. Matching sequences with similar annotations are merged into families of similar descriptions, which are, in turn, further unified, based on assigned GO-profiles retrieved from GOA, into sets of functionally equivalent sequences. As a result, a reliable description will be obtained.
The blantyreESBL R package is a repository for data generated as part of a study into carriage of resistant bacteria in Blantyre, Malawi
Software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.
A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
A tool capable of filtering NCBI BLAST results with user-defined constraints.
BLAST-QC is a tool for automated analysis of BLAST results. It is a quality control filter and parser for NCBI BLAST XML results.
Blast2Fish is a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. It is a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data.
blast2galaxy is a Python package providing a CLI and API for performing BLAST+ and DIAMOND searches on Galaxy servers. It allows users to leverage the Galaxy API for sequence alignments and is available through package managers like Bioconda and Docker.
Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation.
Tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
Returns the list best hits from a list of BLAST results.
BLAST database focused on the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences.
Find regions of sequence similarity and alignments between a query sequence and database sequences.
This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits.
BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs
Tool that aims at displaying in a graphical way results from the NCBI BLAST software.
Uses NCBI Blast to align nucleotide sequences that have large indels or are difficult to align globally. It selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment. Alternatively, the user can choose which sequence to use as an anchor. It also outputs a matrix representing regions of homology along the sequences.
BlastFrost is a highly efficient method for querying 100,000s of genome assemblies. BlastFrost builds on the recently developed Bifrost, which generates a dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants.
New tool for computing intensive approximate pattern matching in a sequence graph or a de-Bruijn graph. Given an oriented graph and a set of query sequences, it detects paths in the graph on which query sequences align at most at the given edit distance.
BlastGUI is A Python-Based Cross-Platform Local BLAST Visualization Software. Users can build databases and perform sequence filtering and sequence alignment through a graphical user interface. The operation visualization, automatic sequence filtering, and cross-platform use can significantly facilitate the analysis of biological data and the mining of biological information.
BlastKOALA (KEGG Orthology And Links Annotation) is a KEGG Web service for annotating genomes and understanding organisms.
Modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
Recursive psi-blast against the ProDom database.
A new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. We have shown that this approach has better sensitivity and specifity than other softwares with comparable computational cost.
Convert BlastXML results into GFF3 format.
This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers.
Fast, accurate spliced alignment of DNA sequences.
Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE.
A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis.
BLoom-filter-based Error correction Solution for high-throughput Sequencing reads is a novel algorithm that produces accurate correction results with much less memory compared with previous solutions.
Basic Long-read Enabled Toolkit for Interspersed DNA Elimination Studies (BleTIES) is a tool for prediction and targeted assembly of internally eliminated sequences (IESs) in ciliate genomes, using single-molecule long read sequencing. The design and name of the software was inspired by ParTIES.
A Python package for integrating BioLector microcultivation devices in the Design-Build-Test-Learn cycle.
Blight is an associative data structure, similar to a hashtable, able to index a kmer set. It associates each kmer with a unique identifier and can identify alien kmers (kmer absent from the index) associated with the identifier -1. The kmer identifiers are in[0, N[ where N is the number of kmer in the index. Hence, one can see Blight as a Minimal Perfect Hash Function (MPHF) that handle alien kmers.
Includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level, methods for data summarization and t-test performance.
BLIMP: Software for Best Linear IMPutation
Server for performing blind docking calculations. Unique approach where user only inputs ligand and protein, and where the whole protein surface area is processed in order to find potential ligand interaction spots. Main application case can be found at: https://www.nature.com/articles/s41589-019-0278-6
Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.
Parallelised Computing for Big Linear Mixed Models. Within neuroimaging large-scale, shared datasets are becoming increasingly commonplace, challenging existing tools both in terms of overall scale and complexity of the study designs. As sample sizes grow, researchers are presented with new opportunities to detect and account for grouping factors and covariance structure present in large experimental designs. In particular, standard linear model methods cannot account for the covariance and grouping structures present in large datasets, and the existing linear mixed models (LMM) tools are neither scalable nor exploit the computational speed-ups afforded by vectorisation of computations over voxels. Further, nearly all existing tools for imaging (fixed or mixed effect) do not account for variability in the patterns of missing data near cortical boundaries and the edge of the brain, and instead omit any voxels with any missing data
An algorithm for Fluorescent microsphere detection. BlobFunct uses RGB-image, isolates tissue and detects microspheres. Final detection can be used to calculate bloodflow to brain region.
Visualisation, quality control and taxonomic partitioning of genome datasets.
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.
detect blocks of overlapping reads using a gaussian-distribution approach
Web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments.
Tool for accurate polishing of long-read assembly via block divide-and-conquer
The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.
A tool for fast multiple structure alignment. The main difference of BLOMAPS from other existing algorithms for multiple structure alignment is the use of conformational letters, which are discretized states of 3D segmental structural states.
Blood cells tracking and measurement by using spatiotemporal images analysis
Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach | The exposome represents the sum of all exposures during the life-span of an organism (from chemicals to microbes, viruses, radiation and other sources)
A blood glucose model of type-1 diabetics.
Control blood sugar levels by adjusting insulin injection pump rate
Blood Glucose Regulation in a Type-I Diabetic in Simulink
Blood vessel segmentation in retinal images using mathematical morphology
BloodGen3Module: Modular Repertoire Analysis and Visualization. The package provides functions for R users to perform module repertoire analyses and generate fingerprint representations.
BloodGen3Module is an R package for blood transcriptional module repertoire analysis and visualization and generating fingerprint representations.
An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference.
Tracking and diameter estimation of blood vessels using Gaussian process and Radon transform
Blood vessels tracking and diameter estimation using Gaussian process
Blouch is a software tool that implements Bayesian linear Ornstein-Uhlenbeck models for comparative hypotheses, allowing for the estimation of adaptation and phylogenetic inertia in trait evolution. It provides a Bayesian framework incorporating measurement error and allowing for varying effects and multilevel modeling.
Aa script for mining data from BLAST reports. Allows you to specify e.g. an E-value cutoff, a length cutoff and a percent identity cutoff, and extract a list of the hits satisfying these cutoffs.
Python implementation of BoundLess Objective-free eXploration (BLOX)* for discovery of out-of-trend materials using Stein novelty.
Flexible pipeline for haplotype analysis of multiple linked-read technologies. The BLR pipeline is end-to-end Snakemake workflow for whole genome haplotyping and structural variant calling from FASTQs, independent of LongRanger.
Exhaustive comparative discovery of conserved cis-regulatory elements.
Fast, accurate short-read error-correction tool based on k-mer consensus and context. It will correct both Illumina and 454-like data, and accepts sequence data files in both FASTQ and FASTA formats.
Blue Light is a browser-based medical image viewer is primarily maintained by the Imaging Informatics Labs.
An R package and shiny toolkit for comprehensive genetic data analysis in animal and plant breeding.
BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding.
BLUR (BLast Unexpected Ranking) is a tool designed to highlight, on the whole proteome level, protein divergences between species that result from divergence or loss of a domain and/or motif in a specific taxon. It is based on precomputed BLAST searches for a variety of model organism queries, allowing the study of all major life groups.
Electrostatic properties of proteins based on generalized Born radii.
BLVector is a fast BLAST-Like Aagorithm for multicore CPU with vectorization. BLVector produces a list in a similar way than BLAST. BLVector provides a score based on the result of a Smith-Waterman algorithm with affine gaps which is the result of applying a score matrix like BLOSUM62 or PAM30.
BM-BC is a Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the accuracy of the base calls: fading, phasing, and cross-talk between channels.
Bayesian hierarchical model for the inference on the differential gene expression based on RNA-Seq data
Bmap is a tool for efficient and error-tolerant sequencing read mapping.
Fragment-based drug design and compound binding evaluation. Boltzmann Maps provides you, a drug researcher, with tools to design and prioritize small molecules in pre-clinical drug discovery.
The BMAT software is a complete and easy-to-use local open-source neuroimaging analysis tool with a graphical user interface (GUI) that uses the BIDS format to organize and process brain MRI data for MS imaging research studies.
A webtool to identify and analyze bacterial microcompartment types in sequence data.
Probability results are informed plus recall, precision, F factor, G factor, correlation and kappa.
BMDx is a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data.
Bipartite Motif Finder (BMF) is a tool for finding multivalent sequence motifs and their distance dependency in RNA (or DNA) sequences.
Block Mapping and Gathering using Entropy.
A Bayesian framework for multiple genotyping platforms detection of copy number variants.
B-MIPT is a tool using Image Processing and Genetic Algorithm to study the rate of expression of both the proteins in the placenta.
Web server for bipartite motif discovery.
The BiomotionLab Toolkit for Unity Experiments (bmlTUX) helps you design and run experiments in Unity quickly and iteratively without fussing over coding details. The toolkit includes tools to aid in both the design and the execution of experiments in Unity. The toolkit is designed to simplify the setup and reduce the required code needed to get experiments up and running quickly. The toolkit can automatically handle the difficult task creating trial tables, combinatorics randomization, blocking, etc. Such functionality removes one of the most difficult aspects of creating experiments.
Bayesian phylogenetic site model averaging and model comparison.
The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) is a repository for data from NMR Spectroscopy on proteins, peptides, nucleic acids, and other biomolecules.
Bootstrapping Markov Random Field is specifically designed for subnetwork identification by integrating gene expression data and protein-protein interaction data.
Finds, compares, and chooses existing data models, formats, and guidelines, and in particular to promote the use of standards. Quickly shortlist suitable data elements, entities and models either using a simple Google search or by uploading an example data file and ask the system to shortlist data models that provide the most mappings. The registry includes provenance details, links to relevant publications and key contact information, next to the description of model entities and attributes.
BMSS2 is a unified database-driven modelling package for systematic model selection and identifiability analysis.
BMT is a bioinformatics mini toolbox for comprehensive DNA and protein analysis.
Best Match Tagger for removing contaminant reads from metagenomics datasets
The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models.
A variational autoencoder method for clustering single-cell mutation data.
BNA contains some C++ and PERL programs that are useful for studying biological networks, especially protein interaction networks and gene coexpression networks.
Tools to normalize (several) Hi-C data from replicates.
Bayesian negative binomial regression for differential expression with confounding factors
New balanced network deconvolution algorithm to identify optimized dependency matrix without limit on the eigenvalue range in the applied network systems. The algorithm was used to filter contact predictions of five widely-used co-evolution methods.
BnpC is a non-parametric method to cluster individual cells into clones and infer their genotypes based on their noisy mutation profiles. BnpC employs a Chinese Restaurant Process prior to handle the unknown number of clonal populations. The model introduces a combination of Gibbs sampling, a modified non-conjugate split-merge move and Metropolis-Hastings updates to explore the joint posterior space of all parameters. Furthermore, it employs a novel estimator, which accounts for the shape of the posterior distribution, to predict the clones and genotypes.
Steady-state analysis of Boolean molecular network models via model reduction and computational algebra
The Body Network Simulator (BNS) Framework is a WBAN realistic simulation framework.
BoaG is a language and an infrastructure for deeper analysis of the public genomics databases. The BoaG database is a domain-specific language and shared data science infrastructure for genomics, along with a CD-HIT clustering of all these protein sequences at different sequence similarity levels.
BoardION is an interactive web application for real-time monitoring of ONT sequencing runs. BoardION is dedicated to sequencing platforms, the interactive interface of BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the generated data during the experiment. It also enables the comparison of several flowcells to evaluate the library preparation protocols or the quality of input samples.
BOAssembler is a framework that enables end-to-end automatic tuning of RNASeq assemblers, based on Bayesian Optimization principles.
Web interface to the base of bioisosterically exchangeable replacements.
BOTTLENECK BROKEN TOOL is a software for prediction of cis-regulatory motifs in a given set of promoter sequences.
This software allows for requests of up to 1 protein sequence at a time for better predictive performance.
Modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.
R package and Shiny application designed to generate anatomical visualizations of cancer lesions.
A software tool for highly efficient, lossy compression of RNA-seq alignments.
The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials.
Bollito is a Snakemake pipeline that performs a comprehensive single-cell RNA-seq analysis, covering both the basic steps (QC, alignment, quantification and cell specific QC) and more advanced downstream analyses (clustering, diferential expresion, trajectory inference, functional analysis and RNA velocity).
Bolotie is a tool for detecting recombinations in viruses using large data sets with high sequence similarity. Bolotie is a new algorithm designed to conduct mutational analysis and to detect recombinant forms and other anomalies among a very large set of viral sequences. methods implemented in Bolotie are designed such that novel sequences can also be analyzed efficiently without the need to rerun the entire protocol.
BoltzMatch is machine-learning-based peptide-spectrum-matching scoring method for spectrum identification in tandem mass spectrometry, shotgun proteomics. Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics. Authors: Anastasia Voronkova, Pavel Sulimov, and Attila Kertesz-Farkas National Research University Higher School of Economics (HSE), Moscow, Russia.
Machine-learning framework for comparative gene expression analysis across brains and organoids.
BoMiProt is a manually curated, comprehensive repository of published information of bovine milk proteins.
The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.
Software for genetic marker selection and subjects classification from the simultaneous analysis of genome-wide SNP data. It is based on the Naive Bayes classification framework, enriched by three main features: bootstrap aggregating of an ensemble of Naive Bayes classifiers, a novel strategy for ranking and selecting the attributes used by each classifier in the ensemble and a permutation-based procedure for selecting significant biomarkers.
Digital tool for personalized bone health assessment.
BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides free, open source tools for trabecular geometry and whole bone shape analysis. This repository hosts the modern incarnation of BoneJ in development.
Synthesis of Most Permissive Boolean Networks from network architecture and dynamical properties
Bonsai is an algorithm for automatically building pedigrees using identity-by-descent, age, and sex information.
BonZeb is a Bonsai library for high-resolution zebrafish behavioural tracking and analysis. BonZeb provides essential tools for zebrafish behavioural tracking and analysis. In this manual, you will find information and examples for how to use BonZeb to implement behavioural analysis, multi-animal tracking, closed-loop and virtual open-loop visual stimulation, and more. For more information on Bonsai, please check out the forums on Gitter and Google Groups. Behavioural Tracking and Analysis.
A framework for blood type prediction from genotype data.
Bookend is a comprehensive framework for end-guided assembly of short-read, long-read, and end-capture RNA-seq data.
Intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism
Boolink is the open-source software package and GUI for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling. Boolink can simulate user-defined Boolean networks with asynchronous updates. The names of nodes, Boolean connections among nodes, number of time steps for simulation, number of initial conditions are set by the user. The entire network, as well as the activity of any particular node may be visulaized.
Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
Evolution and Controllability of Cancer Networks: a Boolean Perspective.
A python package BOOME, known as BOOsting algorithm for Measurement Error in binary responses and high-dimensional covariates, is used to select informative variables and estimate associated parameters with correction of misclassification in responses and measurement error effects in covariates simultaneously.
Boost is a set of libraries for the C++ programming language that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.
Boost-RS is an innovative general RS framework that enhances RS performance by “boosting” embedding vectors based on auxiliary data.
Inference of differential gene regulatory networks using boosted differential trees.
BoostDM is a method to score all possible point mutations (single base substitutions) in cancer genes for their potential to be involved in tumorigenesis. The method is based on the analysis of observed mutations in sequenced tumors and their site-by-site annotation with relevant features. The compendium of cancer genes and the mutational features for each cancer gene across malignancies have been derived from the systematic analysis of tens of thousands of tumor samples (www.intogen.org). Other relevant features have been collected from public databases.
Spanish Ministry of Economy and Competitiveness
Boosting heritability is a tool for estimating the genetic component of phenotypic variation with multiple sample splitting.
A pipeline for predicting CRISPR-Cas9 cleavage efficiency using feature engineering and LightGBM.
BOOSTNANO is a deep learning tool for preprocessing ONT-Nanopore RNA sequencing reads(before basecalling), it segments/trims the adapter, polyA stall, and the transcription from the raw signal before the basecalling.
An R Package to Derive Confidence Intervals for Combinations of Independent Parameter Estimates. Uncertainty is propagated through by sampling from probability distributions for each estimate and then deriving an empirical interval containing 95% of the resulting distribution (either via highest density interval or quantiles).
BootFam takes as input a set of homologous protein sequences, a species tree, and a sequence-to-species mapping. The output is a set of gene families relative to the species tree.
bootGSEA is a computational pipeline for studying the robustness of Gene Set Enrichment Analysis (GSEA) by performing bootstrap resampling and rank aggregation to combine results from multiple studies or omics levels.
Flexible generation of null sets of genomic ranges for hypothesis testing.
BOPS (Batch OpenSim Processing Scripts) is a Matlab toolbox to batch musculoskeletal data processing for OpenSim.
Tool for generating synthetic next-generation sequencing reads with same nucleotide distribution as model reads.
Borf is a tool for ORF prediction in de-novo assembled transcriptome annotation.
Determination of Bosniak grade for cystic renal masses using MRI.
BOSO, an R package to perform feature selection in a linear regression problem.
Building one-shot semi-supervised (BOSS) learning on CIFAR-10 and SVHN up to attain test accuracies that are comparable to fully supervised learning.
JBoss Data Virtualization is a data integration solution that sits in front of multiple data sources and allows them to be treated as a single source, delivering the right data, in the required form, at the right time to any application and/or user.
Scalable volumetric 3D and 4D database for the cloud.
Is an online platform focuses on providing an up-to-date account of Botryosphaeriales with notes on orders, families and genera and species, keeping abreast of the current literature.
SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.
botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either 'botulinum' or 'tetanus' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.
Bound2Learn is a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments.
BoundedCoalescent is a R package to simulate and compute the probability of phylogenies under the bounded coalescent model. This model is obtained by conditioning the standard coalescent so that the most recent ancestor of the whole sample occurs after a set date.
BounTI is an open-access tool for automatic segmentation of calcified tissues, specifically focusing on craniofacial bones. It utilizes iterative thresholding to preserve boundaries between segments and is available as an Avizo/Amira add-on, a stand-alone Windows executable, and a Python library.
BounTI (boundary-preserving threshold iteration)
Flexible framework to integrate command-line applications in computing platforms.
A deep learning-based software for pose estimation to evaluate nightly behavior and its application to Common Elands (Tragelaphus oryx) in zoos.
BovReg is a project focused on constructing a catalogue of bovine circular RNAs and understanding their origins and functions. It utilizes bioinformatics pipelines and data analysis to characterize circRNAs and identify potential artificial entries.
BOW - Bioinformatics On Windows is essentially a windows port of Linux tools, such as BWA and SAMTOOLS
BOW-GBDT is a GBDT classifier combining with artificial neural network for identifying GPCR–Drug Interaction based on Wordbook Learning from sequences.
A package for analyzing cell velocity from time series of wound healing experiments.
Bowtie is an ultrafast, memory-efficient short read aligner.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Program for creating printouts from multiple-aligned protein or DNA sequences.
RbSP is a tool developed at EBI that integrates GWAS data with protein-protein interaction networks to prioritize proteins involved in blood pressure regulation. The workflow utilizes a Microsoft SQL Server database to store and analyze data from various sources and reconstruct protein interactomes.
An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. You only need to provide the taxa name and the accession code of RNA-seq samples deposited in the National Center for Biotechnology Information (NCBI).
Implementation of a feature detection algorithm for arterial blood pressure.
Data generated through Bioplatforms Australia’s National Framework Initiatives is available via the Bioplatforms Australia Data Portal. The Data Portal API allows programmatic access via the standard CKAN API. The API can be accessed from commonly used programming languages including Python and R.
Predict of transcription factor binding sites based on chromatin accessibility.
A classifier, was developed and trained using Support Vector Machine (SVM) based on the Aac feature extracted using a Bi-profile Bayes model.
A package for Bayesian Paired Comparison analysis with Stan.
Black Pepper Drought Transcriptome Database (BPDRTDb) catalogues all the genomic information like differential expressed genes, microsatellites, variants, transcriptional factors, pathways, domain and families of assembled transcriptome associated with root drought.
This toolkit consists of 5 independent programs, that can be incorporated in a pipeline of various protein structure files. The programs include tools for chirality check for amino acids (ProChiral), contact map generation (CoMa), data redundancy (DaRe), hydrogen bond potential energy (HyPE) and electrostatic interaction energy (EsInE).
BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of biopolymers, BpForms aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. In particular, BpForms was developed to help researchers collaboratively develop whole-cell computational models.
Genome-wide detection of human variants that disrupt intronic branchpoints.
This software provides a platform for running big bioinformatics jobs that consist of a series of processing stages – known as ‘pipelines’.
Base-pairing profile local alignment is a powerful method that evaluates the similarity between a pair of RNAs taking into account secondary structure information. Based on the accurate similarity calculated by BPLA kernel, you can perform a broad range of structural RNA analysis, including family prediction, hierarchical clustering, and remote homology search.
Grid computing framework for enabling large-scale comparative genomics processes.
BPM-Matlab is a numerical simulation tool to efficiently model electric field propagation in a wide variety of optical fiber geometries with arbitrary refractive index profiles even in the presence of bending.
Between-pathway models are network motifs consisting of pairs of putative redundant pathways.
This software is for computing base pair networks found in DNA/RNA. The software also calculates the overlap based network computations.
A database of positive selection projects in ADOPS format.
Program that implements a series of Bayesian inference methods under the multispecies coalescent model. The analyses may include estimation of population size (theta's) and species divergence times (tau's), species tree estimation and species delimitation.
A web-based tool to access and analyse bacterial pesticidal proteins.
BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso
This package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.
Uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.
R package using a probabilistic approach for fully automated database-based identification and quantification of metabolites in local regions of 1H Nuclear Magnetic Resonance (NMR) spectra. The approach is based on a linear mixed model, which accounts for technological characteristics of NMR spectra, and represents the spectra as mixtures of reference profiles from a database.
Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample).
A BRCA1 and BRCA2 copy number alteration caller from Next-Generation sequencing data.
The Brazilian Compound Library (BraCoLi) a repository of chemical and biological information for drug design.
The BReAst Carcinoma Subtyping (BRACS) dataset, a large cohort of annotated Hematoxylin and Eosin -stained images to advance AI development in the automatic characterization of breast lesions.
Package for calculating aggregated isotopic distributions and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm.
MATLAB example using deep learning to classify chronological age from brain MRI images
A MATLAB code for Brain MRI Tumor Detection and Classification
Brain MRI Tumor Detection and Classification
Brain2Mesh is a MATLAB/Octave based 3D mesh generation toolbox dedicated to the creation of high-quality multi-layered brain mesh models.
A database aiming to delineate the genetic components of more than 500 GWAS summary statistics datasets for brain-related traits from multiple aspects.
The Brain Gene Registry is a collaborative repository pairing clinical genetic data with phenotypic data from individuals with variants in brain genes. It aims to accelerate research on neurodevelopmental disorders by providing a centralized resource for data sharing and analysis.
The Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain gliomas in MRI scans to support clinical decision-making in both diagnosis and prognosis.
The Brain Metastasis Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain metastases in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain metastases in MRI scans to support clinical decision-making in both diagnosis and prognosis.
Accessing NHS tissue archives for neuroscience research.
BrainBase is a curated knowledgebase for brain diseases.
Freely-available, biologist-friendly, stand-alone application for exploring the temporal dynamics and genetic control of transcription in the human prefrontal cortex across the lifespan. The BrainCloud applications will contain expression or methylation data, while users will have to register with dbGaP to integrate SNP data.
Database of transcriptomic profiles of human brains of six neuropsychiatric disorders.
Measuring the Intracranial Brain Volume With Fractal Dimension. The validation of the BrainFD software is based on T1-weighted MRI images from the Open Access Series of Imaging Studies (OASIS)-3 brain database, where each participant has multiple MRI scan sessions.
BrainGB is a unified, modular, scalable, and reproducible framework established for brain network analysis with GNNs.
Brain Gene Expression and Network Imputation Engine (BrainGENIE) imputes brain-region-specific gene expression levels from peripheral blood gene expression.
Brain Imaging Analysis Kit (BrainIAK) is a package of Python modules useful for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. BrainIAK applies advanced machine learning methods and high-performance computing to analyzing neuroimaging data. It is tightly integrated with SciKit-Learn, and includes modules for Full Correlation Matrix Analysis (FCMA), Multi-voxel Pattern Analysis (MVPA), a suite of methods for Shared Response Modeling (SRM), Topographic Factor Analysis (TFA), Bayesian-derived methods for Representational Similarity Analysis (RSA), and more.
Fitting Splines to Axonal Arbors Quantifies Relationship Between Branch Order and Geometry.
Brain Network Construction and Classification (BrainNetClass) toolbox to promote more advanced brain network construction methods to the filed, including some state‐of‐the‐art methods that were recently developed to capture complex and high‐order interactions among brain regions. The toolbox also integrates a well‐accepted and rigorous classification framework based on brain connectome features toward individualized disease diagnosis in a hope that the advanced network modeling could boost the subsequent classification.
BrainPainter is a software for the visualisation of brain structures, biomarkers and associated pathological processes.
A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.
A multi-modal neurodata processing software for intracranial stereo-encephalography (SEEG) electrode localization, ictal & inter-ictal data analysis, and cortical surface reconstruction.
brainrender is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set (e.g. Allen Brain atlas) as well as user generated experimental data. The goal of brainrender is to facilitate the exploration and dissemination of neuro-anatomical data by providing a user-friendly platform to create high-quality 3D renderings.
Interactive visual exploration of the spatial and temporal human brain transcriptome.
This package can search and get gene expression data and plots from the BrainStars quantitative expression database of the adult mouse brain, which has genome-wide expression profile at 51 adult mouse CNS regions.
Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology. Our objective is to share a comprehensive set of user-friendly tools with the scientific community using MEG/EEG as an experimental technique. For physicians and researchers, the main advantage of Brainstorm is its rich and intuitive graphic interface, which does not require any programming knowledge. We are also putting the emphasis on practical aspects of data analysis (e.g., with scripting for batch analysis and intuitive design of analysis pipelines) to promote reproducibility and productivity in MEG/EEG research. Finally, although Brainstorm is developed with Matlab (and Java), it does not require users to own a Matlab license: an executable, platform-independent (Windows, MacOS, Linux) version is made available in the downloadable package.
Analysis and automatic identification of dendritic spines using machine learning.
BrainWiki is a Wiki-Style, User Driven, Comparative Brain Anatomy Tool.
Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.
BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
Matlab Simulator of Continuous-time Multi-type Branching Processes in Random Environment with Immigration.
Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.
BRANEart is a fast and accurate method to evaluate the contribution of each residue to the overall stability of membrane proteins and to identify interesting residues to mutate in view of modulating stability.
BraneMF: Integration of Biological Networks for Functional Analysis of Proteins
BRANEnet is a novel multi-omics integration framework for multilayer heterogeneous networks. In particular, it embeds graph-based information from multi-omics data in a lower-dimensional space.
A MS Excel workbook for the analysis and display of rhythmic data series. Many in the circadian biology community use the FFT NLLS suite of programs, to estimate period and phase values from rhythmic experimental data. A user interface is developed to act as a front end to these programs. It imports data from most of the data acquisition packages commonly used in plant circadian research, and from a generic block of data. Then it runs FFT-NLLS on this data, and import the results into MS Excel.
This resource hosts Brassica genome databases. B. rapa genome browser: including comprehensive annotation of the repeat fraction of the genome using the genome viewer GBrowse2. B. oleracea pan genome browser: including SNPs and functional annotation of genes. BlastGbrowse: A portal for blasting a query sequence to B. rapa and B. oleracea pan genome and allow conveniently link hits to the above Genome Browsers.
The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers.
accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Both single and paired ends are supported.
The Biomarker Reliability Assessment Tool (BRAT) was developed to help researchers set targets to improve exposure assessment in studies of chemicals with a short half-life. The BRAT software uses a simple pharmacokinetic model to simulate exposure, internal levels, and resulting urinary levels in individuals from a population based on user-specified inputs (e.g., biological half-life, within- and between-person variability in exposure). Based on internal levels (a toxicologically-relevant exposure metric) and urinary levels in the simulated population, the tool evaluates – through linear regression and quantile classification – the accuracy of the estimation of internal levels depending on the number of urine samples.
BraTS Toolkit is a holistic approach to brain tumor segmentation and consists out of out of three components: First, the BraTS Preprocessor facilitates data standardization and preprocessing for researchers and clinicians alike. It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction. Second, BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. Finally, BraTS Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion
Open-source software for automated electrocardiographic and vectorcardiographic analysis.
BRAVIZ is a software tool that integrates interactive visualization with real-time statistical analyses, facilitating access to multi-facetted neuroscience data and automating many cumbersome and error-prone tasks required to explore such data.
BRowse All Variants Online - Variant Visualization Tool
An integrated software package for the analysis of DNA microarray data.
A software for testing known mutations in BRCA1 and BRCA2 genes from a whole genome sequencing data.
Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases.
Precise identification of breast cancer from expression data using a minimal set of features.
BRCAIndica is a resource providing ACMG/AMP classified variants in BRCA1 and BRCA2 genes. It encompasses over 10,000 variants contributed by clinicians and curated from several sources to enable uniform genomic interpretation.
A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images.
A general semiparametric Bayesian discrete-time recurrent events model | Event time variables are often recorded in a discrete fashion, especially in the case of patient-reported outcomes. This work is motivated by a study of illicit drug users, in which time to drug use cessation has been recorded as a number of whole months. Existing approaches for handling such discrete data include treating the survival times as continuous (with adjustments for inevitable tied outcomes), or using discrete models that omit important features like random effects. We provide a general Bayesian discrete-time proportional hazards model, incorporating a number of features popular in continuous-time models such as competing risks and frailties. Our model also provides flexible baseline hazards for time effects, as well as generalized additive models style semiparametric incorporation of other time-varying covariates
A Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations.
Application for detecting structural rearrangements and indels in short read sequencing data.
BreakFusion is a software that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.
A deep learning method to detect deletion from long reads alignment.
An R/Bioconductor package to localize strand state changes in Strand-seq data | Find breakpoints in Strand-seq data | This package implements functions for finding breakpoints, plotting and export of Strand-seq data | Coverage, DNASeq, Sequencing, SingleCell, Software
Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs.
Database of known human breakpoint junctions and software to search short reads against them.
BreakTrans is a computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events.
Suite of programs that take aligned genomic data and report structural variation breakpoints.
Functions to resize, place, and fuse breast phantoms to a whole-body voxel model
This Code is about Image improvement of breast to show the cancer's cells
The tool takes a digital mammogram and performs an automatic segmentation of the breast area and the dense tissue. After the mammogram segmentation, the tool returns a DICOM-SEG image with both the dense tissue and the breast tissue mask combined.
Instituto Tecnológico de Informática (ITI)
BreastAnalyser is a software designed for the semi-automatic analysis of breast cancer immunohistochemical images, enabling quantification, cell nucleus counting, and annotation. It features a user-friendly interface and is validated for accuracy and usability.
BreastDeformNet is a deep learning tool for predicting non-rigid breast deformations between preoperative and intraoperative configurations. It uses volumetric distance-field representations derived from MRI and surface data to estimate patient-specific displacement vector fields (DVFs). The model enables fast, anatomically consistent deformation estimation to support image-guided breast surgery planning.
BreastImplantAnalyzer is an easy-to-use, validated tool for calculating breast implant volume from MRI data. BreastImplantAnalyzer was designed to be as easy-to-use as possible for plastic surgeons. Using a simple interface, a patient's MRI can be loaded into the application and a semi-automated algorithm will determine the volume of the implant.
Easy and reliable identification of respiration-related artifacts in EDA data (data inspection and cleaning).
BreathXplorer is an open-source Python package designed for processing real-time exhaled breath data generated from high-resolution mass spectrometry. It provides modules for exhalation detection, metabolic feature clustering, and feature alignment.
BREC is R package/Shiny app for an automated, computational and non-genome-specific solution based on the Marey maps method in order to identify eu-heterochromatin boundaries along chromosomes, and provide local recombination rate estimates. This approach allows to determin the location of the centromeric and telomeric regions known to present a reduced recombination rate in most eukaryotic genomes.
Using population-based data to evaluate the impact of adherence to endocrine therapy on survival in breast cancer through the web-application BreCanSurvPred.
Relational database which aims to support breeding for quantitative agronomical traits. The database can be explored through a web-based interface, which offers tools to present basic statistical overviews such as box plots, histograms, but also multivariate tools. The tool is designed to store data from both inbreeding and out-breeding crop species and the analysis and visualization methods adapt automatically to the type of population on hand.
Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high density genotypic information, and provide Genomic Selection related analyses and predictions. Breedbase supports the BrAPI standard.
BREEZE is a web based interactive application for analyzing drug screening data. BREEZE application combines the comprehensive quality control, dose response fitting and calculates the quantitative scoring parameters such as EC50, IC50, drug sensitivity score (DSS) and area under the curve (AUC). The interactive visualizations generated at each step helps the understanding data and exploratory analysis.
BREM-SC is an R package (with core functions jointDIMMSC and BREMSC) for joint clustering droplet-based scRNA-seq and CITE-seq data. jointDIMMSC is developed as a direct extension of DIMMSC, which assumes full indenpendency between single cell RNA and surface protein data. To take the correlation between two data sources into consideration, we further develop BREMSC, which uses random effects to incorporate the two data sources. This package can directly work on raw count data from droplet-based scRNA-seq and CITE-seq experiments without any data transformation, and it can provide clustering uncertainty for each cell.
Internationally leading information system on all aspects of enzymes, including function, structure, involvement in diseases, application, engineering, and molecular properties. The database includes hundreds of milllions of enzyme data and is compiled from manual literature annotation, data integration from other databases and predicted enzyme functions and locations.
BrepConvert is a software developed to identify gene conversion events in immunoglobulin genes, particularly in chickens. It was instrumental in identifying over 1 million gene conversion events, contributing to a better understanding of antibody diversification.
Runs Breseq software on a set of fastq files.
Display reads aligned to the specified region or regions.
Create a coverage plot or table for the specified region.
Brewery uses a suite of ab initio predictors of 1D PSAs. Brewery uses multiple sources of evolutionary information to achieve state-of-the-art predictions of secondary structure, structural motifs, relative solvent accessibility and contact density.
Analyzing high-resolution genomics data in R.
The Biomedical Research Hub (BRH) is a cloud-based and multifunctional web interface that provides a secure environment for discovery and analysis of scientific results and data.
Brain Research Hotspot Database (BRHD) a A comprehensive platform for the latest advances in brain research
Brian2GeNN is a software package that enables the users to make use of GeNN GPU acceleration when developing their models in Brian, without requiring any technical knowledge about GPUs, C++ or GeNN. The new Brian2GeNN software uses a pipeline of code generation to translate Brian scripts into C++ code that can be used as input to GeNN, and subsequently can be run on suitable NVIDIA GPU accelerators.
Monte Carlo (MC) simulation code Brick-CFCMC for phase- and reaction equilibria calculations
Brick Plots is an intuitive platform for visualizing multiparametric immunophenotyped cell clusters. It is a visualisation tool for clustered high dimensional cytometry data.
This package fits a Bayesian hierarchical model for testing DE genes from microarray data, modelling outliers using a t-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing DE genes among multiple samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo.
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) is an open-source web platform developed with the aim to provide an environment for the design of reliable methods to conduct reproducible biomolecular simulations. It is built on the well-known Galaxy bioinformatics platform. Through this, BRIDGE hosts computational chemistry tools on public web servers for internet use and provides machine- and operating-system-independent portability using the Docker container platform for local use.
A graph-based algorithm to analyze dynamic hydrogen-bond networks in membrane proteins.
BRIDGEcereal provides a user-friendly interface to efficiently identify large indels from pan-genomes of major cereal crops, accelerating gene discovery for important traits.
BridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.
BridgeDb is a framework for finding and mapping equivalent database identifiers. It has many facets: it is both a framework, live services, and are identifier mapping files for genes, proteins, and metabolites.
Use BridgeDb functions and load identifier mapping databases in R.
A Novel Graph Neural Network for Predicting Drug-Protein Interactions.
De novo transcriptome assembler for RNA-Seq data. It uses RNA-Seq reads as input in fasta or fastq format, outputs all transcripts in fasta format, without using a reference genome. It works in two steps: First, Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes. Then, it uses a rigorous mathematical model called minimum path cover to search an optimal set of paths.
Bridging Age Gap is a prognostic model that predicts survival and aids in primary treatment decisions for older women with oestrogen receptor-positive early breast cancer. A tool designed to allow for the comparison of breast cancer treatments for older women. The treatments considered within this tool are surgery, primary endocrine therapy and chemotherapy. This tool is designed for use by clinicians with appropriate knowledge of breast cancer and the two types of treatment that are addressed here.
BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
A practical guide to adjust micronutrient biomarkers for inflammation using the BRINDA method. The BRINDA inflammation adjustment method uses regression correction to adjust for the confounding effects of inflammation on select micronutrient biomarkers and has provided important insights to micronutrient research, policy, and programming.
BRIO (BEAM RNA Interaction mOtifs) is a web server designed for searching known sequence and structure protein binding motifs in RNA molecules of interest.
Biomedical Research Software as a Service that enables biomedical & translational researchers to securely manage and combine datasets, typically for patient cohorts. A suite of cloud enabled & integrated open source applications can be accessed in a browser, which make it easier for researchers to manage their studies. Sensitive data can be secured and only accessible to those with permission.
Vast database of protein fragments, clustered on their backbone similarity. It contains fragments from 7290 proteins from the Astral40 set, fragmented in lengths ranging from 4 to 14 amino acids and clustered against 6 different distance thresholds on similarity of the protein backbone. Loop subset contains loop fragments from 14.525 proteins from the Astral95 set, clustered according to end-to-distance and anchor residue superposition.
Algorithm for the identification of broad peaks from diffuse ChIP-seq datasets.
It converts genomics data into DNA k-mer words representing the regions associated with a chromatin mark, and then analyzing these k-mer sets to see how samples differ from each other. This approach is primarily intended for single cell genomics data, and was tested most extensively on single cell ATAC-seq data. The bash scripts in particular may require some alteration for other types of genomics data.
Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations.
Berlin-Tübingen-Oncology corpus (BRONCO) is a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and speculation. The aim of BRONCO is to foster reproducible and openly available research on Information Extraction from German medical texts.
The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.
This software estimates the incubation time and the docking ratio of nanoparticles to a target spot. The results are diagrams about the docking ratio and the incubation time.
Interactvive graphics in a web browser from R, using websockets and JSON.
A BrowserViz subclassing example, xy plotting in the browser using d3.
BRS-nonint (Balanced Random Sampling of Non-interactions) is a method of sampling non-interactions randomly from the complement graph of protein-protein interactions, while the degree of each protein in the ‘positive’ dataset (interactions) equals to that in the ‘negative’ dataset (non-interactions).
BrumiR is a toolkit for de novo discovery of microRNAs from sRNA-seq data using a de Bruijn graph.
Drug-Protein Interaction Prediction by Correcting the Effect of Incomplete Information in Heterogeneous Information.
A versatile aligning pipeline for bisulfite sequencing data.
An ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling.
Bisulfite Sequencing Virus integration Finder.
Mapping tool for bisulfite treated reads.
BSAseq is an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations
A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple.
BiSuflite Bolt (BSBolt) is a fast and scalable bisulfite sequencing processing platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of BWA and WGSIM for read alignment and read simulation respectively. BSBolt is released under the MIT license.
Buffalo Subclinical Mastitis Methylome–Transcriptome database (BSCM2TDb) is a three-tier architecture-based relational database in Water Buffalo.
Provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. Information on the possible types of the mechanical clamps (the motifs which are responsible for a protein's resistance to stretching) are also given.
BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.
A single-cell RNAseq differential expression analysis approach in case-control study
Quality control package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.
The Blazing Signature Filter is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. The algorithm transforms datasets into binary metrics, allowing it to utilize the computationally efficient bit operators and provide a coarse measure of similarity.
A template for parallelization of iterative numerical algorithms on cluster computing systems.
Tool for predicting the binding sites for the given proteins. It is implemented in Java.
Infrastructure shared by all the Biostrings-based genome data packages.
BSHMM is a software of methylation profile analysis using hidden Markov models.
The Biological Structure Model Archive (BSM-Arc) aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. It is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner.
short reads mapping software for bisulfite sequencing
Bi-Similarity Network (BSNet) consists of a single embedding module and a bi-similarity module of two similarity measures. After the support images and the query images pass through the convolution-based embedding module, the bi-similarity module learns feature maps according to two similarity measures of diverse characteristics.
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology.
New method for ligand-protein blind docking using low-resolution protein structures.
Neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids.
Web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. It recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.
A repository for bacterial small regulatory RNA.
A collection of tools for analyzing and visualizing bisulfite sequencing data.
Sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites.
Lightweight, genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data.
BSXplorer is a Python package designed for exploratory analysis of bisulfite sequencing data. It offers tools for creating visualizations, performing comparative analyses, and identifying modules with shared methylation signatures.
The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.
BRENDA Tissue Ontology is a structured encyclopedia of tissue terms. BTO contains different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues.
An algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
Fast and lightweight software to trim adapters and low quality regions in reads.
BTS (Bayesian Tissue Score) is a scalable algorithm designed to identify affected cell types and functional elements in GWAS analyses. It leverages annotation-specific Bayesian models to prioritize variants and provides context-specific fine-mapping.
BtToxin_Digger is a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis. BtToxin_Digger is a Bt toxin mining tool which integrated BLAST, HMM (Hidden Markov Model) and SVM (Supporting Vector Machine) prediction modules.
Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.
Calculate the twisting in a B-DNA sequence.
The aim of BTXpred server is to predict bacterial toxins and its function from primary amino acid sequence using SVM, HMM and PSI-Blast
BTyper3 is a command-line tool for taxonomically classifying Bacillus cereus group genomes using a novel, standardized nomenclature. Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus group with Historical Typing Methods.
Bundle Analytics (BUAN) is a computational framework for investigating the shapes and profiles of brain pathways across populations.
An ontology change tool which is able to analyse two ontologies (typically two versions of the same ontology) to highlight logical changes which have occurred and to present these changes in more or less detail, as required.
Computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row.
BubbleGun is a tool for detecting Bubbles and Superbubble in De-bruijn graphs. BubbleGun outputs runs of bubbles and superbubbles we call bubble chains.
A method for detecting variants directly from next-generation reads without a reference sequence. It uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively.
CNV analysis in groups of tumor samples (Publication Pending).
BUild Connected C-Alphas, Nautical Excuse for Eponym Required performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.
Open-source cheminformatic software platform developed for MS-based metabolomics research.
Collection of four independent, yet interrelated, command line programs that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction.
BufBOSS is a tool for Buffering Updates Enables Efficient Dynamic de Bruijn Graphs.
Tool that performs the unbiased miRNA functional enrichment analysis (Bleazard et al.) requiring significantly reduced excution times (less than 10 minutes for 1 million iterations).
Web application for designing thermodynamically corrected monoprotic buffers used in biological systems, with corrections for the temperature and ionic strength.
A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.
Microarray analysis methods that use BufferedMatrix objects.
A relational database containing microbial gene expression and comparative genomic hybridisation experimental data. The data is mostly derived from whole genome microarrays designed by the BµG@S group, however data from other microarrays is included and the database is being modified to support RNA-Seq analysis. Public access is available for datasets that have been published and login credentials can be obtained for data submission.
BugBuilder is a pipeline for the automated assembly and annotation of microbial genomes from high-throughput sequence data. It is configurable so as not to be tied to any assembler or scaffolder, and is designed to run in a cluster environment facilitating high-throughput processing of genomes.
BugSeq will perform rapid search and classification against our index of bacterial, viral, fungal and protozoal genomes.
Taxonomic binning of metagenomic assemblies enables genome-resolved metagenomics.
BuildAMol is a Python toolkit for fragment-based molecular assembly designed for flexibility and expert-driven model construction. It caters to a broad range of applications, from metal complex generation to integration into drug discovery pipelines.
Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.
Range of bioinformatics tools including Blast, PsiBlast, PhyloTable.
Spatially resolved single-cell deconvolution of bulk RNA-seq using Bulk2Space.
This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide.
Tools for finding bumps in genomic data.
Web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles.
This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).
BUS-GAN is consisting of a segmentation base network - BUS-S and an evaluation base network - BUS-E, is proposed. The BUS-S network can densely extract multi-scale features in order to accommodate the individual variance of breast lesion, thereby enhancing the robustness of segmentation for semi-supervised Segmentation of Tumors from Breast Ultrasound Images with Attentional Generative Adversarial Network.
A benchmark for quantitative evaluation of breast ultrasound segmentation networks with public datasets.
Prediction of protein subcellular localization from sequence
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
A webserver for Busco-Based Phylogenomic Analysis for Non-specialists.
Automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies).
Collection of tools whose goal is to aid researchers in carrying out scientific analyses on a multitude of cloud computing platforms. It concerns itself with providing functionality in four broad areas: Provisioning; Configuration Management; Workflow Management; Operations Management.
Accelerated nanopore basecalling with SLOW5 data format.
Bacterial and Viral Bioinformatics Resource Center (BV-BRC). A resource combining PATRIC, IRD and ViPRA with a suite of command line tools and a web application.
Fast, accurate, memory-efficient aligner for short and long sequencing reads
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
BWA-MEME is a practical and efficient seeding algorithm based on a suffix array search algorithm that solves the challenges in utilizing learned indices for SMEM search which is extensively used in the seeding phase
Probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.
Fast, accurate, memory-efficient aligner for long sequencing reads
Tools and applications for integrative analysis of DNA methylation in social insects.
BWDAT (Binge-watching Data Analysis Tool) is a research tool for analyzing the consumption of video-on-demand content at home.
A package to describe image patterns in natural structures. Describe Image Patterns in Natural Structures. A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure. The facility to obtain high quality digital images creates the opportunity to measure natural variables using image analyses. Bwimage is an R package to analyze patterns in black and white images from natural structures. A computational tool to describe patterns from black and white images
Illustrates the Burrows-Wheeler Matrix (BWM) Transform.
BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments, BWT-SW finds all local alignments.
Command-line utility for bigWig files. BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth).
Tools for manipulating biological data, particularly multiple sequence alignments.
Learning to reconstruct 3D spinal structures from bi-planar X-ray images.
BYASE is a Python package that uses Bayesian inference to identify gene-level and isoform-level ASE (Allele-specific expression) in polyploid (diploid or higher) organisms from single-end or paired-end RNA-seq data.
Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.
Implementation of a new method for inferring branch lengths and site-specific substitution rates from nucleotide sequences. It makes use of the Bayesian Markov Chain Monte Carlo method and of the uniformization (randomization) technique to calculate sequence substitution probabilities in complicated DNA substitution models such as general time reversible model (GTR).
Variant annotation & filtering for any size data.
Web-tool that allows to compute mutation rates from fluctuation assays.
BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures.
C-BIG Repository is an open science resource that promotes scientific research and discovery in neurological diseases and accelerates the development of new treatments.
c-CSN is a script for single-cell RNA sequencing data analysis by conditional cell-specific network.
Software to detect remote/distant homologues from protein sequence databases. It is based on HMMs(Hidden Markov Models) for identifying the deep evolutionary relationships of protein sequences.
C-IMMSIM is an immunoinformatics tool used to predict and simulate immune responses, specifically for the development of broad-spectrum vaccines against viruses like Bluetongue. It integrates protein docking, molecular dynamics, and cytokine response prediction for vaccine design.
The Canadian Open Parkinson Network (C-OPN) is a national initiative connecting Parkinson's disease participants, clinicians, and researchers to accelerate discovery. It provides a database of participant data, including biomaterials such as DNA, PBMC, and serum, accessible through web-based data management systems like REDCap.
C-RNNCrispr is a framework for CRISPR/Cas9 single guide RNA (sgRNA) on-target activity prediction using convolutional and recurrent neural networks.
Webapp written using Vue and d3.js for epigenetic data visualization by biologists.
A System for Predicting Mortality of Patients with COVID-19 Pneumonia at the Time They Require Mechanical Ventilation.
Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched.
C2CDB is a database and platform for cancer-related circular RNAs (circRNAs), integrating information, expression values, biological traits, and molecular mechanisms. It provides analysis tools for miRNA binding, RNA-binding protein interaction, and circRNA biogenesis.
Non-rigid point cloud registration for middle ear diagnostics with endoscopic optical coherence tomography.
A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence | cAb-Rep is a database of curated antibody repertoires. It currently includes 306 B cell repertoires collected from 121 human individuals, including healthy, vaccinated, and autoimmune disease donors. The database has a total of 267.9 and 72.9 million curated full-length V(D)J heavy and light chain transcripts respectively, which were generated using illumina sequencing technology in previous studies. We removed redundancy and sequencing errors in the raw datasets, and annotated each transcript including gene origin, antibody isotype, mutations, post-translational modification, and other characteristics
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
Accurate loop calling for 3D genomic data with cLoops | Accurate and flexible loops calling tool for 3D genomic data | cLoops: loop-calling for ChIA-PET, Hi-C, HiChIP and Trac-looping | Chromosome conformation capture (3C) derived high-throughput sequencing methods such as ChIA-PET,HiChIP and Hi-C provide genome-wide view of chromatin organization. Fine scale loops formed by interactions of regulatory elements spanning hundreds kilobases can be detected from these data. Here we introduce cLoops ('see loops'),a common loops calling tool for ChIA-PET, HiChIP and high-resolution Hi-C data. Paired-end tags (PETs) are first classified as self-ligation and inter-ligation clusters using an optimized unsupervisied clustering algorithm. The significances of the inter-ligation clusters are then estimated using permutated local background
Identification of disease-associated loci using machine learning for genotype and network data integration.
R Tools for Estimating Climate from Vegetation.
R package for accessing microRNA and transcription factor-gene expression correlations in cancer.
C-GWAS is a powerful method for combining GWAS summary statistics of multiple potentially related traits and detect SNPs with multi-trait effects.
CA-Net is a Comprehensive Attention Comvolutional Neural Networks for Explainable Medical Image Segmentation.
a novel end-to-end fully convolutional network, named Class-Aware Attention Network (CAA-Net), for automatically diagnosing infectious keratitis (normal, viral keratitis, fungal keratitis, and bacterial keratitis) using corneal photographs
Contact area-based alignment is a flexible protein structure alignment method based on the residue-residue contact area.
CABEAN is a Software Tool for the Control of Asynchronous Boolean Networks. Combining the two categories, there are six different control strategies. CABEAN provides the following methods to solve the six source-target control problems:.
A Cytoscape 3.2.0 app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness.
A Web Application for the Bioinformatic Analysis of Bacterial Genomes.
CABNet is a category Attention Block for Imbalanced Diabetic Retinopathy Grading
Celera Assembler is scientific software for DNA research.
Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)
Common Access to Biological Resources and Information - A collection of European Biological Resource Centre catalogues.
Efficient procedure for the simulation of structure flexibility of folded globular proteins.
CABS-fold is a web server for the de novo and consensus-based prediction of protein structure. The web server output is a coarse grained trajectory of generated conformations.
A web based (Coronary artery calcification) CAC calculator
Generate server cache file for DAS servers or for the DAS registry.
Generate server cache file for Dbfetch/WSDbfetch data sources.
Generate server cache file for EB-eye search domains.
Generate server cache file for an Ensembl server.
CACHET-CADB is 259 days long contextualised single-channel ECG arrhythmia database from 24 patients recording under a free-living ambulatory setting
Classification of anticancer peptides via deep neural network and skip-gram-based word embedding model.
Cactus is a reference-free whole-genome multiple alignment program.
CACTUS is a tool for integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.
Cancer Antigens Database (CAD) designed to facilitate users to perform a complete exploration of cancer antigens online.
New evaluation function quantifying differences between physical contacts in a model and the reference structure.
CADA (Case Annotations and Disease Dnnotations) is a phenotype-driven gene prioritization tool for rare syndromes. The tool utilizes both disease-level annotations from Human Phenotype Ontology (HPO) and clinical cases-level annotations to construct a gene-phenotype association network. Later, by applying network representation learning method on the network, disease-causing genes are prioritized by a link prediction task. gene prioritization from case annotations and disorder annotations. Web site created using create-react-app. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/genetalk (GENE-TALK.DE)
The purpose of this software, Comparing Alignment results of user Data Based on the relative reliability and advantage of Uniquely aligned REads, is to evaluate spliced aligner performance on user’s RNA-Seq data by comparing a pair of alignment results obtained either from two different aligners with the similar parameter set or from two different parameter sets with the same aligner.
Combined Annotation Dependent Depletion (CADD) - tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.
Cancer Driver Drug Interaction Explorer (CADDIE) It provides an interface for a variety of CADDIEs functionalities, giving the user the possibility to execute tasks on CADDIE programmatically without using the website.
Comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others.
This software simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs.
Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available.
Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures.
Category encoding (CAEN) method is proposed to select feature genes for bulk and single-cell RNA-seq data classification. This novel method encodes categories by employing the rank of sequence samples for each gene in each class. Correlation coefficients are considered for gene and class with the rank of sample and a new rank of category. The highest gene correlation coefficients are considered feature genes, which are the most effective for classifying bulk and single-cell RNA-seq dataset.
CaeNDR, the Caenorhabditis Natural Diversity Resource. CaeNDR enables quantitative genetics and genomics studies across three Caenorhabditis species. The platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CarNDR provides interative tools to explore natural variation and enable GWAS mappings.
Computes the entropy for Cellular Automata
Capillary Automated Footprinting Analysis algorithms. The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping (‘footprinting’).
Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input.
A software suite for analysis of paired-sample transposon insertion sequencing data. CAFE – Coefficient-based Analysis of Fitness by read Enrichments. The R package part of CAFE can be installed in R using the devtools package and: install_github("bengtssonpalme/cafe").
The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
aCcelerated Alignment-FrEe sequence analysis. Compute overall 28 distance/dissimilarity measures including (1) conventional measures based on k-mer counts, (2) newly developed measures based on background adjusted k-mer counts, and (3) measures based on presence/absence of k-mers.
CAFEH is a method that performs finemapping and colocalization jointly over multiple phenotypes. CAFEH can be run with 10s of phenotypes and 1000s of variants in a few minutes.
Client-based Application for Fast Electrophoresis Simulation (CAFES) a client-side web-based simulator for complex electrophoresis phenomena, including isotachophoresis.
Scientific abstracts annotated across different food semantic resources.
An scRNA-seq data clustering method based on cluster-aware feature weighting. Useful for scRNA-seq data analysis.
caffsim is a R package for simulating plasma caffeine voncentrations by using population pharmacokinetic model.
Database for cancer-associated fibroblasts related genes and their functions in cancer.
CAFTOOLS comprises a set of libraries and programs for manipulating DNA sequence assemblies using CAF files, a comprehensive representation of a sequence assembly as a text file.
iCageCavityCalc is a Python-based tool for calculating the cavity size of molecular cages. It utilizes a novel algorithm that enables rapid calculations and facilitates visualization of results, and is designed to streamline cage cavity calculations.
Mapping genes for calcium signaling and their associated human genetic disorders.
Computational analysis of gene expression evolution.
It is an R/Bioconductor package for performing a wide range of common CAGE data analysis tasks. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, calculation of TSS shapes and quantification of CAGE expression as expression matrices.
R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks.
Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).
R package that facilitates the detection and visualization of changes in the relative transcription from promoter regions in multi-promoter genes, all in the context of overall gene expression. Multiple samples can be compared simultaneously.
Freeware comparative analysis package to find and calculates phylogenetically independent contrasts in one or more variables enabling you to test hypotheses of correlated evolution.
A comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Stochastic simulation tool for gene regulatory networks
A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing-
Bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
CALANGO is a first-principles, phylogeny-aware comparative genomics package to search for annotation terms (e.g Pfam IDs, GO terms or superfamilies), formally described in a dictionary-like structure and used to annotate genomic components, associated with a quantitative/rank variable (e.g. number of cell types, genome size or density of specific genomic elements).
CalCEN is a comprehensive and unbiased coexpression network for C. albicans.
A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. Each query is passed to the semantically-annotated tools repository, and based on similarity matches, it ranks the available resources.
This is for calcification reduction from left coronary artery.
Calcifications Attenuation in Left Coronary Artery CT Images Using FDA Domain
Automated characteriztion of single and multi-peaked transient calcium responses from time series data. Signals are decomposed into drift and response components and the entirety of the signal is reconstructed using a mathematical model of a transient response and drift. Measures time of onset, activation time (10% to 90% of total amplitude),amplitude of response, full width at half maximum, decay time constant.
Given two genomes, find the shortest sequence of 2-Breaks transforming one genome into another
Calculate number of cycles in genetic 2-Break distance problem
Calculation of CT MTF and NPS using the ACR accreditation phantom. This code enables measurements of CT MTF and NPS from images of an ACR accreditation phantom.
CalcUS is a quantum chemistry plateform. It strives for simplicity, clarity and efficiency. It brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
A tool for finding all significant de Bruijn subgraphs for bacterial GWAS.
The web-server was developed to identify cancerlectin based on the sequence information.
Open source visual analysis framework targeted at biomolecular data. The biggest strength of this software is the visualization of interdependencies between multiple datasets. It can load tabular data and groupings/clusterings. You can explore relationships between multiple groupings, between different datasets and see how your data maps onto pathways.
Ministry of Education of the Czech Republic
Unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. Allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways.
Brno University of Technology, Brno, Czech Republic
International Centre for Clinical Research, Brno, Czech Republic
This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.
CALIBER is a machine learning tool for predicting linear and conformational B cell epitopes. It utilizes a BiLSTM GCN boosting model with random or ESM-2 projections to improve accuracy over existing methods.
A highly useful and flexible tool for calibration of targeted MS‐based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.
CalicoST is a software tool that infers allele-specific copy number aberrations and reconstructs spatial tumor evolution from spatially resolved transcriptomics data. It improves upon existing methods by identifying key CNA classes and achieving an accuracy of 86% in analysis of tumor data.
Python package that implements the CaliForest algorithm presented in ACM CHIL 2020.
Directly extract stable carbon isotope fingerprints (SIFs) of individual species in a microbial community from a metaproteomic dataset. It takes the scored peptide-spectrum match (PSM) tables for samples and the calibration material, and the raw MS data in mzML format as input.
Clustering and Lineage Inference in Single-Cell Transcriptional Analysis (CALISTA), a numerically efficient and highly scalable toolbox for an end-to-end analysis of single-cell transcriptomic profiles. CALISTA includes four essential single-cell analyses for cell differentiation studies, including single-cell clustering, reconstruction of cell lineage specification, transition gene identification, and cell pseudotime ordering, which can be applied individually or in a pipeline.
callback is a method for protecting against over-clustering in scRNA-seq data by controlling for the impact of double-dipping, compatible with various clustering algorithms and the Seurat library.
Retention time prediction of small molecules with generalized calibration.
CALLR is a semi-supervised cell type annotation method for scRNA-seq data. It requires a small number of cell type labels, and annotate the remaining cells by combining clustering and sparse logistic regression.
CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
CalmBelt, an integrated framework for on-site whole genome characterization and outbreak tracking.
Program that outputs a large amount of data on cell cycle phase, cell forms, etc., for individual cells, from a set of pictures of cell walls, cell nuclei, and actins.
CALR-ETdb is a database of calreticulin variants diversity in essential thrombocythemia
CalTrack is a script for high-throughput automated calcium transient analysis in cardiomyocytes.
CAM3.0 is an R package for unsupervised deconvolution of bulk tissue data to estimate cell type compositions and expression. It utilizes novel algorithms and offers improved accuracy in identifying cell markers and determining cell proportions.
CAMAMED is a pipeline for composition-aware mapping-based analysis of metagenomic data. This pipeline can analyze metagenomic samples at both taxonomic and functional profiling levels.
Codon Arrangement MAP Predictor, predicting MHC-I Associated Peptides presentation form mRNA
Cambridge Cognitive and Psychiatric Test Kit (CamCOPS) an open-source application for capturing information relevant for cognitive and psychiatric assessment, on tablets, laptops, and desktops. It offers simple questionnaires and more complex tasks, and sends its data securely to your server.
CaMelia (CAtboost-based method for predicting MEthyLatIon stAtes) is a computational imputation method based on the CatBoost gradient boosting model for predicting single-cell methylation states to address the sparsity of the data. CaMelia imputed the missing methylation states in a cell by borrowing information of the same locus in other cells, based on the locally paired similarity of methylation patterns around the target locus between cells or between cell and bulk data.
In silico prediction of calmodulin binding proteins and their binding sites.
Continuously evaluates the accuracy and reliability of protein structure prediction methods in a fully automated manner. CAMEO currently assesses predictions in two categories (3D protein structure modeling and protein structure model quality predictions). The project is open to everyone and has been used by several method developer groups to benchmark and monitor their servers and new developments.
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.
cameratransform is a python package which can be used to fit camera transformations and apply them to project points from the camera space to the world space and back.
CaMeRe is a novel tool for inference of cancer metabolic reprogramming. CaMeRe identifies metabolic pathways connecting the two compounds via collection of compatible enzymes, which are most consistent with the provided gene-expression data. In addition, cancer-specific knowledge, such as the expression level of bottleneck enzymes in the pathways, is incorporated into the search process, to enable accurate inference of cancer-specific metabolic pathways.
Camfi is a tool for long-term, non-invasive population monitoring of flying insects using images and videos from wildlife cameras, employing automated detection and annotation using Mask R-CNN. It facilitates large-scale monitoring programs and behavioral observation with high throughput.
The Cameroon health research and evidence database.
AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation.
CAMITAX is a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance–, 16S ribosomal RNA gene–, and gene homology–based taxonomic assignments with phylogenetic placement.
CAMLU is an R package that provides an autoencoder based method for annotating cell types from scRNA-seq data. The function can identify unknown cells with the input training data. It also can annotate the full lists of cell types with consideration of unknown cell types.
CAMMiQ is a software tool for microbial identification and quantification. Specifically, it builds a compact index to manage a database of microbial genomes (in particular, bacterial/viral genomes in NCBI RefSeq database) and answers queries of the following form: given a set of high throughput sequencing (HTS) reads obtained from a mixture of genomes in the database, identify the corresponding genomes (in the database) and compute their relative abundance.
Cell-Typing using Variance Adjusted Mahalanobis Distances with Multi-Labeling. Creates multi-label cell-types for single-cell RNA-sequencing data based on weighted VAM scoring of cell-type specific gene sets.
A Web Server for Comprehensive Analysis on Multi-Omics of Immunotherapy in Pan-cancer.
Collection of Anti-Microbial Peptides is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated and predicted datasets based on their reference literature. Information like source organism, activity, reference literature, target and non-target organisms of AMPs are captured in the database. Prediction and sequence analysis tools, including BLAST, are integrated in the database.
CAMP is a sequence-based deep learning framework for multifaceted prediction of peptide-protein interactions, including not only binary peptide-protein interactions, but also corresponding peptide binding residues.
CAMPAREE is a RNA expression simulator that is primed using real data to give realistic output.
CAMPO is a tool to analyze conserved regions from a multiple sequence alignment
CAncer bioMarker Prediction Pipeline (CAMPP) is a standardized framework for the analysis of quantitative biological data
Open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.
The Camelina Gene Expression Database (CamRegBase) is a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide orthologs in the close-relative reference plant Arabidopsis.
Tool for comparative analysis and merging of scaffold assemblies.
New method and software package able to extract multiple, alternative, and equivalent classification models.
CaMutQC is an R/Bioconductor package designed for integrative quality control and filtration of cancer somatic mutations. It removes false positives, selects candidate mutations, and estimates Tumor Mutation Burden, offering a detailed filter report and code log.
Charge atomtype naming (CAN) a program to streamline preparation of molecular coordinate files for molecular dynamics simulations.
The Canadian VirusSeq Data Portal provides open access to Canadian SARS-CoV-2 genomic sequences and contextual data, while Duotang presents dynamic analyses and visualizations of circulating variants. Both resources are part of a larger network focused on open data sharing and public health communication.
Self contained amplicon NGS pipeline that takes a pair of zipped Fastq files and generates an annotated VCF file of variants.
Canary is a bioinformatics tool that allows for the automatic conversion of MaCH dosage files (mlinfo and mldose) into PLINK1 and PLINK2 compatible files.
CanBind is a pipeline to identify genes significantly mutated in cancer
This package is a user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available cancer data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Cancer SIGVARA is a semiautomated interpretation tool for germline variants of hereditary cancer-related genes.
CancerCRCdb is a comprehensive database of human core regulatory circuitry.
An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers
CancerHallmarks.com is an interactive web tool that analyzes gene lists based on the ten canonical hallmarks of cancer. It integrates 6,763 hallmark-associated genes (core set: 1,574) from multiple databases and offers enrichment analysis with clear bar and distribution plots.
Tools for cancer center catchment area geographic data collection and visualization.
Cancer Stemness Online is a web server for scoring cancer stemness potential and exploring associations with immune response, integrating eight predictive algorithms and 27 signature gene sets.
Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders. The purpose of the project is to stratify the cancer patients into clinical associated subgroups to assist the personalized diagnosis and treatment.
CancerABC is a manually curated comprehensive database containing information of the cell-free Nucleic Acid biomarkers against cancer
Pytorch implementation for cancerAlign: use adversarial learning to align different cancer types. Tumor stratification, which aims at clustering tumors into biologically meaningful subtypes, is the key step towards personalized treatment.
cancercelllines.org is a resource containing genomic profiling data, somatic mutation information, and associated metadata for thousands of human cancer cell lines, curated from multiple resources and providing data with mappings to the GRCh38 reference genome. The resource is accessible through a GA4GAH Beacon v2 API and a graphical user interface.
CancerCellNet is a R package that allows cancer type classification and evaluation of transcriptional fidelity for cancer models across species and platform (bulk RNA-seq, microarray). Alternatively, you can visit our web-app. You can also read about the applications of CancerCellNet in our bioRxiv preprint.
A framework, CancerCellTracker to process the time-lapse microscopy images and track the behavior of thousands of MM cells simultaneously for drug response prediction of patients
The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.
Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.
CancerCSP (clear cell renal cancer stage prediction) is a web-bench developed for predicting Early and Late stage of clear cell renal cell carcinoma (ccRCC) patients using gene expression data derived from RNA-seq experiments in the form of RNA-Seq by Expectation Maximization (RSEM) values.
cancerdp: Prioritization of anticancer drugs
CancerDR is the compilation of mutation data and pharmacological drug profiles from Catalogue Of Somatic Mutations (COSMIC)and Cancer Cell Line Encyclopedia (CCLE)
Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeR.
CancerEMC (bagging Ensemble Meta Classifier) is a method for frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA
A database of cancer associated enhancers. A comprehensive resource on enhancer information for TCGA cancer types. CancerEnD Genome-wide association studies have successfully identified thousands of genomic loci potentially associated with hundreds of complex traits in the past decade.
CancerGram identifies anticancer peptides using random forests and n-gram encoding. Antimicrobial peptides (AMPs) constitute a diverse group of bioactive molecules that provide multicellular organisms with protection against microorganisms, and microorganisms with weaponry for competition. Some AMPs can target cancer cells; thus, they are called anticancer peptides (ACPs). Due to their small size, positive charge, hydrophobicity and amphipathicity, AMPs and ACPs interact with negatively charged components of biological membranes. AMPs preferentially permeabilize microbial membranes, but ACPs additionally target mitochondrial and plasma membranes of cancer cells.
Human endogenous retrovirus (HERV) expression database for human cancer accelerates studies of the retrovirome and predictions for HERV-based therapies.
CancerImmunityQTL is a database to systematically evaluate the impact of genetic variants on immune infiltration in human cancer. Tumor-infiltrating immune cells, as the component of tumor microenvironment, could influence tumor progress, prognosis and response to therapy profoundly. Genetic variants are considered as crucial factors that affect immune response. So far, tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches based on immune-specific marker genes or expression signature. Therefore, we systematically explored the effects of single nucleotide polymorphisms (SNPs) on tumor-infiltrating immune cells, and identified immunity quantitative trait loci (immunQTLs) across 33 cancer types from TCGA.
This package provides an R interface for running mathematical models of tumor progression. It has the underlying models implemented in C++ and the output and analysis features implemented in R.
CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting and analyzing data.
CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus (GEO) and ArrayExpress.
This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver and passenger genes, and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.
Cancermuts is a package for the automtic retrieval and annotation of cancer mutations.
A VAE based deep learning approach to cancer tissue of origin classification.
A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines
Comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains.
CancerPDF is a manually curated database of cancer-associated peptides found in different human bodyfluids (e.g., serum, urine, plasma and saliva).
A repository of experimentally verified anticancer peptides (ACPs) and anticancer proteins. Data were manually collected from published research articles, patents and from other databases.
CancerPred is a web-server specially trained for predicting the Cancerlectins. Lectins are important biomolecules and play important functions in many processes e.g cell to cell recognition, host-pathogen interactions etc. In the same way Cancerlectins are those lectins which are known to play roles in cancer metastasis and tumor progress, oncogenesis etc. CancerPred is mainly designed for distinguishing Cancerlectins from Non-cancer lectins.
Resource to functionally decipher the proteome landscape in cancer.
CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine.
Database of single-cell expression map across various human cancers.
CancerSiamese is a tool for one-shot learning for predicting primary and metastatic tumor types unseen during model training.
CANCERSIGN is a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes.
CancerSP is a web bench developed for analyzing genomics data and for predicting Early and Late stage of cancer using genomics data.
This tool integrates the current common computational biology methods for cancer subtypes identification and provides a standarized framework for cancer subtypes analysis based on genomic datasets.
In silico Platform for designing genome-based Personalized immunotherapy or Vaccine against Cancer.
CancerTSP is a web-bench designed for stage prediction of Papillary Thyroid Carcinoma (PTC) using RNA expression data (derived from RNA-seq experiments in the form of RNA-Seq FPKM values). Primarily Early v/s Late stage prediction module predicts stage of PTC tissue sample. Further Cancer v/s Normal prediction module predicts whether tissue sample is cancerous or normal. Analysis module allows the user to analyze data regarding expression of an RNA transcript in Early or Late stage of PTC.
CancerUBM is a web bench developed for analyzing proteomics data and for predicting cancer status of a urine sample from its proteomics data.
A library of peptide-based cancer vaccines and their clinical attributes, named CancerVaccine
CancerVar is a web server for improved evidence-based clinical interpretation for cancer somatic mutations. CancerVar is a bioinformatics software tool for clinical interpretation of somatic variants.
Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall p-value will be returned for each test. Plotting functions are also available.
CanDI - A global cancer data integrator.
CandiHap is a user-friendly local software, that can fast preselect candidate causal SNPs from Sanger or next-generation sequencing data, and report results in table and exquisite vector-graphs within a minute. Investigators can use CandiHap to specify a gene or linkage sites based on GWAS and explore favourable haplotypes of candidate genes for target traits.
Causal Network of Diseases (CaNDis) is a web server for the exploration of a human causal interaction network, which we expanded with data on diseases and FDA-approved drugs, on the basis of which we constructed a disease–disease network in which the links represent the similarity between diseases.
New pipeline to automatically identify the candidate polymorphic SSRs for a given species or genus based on their assembled sequences.
CANDOCK (Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials) is a novel docking algorithm, that utilizes a hierarchical approach to reconstruct ligands from an atomic grid using graph theory and generalized statistical potential functions to sample biologically relevant ligand conformations. Our algorithm accounts for protein flexibility, solvent, metal ions, and cofactor interactions in the binding pocket that are traditionally ignored by current methods.
Cancer-Driving Site Profiling DataBase (CanDriS) is a platform to comprehensively proflie the cancer-driving sites at the pan-cancer and tumor-type level for the somatic mutations collected from The Cancer Genome Atlas (TCGA PanCanAtlas project) and International Cancer Genome Consortium (ICGC) (ICGC Release 25) by an in-house method CanDriS.
CandyCodes is a simple universally unique edible identifiers for confirming the authenticity of pharmaceuticals.
CandyCrunch is a package for predicting glycan structures from liquid chromatography-tandem mass spectrometry data.
Application for Comprehensive automated Analysis of Next-generation sequencing Experiments.
Query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. It stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information.
CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database
Machine Learning-Based Mortality Prediction Model for Critically Ill Cancer Patients Admitted to the Intensive Care Unit (CanICU).
Database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects
Functional tool useful for comparative analyses of human and canine mitochondrial genomes.
Database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). CanISO enables to facilitate expression-based analysis at gene- and transcript isoform-level in each sample, in a group (normal or tumor), and between both conditions. Since GTEx data in human is included into CanISO database, comparison function can also be supported between samples of dogs and humans.
Database to study the functional impact of isoform switching events in diseases.
A database for genome-wide DNA methylation annotation in cancers.
CANNUSE is a database containing the traditional uses of Cannabis.
A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis | The Molecular Bioinformatics Center provides an integrated approach to the use of gene and protein sequence information, molecular structures, and related resources, in molecular biology | (A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis) | Step 1: Upload genome contig files | YY Liu, JW Lin and CC Chen (2019) cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis . Front. Microbiol. 10 :1687. doi: 10.3389/fmicb.2019.01687
CANOPUS is a tool for predicting compound classes directly from MS/MS. Because it does not depend on any database, CANOPUS is suitable for the classification of unknowns.
Our variation of canopy clustering focuses on efficient clustering of points in multi-dimensional pearson correlation space. The basic notion of the heuristic is choosing a point(seed point) at random, and upon establishing it's distance to all the other points, single out those that are within a specified canopy distance. A median profile of those points is then calculated creating a canopy centroid. The canopy creation process is then repeated perpetually(canopy walk) from the previously created centroid until the distance between previous centroid is small enough. All points from the last canopy are then marked, and will not become seed points again. The above will be repeated for all possible seed points.
Combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
CanProSite is developed in IIT Madras from Protein Bioinformatics Lab. It is useful for the identification of disease prone sites in lung cancer using deep neural network
The CanRisk tool is a web interface to BOADICEA, the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm, risk prediction model used to calculate future breast and ovarian cancer risks in women. This is the first comprehensive model that allows for reliable breast cancer risk prediction in unaffected women on the basis of mutation screening information for rare (high risk and moderate risk) breast cancer genetic susceptibility variants, common cancer genetic susceptibility variants (using polygenic risk scores), explicit family history, personal lifestyle, hormonal and reproductive risk factors, and mammographic density.
canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research.
canSAR is a chemistry registration and standardization pipeline.
Global repository for breast, cervical and colorectal cancer screening programs.
Efficient and user-friendly genotype classification pipeline based on an easily expandable database of predefined canonical single nucleotide polymorphisms.
Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons.
CANTARE (Consolidated Analysis of Network Topology And Regression Elements) is a workflow for building predictive regression models from network neighborhoods in multi-omic networks.
CANTATA is an approach to find missing interactions in Boolean networks using prior network knowledge and experimental results. Using genetic programming the prior network is adapted to match the desired behavior as specified in the experimental results.
De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.
Variant level frequency data from cancer germline sequencing studies.
CanVaS is a Greek cancer patient genetic variation resource.
CANVS is an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. The elucidation of a protein's interaction association network is important for defining its biological function. Mass spectrometry-based proteomic approaches have emerged as powerful tools for identifying protein-protein interactions (PPIs) and protein-protein associations (PPAs). However, interactome association experiments are difficult to interpret, considering the complexity and abundance of data that are generated. Although tools have been developed to identify protein interactions associations quantitatively, there is still a pressing need for easy-to-use tools that allow users to contextualize their results. To address this, we developed CANVS, a computational pipeline that cleans, analyzes, and visualizes mass spectrometry-based interactome association data
Package that provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.
CaosDB is a software toolbox for data management. Its focus lies on managing data in dynamic environments of research and development where changes are too frequent or projects are too small to bear the great cost of implementing a traditional specialized and but inflexible data management system. The research data management system (RDMS) CaosDB uses a semantic data model that allows to grow and change in those dynamic environments!
Software package for the analysis of Capture-C data.
An extension of DSD that takes in to account a measure of interaction confidence while also incorporating directed pathway data.
Combine complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations.
CapiPy (Computer Assistance for Protein Immobilisation – Python) is a small collection of 4 main packages to retrieve useful information for the immobilisation of a query protein. Information from each module, specially the Blast and modeller is preferentially used by the others. In case no such information is given, the user will have to input the necessary information.
Novel approach for clustering samples (treatments, patients, condition etc) by using annotational information about the genes. The algorithm searches all pre-defined gene classes for classes that exhibit a strong clustering of the samples. These are then used to split the samples in two groups until no significant splits can be found. The result is visualized as a tree with gene classes as nodes and groups of samples as leaves.
capl is an R package for use with data collected using the Canadian Assessment of Physical Literacy. The package contains functions that will calculate CAPL scores and interpretations from raw data.
The software calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences.
Bioinformatics Tool for Comparative Analyses of Proteins In Bacteria (CAPRIB) is a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. CAPRIB efficiently finds through an easy-to-use graphical interface amino-acid changes that are strictly associated to the emergence of a phenotype.
Structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. The tool is fully browsable and searchable and is regularly updated.
Simulation of targeted sequencing. Given a genome sequence and a set of probes, it simulates the fragmentation, the dynamics of probe hybridization and the sequencing of the captured fragments on Illumina and PacBio sequencing platforms. The simulated data can be used for evaluating the performance of the analysis pipeline, as well as the efficiency of the probe design.
CapsNet-SSP is a multilane capsule network for predicting human saliva-secretory proteins. Compared with disease biomarkers in blood and urine, biomarkers in saliva have distinct advantages, as they can be examined with convenient clinical tests and through noninvasive sample collection.
Capsule network-based prediction of lysine crotonylation sites in human non-histone proteins.
Capsule-LPI is a LncRNA-protein interaction predicting tool based on a capsule network.
An interactive web tool to provide taxonomic context for a given phylogenetic tree.
Captor is a tool for O-glycosylation site prediction in Homo sapiens. It works by combining properties and sequence features with support vector machine.
CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems.
CaptureCompendium is a comprehensive toolkit for 3C analysis.
CAPTVRED is an automated pipeline designed for viral tracking and discovery from capture-based metagenomics samples. It provides a user-friendly approach to virome description, particularly suited for environmental matrices, with a setup module for customization to different capture panels.
Tool for storing, analyzing and visualizing CGH-array data.
Capybara is a R tool to measure cell identity and fate transitions. This approach is designed to measure cell identity as a continuum, at a single-cell resolution. Capybara enables classification of discrete identities as well as cells with multiple identities.
Contig assembly of prokaryotic draft genomes using rearrangements.
Interactive web server for comprehensive analysis of renal allograft rejection in immune microenvironment.
Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART) is a software tool for glycan microarray experimental design, data storage, processing, presentation and reporting.
Novel tool that applies support vector machine (SVM) for identifying carboxylation sites on glutamate residue.
CarDEC (Count adapted regularized Deep Embedded Clustering) is a joint deep learning computational tool that is useful for analyses of single-cell RNA-seq data.
This R package contains a Bayesian method to infer clonal structure for a population of cells using single-cell RNA-seq data (and possibly other data modalities).
CardIAc is an open-source application designed as an alternative to commercial software for left ventricle myocardial strain quantification in short-axis cardiac magnetic resonance images. CardIAc was developed as a 3D Slicer extension for an easy installation and usability. The source code is available opon request to the corresponding author.
Software for semi-automatic segmentation of cardiac ischemia tissues from histological images.
CardIAP web app, an automated method for the identification of spatio-temporal patterns in a calcium fluorescence imaging sequence. Through this tool, users can analyze single or multiple Ca2+ transients from confocal line-scan images and obtain quantitative information on the dynamic response of the stimulated myocyte
Implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
CardioAtlas is a resource providing a comprehensive analysis of single-cell transcriptome data in cardiovascular tissues and diseases. It offers analytical modules for cell-type prediction, marker gene identification, and cell-cell communication analysis, alongside the ability for users to upload their own data for personalized analysis.
CardioBoost is a disease-specific machine learning classifier to predict the pathogenicity of rare (gnomAD Allele Frequency <=0.1%) missense variant in genes associated with cardiomyopathies and arrhythmias that outperforms existing genome-wide prediction tools.
CardioPy is an open-source heart rate variability toolkit for single-lead EKG. A flexibile package for R-peak detection and heart rate variability analysis of single-lead EKG data.
A convolutional neural network for cross vendor automated sorting of cardiac MR images.
Automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database.
CARE is an alignment-based scalable error correction algorithm for Illumina data using the concept of minhashing. Minhashing allows for efficient similarity search within large sequencing read collections which enables fast computation of high-quality multiple alignments. Sequencing errors are corrected by detailed inspection of the corresponding alignments.
Caretta is a web suite for multiple protein structure alignment and feature extraction.
Portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.
Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.
The software was developed to support functional and comparative genome analysis. It provides the visualization of automatically obtained metabolic networks based on KEGG database information and stores the generated data in standardized SBML format. SBML is an open source XML-based format that facilitates the description of models and their exchange between various simulation and analysis tools.
Computational Assessment of the Regulation-Modulating Potential for Noncoding Variants. Large-scale genome-wide association and expression quantitative trait loci studies have identified multiple noncoding variants associated with genetic diseases via affecting gene expression.
Web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies.
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
Creating connectomes for different atlases when raw data is not available.
CaRpools is an R package for exploratory data analysis of pooled CRISPR/Cas9 screens.
Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.
CARROT is a tool for relationship inference that leverages linkage disequilibrium to differentiate between rotated relationships, such as (first-, second-, etc) uncle-niece.
CarrotOmics is an integrated web-based relational database, developed to house and integrate genomic, genetic and breeding data for carrot and related species. CarrotOmics includes genome assemblies, annotated transcripts, traits, maps, and markers being generated and used by carrot researchers.
A database of polar amylodogenic peptides from disordered proteins.
CarSite-II is an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques.
This software automatically predicts the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the canonical Watson–Crick pairings.
Genetic/radiated hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. It solves marker ordering problems and can also join maps (genetic or radiated hybrid) on various pedigrees: backcross, RI (ri self, ri sib), F2 intercross, phase known outbreds, haploid and diploid radiation hybrids up to now.
CARTmath is a mathematical model of CAR-T immunotherapy in preclinical models. It simulates a three-cell mathematical model to describe tumor response to CAR T cell immunotherapy in immunodeficient mouse models.
CartograTree is a web-based application that allows researchers to identify, filter, compare, and visualize geo-referenced biotic and abiotic data. Its goal is to support numerous multi-disciplinary research endeavors including: phylogenetics, population structure, and association studies.
CarveMe is a python-based automated tool used for top-down genome-scale metabolic model reconstruction. It can predict an organism's uptake and secretion capabilities without requiring gap-filling, although gap-filling is also supported. Additionally, CarveMe allows the generation of microbial community models by merging single species models. The tool offers advanced features such as manual adjustment of blasting options, an orthology-based search using eggNOG-mapper (kegg-bigg branch), the ability to provide a custom media library for gap-filling, and the generation of models compatible with various SBML formats. Furthermore, CarveMe supports ensemble modeling, which helps explore how different alternative solutions can lead to diverse network structures and predict various phenotypes. During the model carving process, users can select from provided templates or create their own customized universe model to suit their specific needs.
European Molecular Biology Laboratory (EMBL)
Application for viewing gene expression data in a whole-genome context. It has been used to “draw” microarray data onto a set of chromosomes so that changes in DNA copy number can identify regions of chromosome loss or duplication within the genome of tumor cells (Nat Genet. 1999 Sep;23(1):41-6).
It is a software for simulating radiogenic aberrations in detail.This software simulates chromosomal rearrangements produced by ionizing radiation during the G0/G1 phase of the cell cycle. It gives a cell-by-cell record of simulated rearrangements, much as in an actual experiment.
This software provides all possible RGEN targets in the given input sequence (e.g. exon), with the useful information including potential off-target numbers within 2nt mismatches and optional 3nt bulge via Cas-OFFinder, and out-of-frame scores via Microhomology-predictor.
Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
Context-aware seeds (CAS) is a seeding framework for finding finding all valid mappings but uses fewer (and longer) seeds, which reduces seed frequencies and increases efficiency of seed-and-extend NGS read mappers. CAS achieves this improvement by attaching a confidence radius to each seed in the reference genome.
CAS Common Chemistry is an open web resource that provides access to reliable chemical substance information for the scientific community.
Cell Annotation Software was designed for neuroscience research by researchers specializing in an image processing domain.
A database resource for the COVID-19 Alternative Splicing Atlas.
Interactive survival analysis and visualization. Perform the following types of survival analysis: quantile, landmark and competing risks, in addition to standard survival analysis.
CASAVA provides a comprehensive annotation of disease risk in 24 disease categories for any non-coding variant in the genome.
BERT-Based Retrieval for Compositely Annotated Biosimulation Model Entities.
Casboundary is a method which is able to automatically define CRISPR cassette boundaries. In addition. It contains a Cas type predictive model used to assign each gene located in the region defined by a cassette’s boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules.
This package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.
Cascade is a web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments.
CasCollect is a pipeline for the detection of Cas genes and CRISPR arrays from unassembled raw illumina sequencing reads.
A lightning transfer-learning model directly used to discriminate cancer/normal cells from scRNA-seq.
Caserel (Computer-aided Segmentation of Retinal Layers in Optical Coherence Tomography Images) os an open-source software suite for computer-aided segmentation of retinal layers in optical coherence tomography (OCT) images written in Matlab.
A versatile CRISPR package for in silico CRISPR RNA designing for Cas12, Cas13, and Cas14.
Database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, it will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study. It also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.
CASowary is a command line machine learning tool written in Python 3.6.8 for predicting the efficacy of sgRNAs for CRISPR Cas13 and other transcript targeting systems.
Image analysis tool in comet assay. It has been developed to work with either color, or gray-scale images of fluorescence-stained comets saved in TIF format. In its present version it does not control a video or CCD camera. Comets stained with silver (dark cells on white background) must be converted into negative images in order to be analysed correctly.
Computerized Affected Sibling Pair Analyzer and Reporter, main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing.
Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
A method to identify chromatin topological associated domains based on spatial density cluster.
Web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.
An analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long noncoding RNAs.
Web service for identifying Cas proteins.
CaSQ converts CellDesigner models to Boolean models encoded in SBML-Qual
Software package for simulating and sampling protein sequences with an explicit genotype-to-phenotype map.
cluster assignment by islands of sites, is a tool to predict secondary metabolite (SM) gene clusters around a given anchor (or backbone) gene.
An integrated system that supports all steps of computational ChIP-seq data analysis and supersedes the laborious application of several single command line tools. It provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses.
CAST-HSROC is a web application for calculating the summary points of diagnostic test accuracy from the hierarchical summary Receiver Operating Characteristic model.
An application to visualize circadian and heat stress-responsive genes in plants.
Castanet is a pipeline designed for rapid analysis of targeted multi-pathogen genomic data, providing end-to-end processing and consensus sequence generation with features like a graphical interface and installer script. It’s designed for flexibility, working with existing methodologies and supporting multi-pathogen enrichment experiments.
Cell Adhesion Supervised Training and Learning Environment (CASTLE) is a series of ImageJ plugins. CASTLE combines effective techniques for phase-contrast image processing with statistical analysis and machine learning algorithms to interpret the results.
CASTLE (Computational Analysis of SynThetic LEthals) is a collection of synthetic lethal data for various pathogenic organisms, generated computationally. Here, you can find synthetic lethal genes and reactions for more than 70 organisms.
Phylogenomic branch length estimation using quartets.
Systems-level sequence evolution simulator.
Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters.
Locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.
CASTpFold is a web server that provides detailed analysis of protein topography, building upon the CASTp server and incorporating AlphaFold2 protein structures. It offers functionalities for locating and quantifying surface pockets, cavities, and channels, along with functional pocket prediction and similarity search.
a tool for pathway analysis of proteomic and phosphoproteomic datasets
A Cross-Slice Attention Transformer Model for Prostate Zonal Segmentation in MRI.
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.
CAT Bridge (Compounds And Transcripts Bridge) CAT Bridge is a comprehensive multi-omics integration and analysis tool, It stands out in its ability to identify gene-metabolite pairs with biological association by fusing transcriptomic and metabolomic data. This is accomplished through the combined use of causality modeling and artificial intelligence.
CAT is a collection of tools designed for the construction of various chemical compounds.
A comprehensive web tool for exploring cancer targeting strategies.
CATA (The chromatin accessibility of cancer database) is a comprehensive Cancer ATAC-seq database that aim to provided a large number of available resources on cancer ATAC-seq datas. The database was annotated with potential functions of ATAC-Peak in the cancer.
Web application to download correlations between DNA methylation and expression of nearby genes (eQTMs) in child blood. It will help biological interpretation of epigenome-wide association studies (EWAS) in children.
A web-platform for sharing data and software for computational catalysis research.
Mass cytometry uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. Cytometry dATa anALYSis Tools is designed to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.
Provides the ability to find structural matches to a user-specified catalytic site among all Protein Data Bank (PDB) proteins. The web server can also examine a user-specified protein to identify structural matches to a library of catalytic sites.
A user-friendly, web-based modelling tool to design and manipulate proteins, DNA and DNA nanostructures. State-of-the-art features from standalone tools for modelling, manipulation, and visualization of complex molecular systems
Combining dATa Across species using Positive-Unlabeled Learning Techniques, is a supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network.
Catapult is an automated mass spectrometry search runner and analysis software.
CATAStrophy is a classification method for describing lifestyles/trophic characteristics of filamentous plant pathogens using carbohydrate-active enzymes (CAZymes). The name CATAStrophy is a backronym portmanteau hybrid where "CATAS" means CAZyme Assisted Training And Sorting.
A tool for exploring patterns in ChIP profiling data.
Estimate ecological diversity with both parametric and non-parametric estimators.
This database contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples).
Complete Arabidopsis transcriptome database
Unité de Recherche en Génomique Végétale
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
A collection of tools for performing categoric analysis.
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis.
Cluster analysis tool for healthcare-associated infections.
HIV drug resistance prediction with weighted categorical kernel functions | BACKGROUND:Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. Predicting drug resistance to previously unobserved variants is therefore very important for an optimum medical treatment. In this paper, we propose the use of weighted categorical kernel functions to predict drug resistance from virus sequence data. These kernel functions are very simple to implement and are able to take into account HIV data particularities, such as allele mixtures, and to weigh the different importance of each protein residue, as it is known that not all positions contribute equally to the resistance.
CATKINAS is a Catalytic MicroKinetic Analysis Software, which is aimed for the Mechanism Auto-analysis and Catalyst Screening.
Considering protease-as-substrate interactions in proteolytic networks. Enzymes are catalysts in biochemical reactions that, by definition, increase rates of reactions without being altered or destroyed. However, when that enzyme is a protease, a subclass of enzymes that hydrolyze other proteins, and that protease is in a multiprotease system, protease-as-substrate dynamics must be included, challenging assumptions of enzyme inertness, shifting kinetic predictions of that system. Protease-on-protease inactivating hydrolysis can alter predicted protease concentrations used to determine pharmaceutical dosing strategies
Cross-event attention-based time-aware network for medical event prediction
A machine learning and network framework to discover new indications for small molecules. CATNIP = Creating A Translational Network for Indication Prediction. The CATNIP repurposing network can be searched either by specifying one or more drugs or diseases. The probability of CATNIP prediction that two drugs will share an indication is 0.95 by default, but can be changed by the user.
CATO (Clone Alignment Tool) allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences.
CATO is a modular software package for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging data and resting-state functional MRI data.
Aan algorithm to estimate the binding propensity of protein-RNA pairs. By combining secondary structure, hydrogen bonding and van der Waals contributions, catRAPID predicts protein-RNA associations with great accuracy.
This software calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions
CatReNet is an open-source Java application for interactive analysis of catalytic reaction networks, providing algorithms for computing autocatalytic subnetworks and dynamic visualizations for understanding complex biochemical systems. It's available on GitHub under a GPL3 license and has been published in Bioinformatics.
A unification of several software tools for sequence analysis developed at the IPK Gatersleben. The web BLAST server utilizes a homology search against the current cereal genome sequence resources (barley, rye and bread wheat). Kmasker plants is able to mask sequences originating from ten agronomically important plants based on mathematical defined repeats, furthermore, selection of sequences applicable for guideRNA construction for genome editing (CRISPR) or for fluorescence in situ hybridization is also possible. MISA web searches a nucleotide sequence for microsatellites and is able generate molecular markers or primer. Within BRIDGE the complete barley collection of the IPK genebank can be visually explored in an interactive manner through diversity, certain phenotyped traits, and based on sequence polymorphisms. The barley genome explorer (BARLEX) is a system to visually inspect the reference genome sequence of barley.
CATS-rb evaluates transcriptome assemblies using the reference genome of the corresponding species
CATS-rf evaluates transcriptome assemblies using RNA-seq reads without requiring a reference genome
A user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing.
Robust genetic model-based SNP-set association test using CauchyGM.
A pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes.
Extraction of causal molecular interactions from the Reactome database.
The causalBuilder is a prototype web application for the curation of molecular interaction causal statements. This interface takes advantage of the VSM framework (https://github.com/vsmjs/) to generate customized VSM-templates for the annotation of specific causal statements. The causal statements generated are compatible with the MI2CAST (Minimum Information about a Molecular Interaction Causal Statement) checklist that is available at https://github.com/MI2CAST/MI2CAST.
CausalDAG is a Python package for the creation, manipulation, and learning of Causal DAGs.
Text mining algorithm to identify causal relationships in scientific literature.
CausalMGM is a data analysis tool to explore large, complex datasets. The method learns a graphical model of the data where the nodes are variables and edges display the dependencies among variables. The graphical model allows users to query their data to find the direct influences of a target variable of interest, or to find novel associations between pairs of variables.
Causal reasoning methods for biological networks, to enable regulator prediction and reconstruction of regulatory networks from high dimensional data.
Provides causal hypotheses testing using causal bayesian networks (CBN) and the do-calculus. Includes include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface.
Tool for generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints.
Grant Agency of the Czech Academy of Sciences
A tool for identification and analysis of tunnels and channels in static and dynamic protein structures.
A tool for interactive visualization and analysis of tunnels, channels and cavities in protein structures.
University of West Bohemia, Plzen, Czech Republic
A PyMOL plugin for identification and analysis of tunnels and channels in static protein structures.
A web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.
Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.
CAVES (Comparative Analysis of Variant Epitope Sequences) is an tool created to automate comparative epitope analyses.
Statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.
Cavity Identification And Rationalization (CAVIAR) is a method for automatic cavity detection, description and decomposition into subcavities. CAVIAR is an open source tool for protein cavity identification and rationalization, written in python and available as command line and as a GUI. It comprises a subcavity segmentation algorithm that produces meaningful decomposition of cavities, fully focused on the protein structure and agnostic of any ligand information. These subcavities reproduce subpockets as defined empirically with medicinal chemistry knowledge.
Database of cavities and their features in the structural and conformational space of proteins.
CavitomiX is a plugin for PyMOL that analyzes protein cavities. It integrates with NVIDIA’s BioNeMo platform and combines data from AlphaFold 2, OpenFold, and ESMFold to generate a dataset of predicted protein structures for human proteins.
Protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys.
A database of potential ligand binding sites in the human proteome.
cayenne is a Python package for stochastic simulations. It offers a simple API to define models, perform stochastic simulations with them and visualize the results in a convenient manner.
Cayman is a tool for profiling carbohydrate-active enzymes (CAZymes) in microbial communities. It provides a hierarchical substrate annotation scheme and is useful for analyzing CAZyme repertoires and identifying mucin-foraging species.
The database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Carbohydrate-active enzymes database (CAZy)
CB-Dock2 is an improved version of the CB-Dock server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting.
CBA (Consistency Based Alignment) builds multiple structure alignments from pairwise superpositions using consistency as a driving force.The software harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments.
This package contains functions that allow analysing and comparing various gene groups from different cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.
Online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes.
CBCAnalyzer ( compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats (ct, RNAviz ct or Mac ct), and generates a so called “bracket-dot-bracket” format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. It consists of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats and generates a so called “bracket-dot-bracket” format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. The count matrix obtained by CBCDetect is used as input for CBCTree.
CBCR is a curriculum-based strategy for chromosome reconstruction.
MATLAB tool for 3D Cone beam CT (CBCT) backprojection and iterative reconstruction.
CBD2 is a database providing information on 1569 colorectal cancer biomarkers, along with network analysis capabilities and functionality for designing polypharmacological treatments.
Colorectal Cancer Biomarker Database (CBD2)
R package for performing enrichment analysis for microbiome relative abundance data using the CBEA approach.
CBioProfiler is a web server and standalone application for cancer biomarker and subtype characterization. It includes pipelines for identifying biomarkers, performing subtype analysis, and provides curated cancer prognosis data from 268 studies.
cblaster is a tool for finding clusters of co-located homologous sequences in BLAST searches. Given a collection of protein sequences, cblaster can search sequence databases remotely (via NCBI BLAST API) or locally (via DIAMOND). Search results are parsed and filtered based on user thresholds for identity, coverage and e-value. The genomic coordinates of remaining hits are obtained from the NCBI's Identical Protein Group (IPG) database (or a local database in local searches).
Cauchy-based bounded constraint low-rank representation (CBLRR), is a low-rank representation-based method by introducing bounded nuclear norm regulation and cauchy loss function (CLF) to achieve better clustering in single-cell RNA-seq data.
MATLAB toolbox for data preparation and post hoc analyses in neuroimaging meta-analyses.
CBMOS is a GPU-enabled Python framework for the numerical study of center-based models. Cell-based models are becoming increasingly popular for applications in developmental biology.
CBNplot: Bayesian network plot for the enrichment analysis results.
Cell Behavior Ontology, is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, …) and computational models of those behaviors. It is an OWL-2 ontology developed in Protégé 4.
CBP-JMF is an improved joint matrix tri-factorization method for characterizing complex biological processes of diseases.
An AlphaFold-predicted plant kingdom-wide database of the CALMODULIN-BINDING PROTEIN 60 protein family with a novel structural clustering algorithm.
This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics.
CBPtools is a Python package that allows users to run an extensively evaluated rCBP analysis workflow on a given ROI. It currently supports two modalities: resting-state functional connectivity and structural connectivity based on diffusion-weighted imaging, along with support for custom connectivity matrices. Analysis parameters are customizable and the workflow can be scaled to a large number of subjects using a parallel processing environment. Parcellation results with corresponding validity metrics are provided as textual and graphical output. Regional connectivity-based parcellation (rCBP) is a widely used procedure for investigating the structural and functional differentiation within a region of interest (ROI) based on its long-range connectivity.
Protein viewer which uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.
Given a protein structure (PDB file), cbsPredict will identify potential carbohydrate-binding sites based on detection of coplanar, aromatic residues located on the protein surface.
Conformational B cell epitope prediction
CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.
Culture collection of algae and protozoa.
Culture collection of algae and protozoa (CCAP)
One-stop and comprehensive annotation system for individual cancer genome at multi-omics level.
Analysis of ChIP-seq data with negative control.
The Human Cell Cycle Browser (hCCB) is an interactive web tool for visualizing and simulating the human cell cycle to explore the timeline of molecular events during cell cycle progression.
ccbmlib is a Python package for modeling Tanimoto similarity value distributions.
Utilities for CCBR Bioinformatics Software
Coiled-Coil Crick Parameterization is a programs for fitting Crick parameters to coiled-coil structures and generations of ideal structures from parameters.
This software computes the void parts of the proteins, i.e. cavities, channels and pockets.
Crystallization Construct Designer 2 (CCD2) a tool to design protein truncation constructs for recombinant expression
The Cervical Cancer gene DataBase is a manually curated catalog of experimentally validated genes that are involved in the different stages of cervical carcinogenesis. Each record contains details related to gene. It provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search.
A database for exploring inter-chemical correlations in metabolomics and exposomics datasets.
Python framework for natural compound derivatives database.
In Silico Protein (s) Digest s with disulfide bridges.
Find peptides with disulfide bridges within ETD data.
A collection of tools for cancer single cell RNA-seq analysis. Cell clustering and feature gene selection analysis employ maximum likelihood and Bayesian non-negative matrix factorization algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations.
Rapid and accurate prediction of coiled-coil structures.
Many of protein structural characterization tools integrated into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.
An HMM-based predictor of coiled-coil segments in proteins.
cchsflow supports the use of the Canadian Community Health Survey (CCHS) by transforming variables from each cycle into harmonized, consistent versions that span survey cycles. It is an open science approach to transform and combine population health surveys.
CCI (Counterpart Composite Index) is a tool for projecting carcinoma cells into reference cells, to identify their healthy counterparts that could reveal the subtypes and lineage stage of carcinoma cells based on single cell RNA sequencing data (scRNA-seq).
Manually curated cell-cell interaction database with cell context information.
the ccImpute R package is an effective algorithm to correct for dropout events and improve downstream analysis of scRNA-seq data
CCIP is a machine learning method for predicting CTCF-mediated chromatin loops with transitivity.
CCIVR (Comprehensive Cis-NATs Identifier Via RNA-seq data) is a Python package tool that facilitates the identification of total cis-NATs (cis-natural antisense transcripts) from gene datasets.
Novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data.
Boosting medical image segmentation via conditional-synergistic convolution and lesion decoupling.
Databases which contain gene expression levels from next generation sequencing and also drug screening data for a large number of cancer cell lines.
Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles.
CCMDR, Clinical connectivity map drug repurposing. Drug repositioning framework to discover the new indications of existing drugs from electronic clinical information
CCmed is a package for cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression. The goal of CCmed is to provide computationally efficient tools to conduct cross-condition mediation analysis. CCmed identifies trans-associations mediated by cis-effects (e.g. trans-associations of eQTLs mediated by effects on cis-gene expression levels). Mediation analyses can be performed at the gene-level or used to identify trans-associations of complex trait GWAS SNPs/variants.
Consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage. Consensus clustering, also called meta-clustering or cluster ensembles, has been increasingly used in clinical data. Current consensus clustering methods tend to ensemble a number of different clusters from mathematical replicates with similar sample coverage. As the fact of common variety of sample coverage in the real-world data, a new consensus clustering strategy dealing with such biological replicates is required. This is a two-step consensus clustering package, which is used to input multiple predictive labels with different sample coverage (missing labels).
Complex Carbohydrate Magnetic Resonance Database (CCMRD) is a solid-state NMR database for complex carbohydrates. Carbohydrates play key roles in many life activities in living organisms. As an emerging technique with steadily improving resolution, solid-state NMR spectroscopy has the unique capability in revealing the molecular structure and dynamics of insoluble complex carbohydrates. We developed and implemented CCMRD, Complex Carbohydrates Magnetic Resonance Database, a solid-state NMR database for complex carbohydrates. Currently, it holds more than 400 solid-state NMR spectra and expects rapid expansion. The database supports searching by atom, chemical shifts and residue names.
Carbapenemase-encoding gene Copy Number Estimator (ccne) is a tool to estimate the copy number of AMR genes. It uses housekeeping gene as the reference and compares the count of reads that mapped to AMR genes with the count of reads that mapped to the reference gene.
Criss-Cross Network (CCNet) is a method for obtaining full-image contextual information in a very effective and efficient way. Contextual information is vital in visual understanding problems, such as semantic segmentation and object detection.
ccNetViz is a lightweight, high-performance JavaScript library for large network graphs visualization using WebGL. It enables custom styling of nodes and edges in CSS like way, curve edges, dynamic changes of the network, force-directed layout and basic graph interactivity.
Coupled-Clone Nonnegative Matrix Factorization (CCNMF) is a method for joint inference of clonal structure using paired Single-cell DNA-Seq and RNA-Seq data. The framework is based on optimizing an objective function that maximizes clone structure coherence between single-cell gene expression and copy number profiles, in which the two profiles are copuled by the dosage effect. The coupling dosage effect can be estimated a prior either by a linear regression model using publicly aviable paired RNA and DNA bulk sequencing data (TCGA), or by using an uninformative prior. The workflow in CCNMF is illustrated in the figure below.
A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.
Complex COMParison, is a simple command-line tool for comparing ligand/receptor complexes. It can also be used for calculating pairwise all-atom RMSD of slightly different protein structures, taking care of missing atoms, sequence inconsistencies, etc.
Software suite for Macromolecular X-Ray Crystallography, including data processing, phasing and structure refinement.
CCP4 Molecular graphics package Topic: Crystallography.
ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is complied from the literature and the Protein Data Bank (PDB), where all datasets were derived from PDB.
CCPE is a cell cycle pseudotime estimation method characterizing cell cycle timing from single-cell RNA-seq data.
Collaborative Computational Project for Electron cryo-Microscopy
R package for the visualization of cell-cell interactions.
CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells.
A graphical NMR assignment and data analysis program.
CCPRD is a novel analytical framework for comprehensive proteomic reference database construction of non-model organisms.
Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.
CCQTL is a wrapper around the R/qtl2 (Broman et al, Genetics 2019 10.1534/genetics.118.301595) functions, with hard-coded parameters tailored for QTL mapping in the Collaborative Cross.
Case-Control association analysis with RELlated individuals, is a program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers.
The package is designed to assess the significance of general similarity measures in compositional datasets. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.
A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.
Cascade Detection Network with the Convolution Kernel Switch Block and Statistics Optimal Anchors Block in Hypopharyngeal Cancer MRI.
CCSbase is an all-in-one web interface for querying the CCS database and accessing the predictive model to support unknown compound identifications.
Predictor of protein solubility based on the physicochemical properties of amino acid sequences.
CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.
Web-based application providing transmembrane topology prediction.
R package and web application for automated evaluation and selection of weighting factors for accurate quantification using linear calibration curve.
Crowdsourcing condensate database and encyclopedia.
Cluster a nucleotide dataset into representative sequences.
Cross-Dependent Graph Neural Networks for Molecular Property Prediction.
CD-NuSS is web server to predict the nucleic acid secondary structures from the CD spectral data using machine learning algorithms. Circular dichroism (CD) spectroscopy is a profoundly used technique to decipher the protein and nucleic acid secondary structures as well as the structural changes that occur during the biomolecular interactions.
Allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
cd2sbgnml aims to provide the most accurate translation possible between CellDesigner and SBGN-ML file formats. Translation in both direction is possible.
Identify cd47 binding peptides by combining next-generation phage display data and multiple peptide descriptors.
An effective sequence-based predictor named CD8TCEI-EukPath, capable of rapidly identifying eukaryotic pathogen-derived antigen epitopes for host CD8+ T cells from large peptide-coding datasets.
cd-hit-dup: Identifies and removes duplicates from sequencing reads, with an optional step to detect and remove chimeric reads.
Machine learning-based prediction of short-term adverse postoperative outcomes in cervical disc arthroplasty patients.
CDASOR is a Python page for the algorithm of the same name for predicting circRNA-disease association using convolutional and recurrent neural networks. proving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks. License either MIT, or GPLv3 or later
Tool/software developed in Perl to search the chromatin domain boundary element sequences in 12 Drosophila species. It uses recognition sequences of boundary interacting proteins and looks for ‘motif clusters’ under a set of constrains to predict boundary element sequences.
Compressed deBruijn Graph are tools for computing the compressed deBruijn Graph.
A comprehensive directory of bacterial promoters.
Population Level Analysis and Community EStimates (PLACES) that provides model-based estimates for 29 measures among all counties and most incorporated and census-designated places, census tracts, and ZIP Code tabulation areas across the US.
A large and continuously updated drug combination database.
Resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. It includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.
Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD).
Database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to most structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify protein domains flexibility, functional-transitions associated domains, and correlations in molecular motions.
CDeep3M is a tool for image analysis using deep learning. CDeep3M provides a plug-and-play deep learning solution for large-scale image segmentation of light, electron and X-ray microscopy.
Characterizing differences in microbial composition and function in microbiome data.
Semantic modelling of Common Data Elements for Rare Disease registries, and a prototype workflow for their deployment over registry data.
A simple reader of mass spectra in netCDF.
Co-regulation Data Harvester (CDH) begins with a gene of interest and identifies co-regulated genes by accessing the Tetrahymena transcriptome database. It then identifies their closely related genes (orthologs) in other organisms by using reciprocal BLAST searches. Finally, it collates the annotations of those orthologs’ functions, which provides the user with information to help predict the cellular role of the initial query.
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network.
The Chronic Disease Indicators (CDI) tool from the CDC provides national and state estimates for a set of key surveillance indicators of chronic diseases and their risk factors, allowing for data-driven decision-making and public health action.
Open source Java library for bio- and cheminformatics.
Tool to visualize chemical structures in the SMILES line notation as 2D chemical structures.
Classification tool using Discriminative K-mers and Approximate Matching algorithm (CDKAM) is a new metagenome sequence classification tool for the third generation sequencing data with high error rates. CDKAM is a taxonomic classification tool using discriminative k-mers and approximate matching strategies.
A software suite for sequence-based bioinformatics analysis of annotated cDNAs, including tools for the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative structure modeling of the product protein structure, identification of alternative splice forms, and comparative systems biology by metabolic pathway reconstruction.
cDNA-detector is a Python tool for detecting and removing contaminating cDNA from vectors and other sources in DNA-Seq data (ATAC-Seq, ChIP-Seq, WES, etc).
CDpred is a web based approach used to predict the celiac disease associated peptides and motifs.
CDR-Finder is a tool to identify centromeric hypomethylated regions from long-read sequencing data. It generates BED files and plots for visualization and downstream analysis.
Classification of Duplicate gene RetentiOn Mechanisms.
Database for patient-derived gene expression signatures induced by cancer treatment.
Taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences.
CDSImpute is a novel effective method to impute the dropout events of a scRNA-seq expression matrix.
CDSnake Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT-OTU-MiSeq utilities.
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.
A method for constructing a competing endogenous RNA (ceRNA) network from RNA-seq data.
CeAid (C. elegans Application for inputting data) is a smartphone application for logging and plotting C. elegans assays.
Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.
A curated toxicology database with enhanced tools for data integration.
Web server for standardized and visual instationary 13C metabolic flux analysis.
CEDAR (The ComplexomE profiling DAta Resource) facilitates the storage and sharing of complexome profiling data, compliant with the MIACE standard , with the goal to enable and simplify their reuse.
The Cancer Epitope Database and Analysis Resource (CEDAR) . It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of cancer disease.
It is a chrome browser extension that enables users to seamlessly enter ontology-based metadata using existing web-based submission forms provided by metadata repositories. The use of controlled vocabularies for entering metadata can help improve the quality of metadata submitted to repositories and ultimately contributes to the creation of FAIR data.
The CEDAR platform provides an easy-to-use solution for creating and reusing FAIR metadata. CEDAR offers a metadata modeling, a flexible but rigorous semantics, and the ability to quickly produce structured metadata.
A knowledgebase of cellular drug response.
CEEDER is an open access evidence service to help evidence consumers find reliable evidence reviews and syntheses to inform their decision making. The CEEDER project team collates all forms of evidence reviews and syntheses relevant to environmental management, as they are published or otherwise become available globally. The CEEDER database lists available (commercially published and ‘grey’) syntheses of primary research (e.g. critical reviews, meta-analyses, systematic reviews, rapid reviews) conducted to assess evidence on a specific question of environmental policy or management relevance.
CEG (Cluster of Essential Genes) is a database containing clusters of orthologous essential genes developed by CEFG Group in UESTC.
Provides access to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.
CEGMA (Core Eukaryotic Genes Mapping Approach) is a software for building a highly reliable set of gene annotations in the absence of experimental data.
CeL-ID is a method developed for cell line authentication using variant profiles derived from RNA-seq data. Benchmarking studies on independent test sets have shown its robustness. CeL-ID successfully identifies identical, synonymous and derivative cell lines and also estimates about the possible contaminant. We have attempted to provide simple solution to problem associated with cell line authentication and hope this would help in adoption of regular cell line authentication.
CeLaVi (Cell Lineage Visualisation tool) is a web-based visualisation tool that allows to use data derived from multiple technologies to interrogate the cell lineage whilst visualising the spatial context, the identity and the properties of the cells.
A GUI-based Python framework for segmentation, tracking and cell cycle annotations of microscopy data.
Use images of fluorescently labeled nuclei to determine G1, S and G2 staging of cells.
Cell-Dock is an FFT-based docking algorithm adapted to the Cell BE processor.
Cell-ID is a R package for gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
Matlab implementation of several methods for cell detection and cell segmentation
Cell Segmentation Generalized Framework is a generalized framework for cell segmentation.
Region based method for segmenting and splitting images of cells in an unsupervised manner.
Time-lapse microscopy classification of 2D cells based on cell shape (Seiler et al., TERM, 2012)
This macro summarizes the cell viability results from an excel table that summarises the cell numbers of different color channels.
Cell Viability Estimator for 3D Scaffolds
Cell2Chem is a web tool for mining explored and unexplored biosynthetic chemical spaces to find relationship between species and compounds.
Cell4D is a Linux C++-based graphical spatial stochatic cell simulator capable of simulating a wide variety of cellular pathways. Molecules are simulated as particles within a user-defined simulation space under a Smoluchowski-based reaction-diffusion system on a static time-step basis.
Cell-level matching and holistic comparison of single-cell transcriptomes | To understand the molecular pathogenesis of human disease, precision analyses to define alterations within and between disease-associated cell populations are desperately needed. Single-cell genomics represents an ideal platform to enable the identification and comparison of normal and diseased transcriptional cell populations. We created cellHarmony, an integrated solution for the unsupervised analysis, classification, and comparison of cell types from diverse single-cell RNA-Seq datasets. cellHarmony efficiently and accurately matches single-cell transcriptomes using a community-clustering and alignment strategy to compute differences in cell-type specific gene expression over potentially dozens of cell populations
Cell Layers is an interactive Sankey tool for the quantitative investigation of gene expression, coexpression, biological processes, and cluster integrity across clustering resolutions.
Cell++ is a novel stochastic simulation environment which is capable of modelling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signalling.
A curated repository of cell types with multifaceted characterization.
A suite of scripts for analysis of scRNA-seq cell type classification tool outputs. These scripts can be used both for evaluating the existing methods by running pipelines on labelled data and for analysing predicted labels for novel data sets.
A method for comparing expression dynamics within and between single-cell differentiation trajectories.
CellAnn is a web application for predicting cell types of single-cell clusters based on published reference datasets. CellAnn provides a comprehensive scRNA-seq reference database and users can easily find the relevant reference datasets in their analysis.
Cellar is a interactive single cell data annotation tool.
CellBarcode is a Bioconductor package for extracting and filtering cellular DNA barcodes from sequencing data. It supports a range of barcode types and includes a simulation kit (CellBarcodeSim) for optimizing barcode identification.
RESTful Web Services for retrieving relevant biological information.
This package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.
We have released a large-scale, multimodal annotated dataset for cell segmentation, CellBinDB. Based on CellBinDB, we designed a benchmarking pipeline to benchmark eight of the most advanced and widely used cell segmentation techniques/methods, and further analyzed the impact of four cell morphology indicators and image gradients on the segmentation results.
CellCall is a toolkit to infer intercellular communication networks and internal regulatory signals by integrating intracellular and intercellular signaling.
Supervised cell type identification for single-cell ATAC-seq data.
CellChat is a R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
CellCoal simulates the somatic evolution of single-cells. CellCoal generates a coalescent genealogy for a sample of somatic cells - no recombination - obtained from a growing population, together with a another cell as outgroup, introduces mutations along this genealogy, and produces single-cell diploid genotypes (single-nuclotide variants or SNVs).
The Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing one of the major hurdles with computational research. In addition, this platform allows scientists to simulate and analyze the models in real-time on the web, including the ability to simulate loss/gain of function and test what-if scenarios in real time.
Atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.
A collection of genes and proteins involved in human and yeast cell cycle.
A unified repository for scRNA-seq data and visual exploration.
A RShiny application and R package for the visualization and analysis of single-cell lineage tracing data.
CellDetail is an open-source 3D-cell-image analysis platform used to quantitatively determine the spatial distribution of components within cells, particularly focusing on polarity proteins and Septin networks. It uses a dipole moment-based algorithm and has been used to analyze hematopoietic stem cells and human fibroblasts.
Computational framework for ligand-receptor-mediated cell-cell communication analysis III.
Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.
CELLector is an R package and R Shiny application allowing researchers to select the most relevant cancer cell lines in a patient-genomic-guided fashion.
Cellects is an open-source software tool for automatically quantifying growth and motion in 2D image sequences, applicable to a wide range of species and experimental conditions. It provides geometrical descriptors and facilitates validation, contributing to increased reproducibility and accuracy in biological studies.
Cellenics® is an open source, cloud-based analytics tool for single cell RNA sequencing data. It allows you to explore and analyze single cell datasets without the need to develop bioinformatics skills. Cellenics® has a user-friendly interface with a clear workflow. Offers a variety of pre-loaded publication-ready plots. Cellenics® software was developed by © 2020-2022 President and Fellows of Harvard College. Biomage is an open source software company that provided services to Harvard Medical School for the design and development of Cellenics®.
Scalable and interactive visual analytics app for exploring multimodal single-cell data.
CellExplorer is a graphical user interface (GUI) and standardized pipeline for exploring and characterizing single cells acquired with extracellular electrodes.
This package provides functionalities for the fitting of cell population growth models on experimental OD curves.
An R package designed to demultiplex cell hashing data
This package analyzes high-throughput assays performed in microtitre plate formats. The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview of the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries.
This Image Library is a repository for images and movies of cells from a variety of organisms. It demonstrates cellular architecture and functions with high quality images, videos, and animations. This comprehensive and easily accessible Library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research.
Cellinker is a platform of ligand-receptor interactions for intercellular communication analysis.
A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.
CellKb Immune is a manually curated database of mammalian immune marker gene sets optimized for rapid cell type identification. CellKb Immune is a subset of the CellKb database containing immune cell types from mouse. Marker gene sets of all hematopoietic cell types are manually collected from scientific literature and annotated with cell, tissue and disease ontologies. Read more about the data collection process here.
Visualize protein-protein interaction (PPI) networks in the context of subcellular localization.
Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.
A user-friendly tracking tool for long-term migratory and proliferating cells.
CellMeSH is a package and web application for probabilistic cell-type identification using indexed literature.
CellMix , an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.
CellML 2.0 is an XML-based language for describing and exchanging mathematicalmodels of physiological systems. MathML embedded in CellML documents is used to define the underlyingmathematics of models. Models consist of a network of reusable components, each with variables andequations giving relationships between those variables. Models may import other models to create systems ofincreasing complexity. CellML 2.0 is defined by the normative specification presented here, prescribing theCellML syntax and the rules by which it should be used.
CellModeller is a Python-based framework for modelling large-scale multi-cellular systems, such as biofilms, plant and animal tissue.
CellNetAnalyzer (CNA) is a MATLAB toolbox providing various computational methods for analyzing structure and function of metabolic, signaling, and regulatory networks. Metabolic networks can be analyzed by means of stoichiometric and constraint-based modeling techniques while signal transduction and (gene) regulatory networks can be represented and analyzed as logical networks (Boolean or multivalued logic) or as interaction graphs. Computations can be started within a GUI (interactive network maps) or from command line (via API functions).
Web tool for visualization of biological networks using force-directed layout constrained by cellular components.
This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human primary cell, bulk RNA-seq data in the Sequence Read Archive. The CellO Viewer enables exploration of cell type-specific expression signatures across cell types encoded within the graph-structured Cell Ontology.
A knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research, including immortalized cell lines, naturally immortal cell lines (ie stem cell lines), finite life cell lines when those are distributed and widely used, vertebrate cell lines with an emphasis on human, mouse and rat cell lines, and invertebrate (insect and tick) cell lines.
Virtual mesoscope to model and visualize structural systems biology.
CellPAINT is a free-form painting app that allows users to create their own living illustrations of cellular landscapes.
A curated RNAseq database of palmitoylating and de-palmitoylating enzyme expression in human cell types and laboratory cell lines.
Quantifying differences in cell line population dynamics.
CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. This is crucial, as cell-cell communication relies on multi-subunit protein complexes that go beyond the binary representation used in most databases and studies.
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies.
An unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data.
Cellpose is a generalist algorithm for cellular segmentation.
CellPPD is an in silico method, which is developed to predict and design efficient cell penetrating peptides (CPPs). The main dataset used in this method consists of 708 experimentally validated CPPs.
PhageTB is a multilevel prediction method for predicting interactions between bacteriophages and pathogenic bacterial hosts. This study develops a novel host prediction method for predicting hosts of query phages by their genome sequences utilizing alignment-based and alignment-free features.
CellPPD-Mod is an in silico method, which is developed to predict efficient modified cell penetrating peptides (CellPPD-Mods).
CellProfiler Analyst allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complex and subtle phenotypes, for automatic scoring of millions of cells
CellRank is a package for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors
A toolkit for transforming, selecting, and slicing 3D cell structures on the road to morphologically detailed astrocyte simulations.
Trajectory Algorithms to Infer Stem Cell Fate Decisions. New version available! Please, check our updated tutorial. Updates include:. Raw count/UMI data can be provided as input. Perform quality control on genes and cells.
segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells
An E-scape visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.
It contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform.
A robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images.
CellsFromSpace (CFS) is an R package for deconvolving and annotating spatially distributed omics data without a reference dataset. It utilizes independent component analysis (ICA) to analyze data from various spatial transcriptomics technologies, offering a user-friendly interface for interpretation.
CellSium is a cell simulator developed for the primary application of generating realistically looking images of bacterial microcolonies, which may serve as ground truth for machine learning training processes.
A command-line tool for easy and scalable single-cell RNA sequencing analysis
User-friendly tool for single-cell RNA sequencing analysis.
cellsnp-lite is an efficient tool for genotyping single cells. cellsnp-lite was initially designed to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference. Now besides RNA-seq data, cellsnp-lite could also be applied on DNA-seq and ATAC-seq data, either in bulk or single-cell.
Statistical analysis of organelle movement using state-space models.
TiSim-CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multicellular systems in two and three dimensions. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multicellular phenotypes.
CellTalkDB is a manually curated database of ligand-receptor interactions in humans and mice. CellTalkDB contains literature-supported ligand-receptor (LR) pairs for human and mouse, which are curated from protein-protein interactions (PPIs) in STRING database and verified manually in Pubmed by three reviewers.
Explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data.
Integrated graphical user interface written in Matlab that implements a few novel methods for automating cell segmentation/lineage reconstruction. It is designed for biologists without training in image processing or programing to extract single cell information from microscopy images arising in their studies.
A database to dissect the causative multilevel interplay contributing to cell development trajectories.
CellTracker is an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. CellTracker is a highly integrated graphical user interface software, for automated cell segmentation and tracking of time-lapse microscopy images. It covers essential steps in image analysis including project management, image pre-processing, cell segmentation, cell tracking, manually correction, and statistical analysis such as the quantification of cell size and fluorescence intensity, etc. Furthermore, CellTracker provides an annotation tool and supports model training from scratch, thus proposing a flexible and scalable solution for customized dataset analysis.
An R package for fast and flexible analysis of immune cell migration data.
CellTracksColab is a platform for compiling, analyzing, and exploring cell tracking data. It facilitates the integration of data from multiple experiments and utilizes high-dimensional data reduction and clustering to identify behavioral patterns.
interactive browser-based visualization for analyzing cell trajectories and lineages.
Automated tool to quantify stochastic cell state transitions between distinct cell states from FACS and flow cytometry experiments, to estimate equilibrium cell state proportions and the needed time equilibrium.
This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and builds a compact tree modelling the relationship between individual cells over time or space.
A tool for semi-automatic cell type classification
Celluloid is a tool for clustering single cell sequencing data around centroids.
CellVGAE is an unsupervised scRNA-seq analysis workflow with graph attention networks. CellVGAE uses the connectivity between cells (such as k-nearest neighbour graphs or KNN) with gene expression values as node features to learn high-quality cell representations in a lower-dimensional space, with applications in downstream analyses like (density-based) clustering, visualisation, gene set enrichment analysis and others. CellVGAE leverages both the variational graph autoencoder and graph attention networks to offer a powerful and more interpretable machine learning approach.
CellWalker is a tool that integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.
CellWalkR is an R Package for integrating single-cell and bulk data to resolve regulatory elements.
cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas.
A fast and user-friendly platform for profiling cellular phenotypes.
celseq2 is a Python framework for generating the UMI count matrix from CEL-Seq2 sequencing data.
CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Combined Embedding Model for MiRNA-Disease Association Prediction (CEMDA).
Prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.
It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.
An interactive medical imaging application with image processing, computer vision, and machine learning toolkits for cardiovascular research.
CEN-tools is an integrative tool that identifies the underlying context that is associated with the essentiality of a gene from large-scale genome-scale CRISPR screens.
CEllular Niche Association (CENA) is a method for a joint identification of pairwise association together with the particular subset of cells in which the association is detected. In this implementation, CENA is limited to associations between the genes' expression levels (data from scRNA-sequencing) and an additional cellular meta-data of choice.
CeNet Omnibus is an R/Shiny application to the construction and analysis of competing endogenous RNA network.
Deep-learning pipeline for efficient centriole detection in microscopy datasets.
Comprehensive cancer enhancer database for primary tissues and cell lines.
censcyt is an R package extending the diffcyt (differential discovery in high-dimensional cytometry via high-resolution clustering) pipeline. censcyt (Censored diffcyt) includes methods for differential abundance analysis in the presence of a covariate subject to right censoring. It uses the reversed association testing approach (like diffcyt) meaning the censored variable (e.g. survival time) is modeled as a predictor. Classical survival analysis methods on the other hand model the censored variable as the response.
Protein and nucleotide sequence repeat identification and masking. Screens query sequences against a reference collection of repeats and "censors" (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.
Co-motif scanning program to identify co-transcription factors. It ranks co-transcription factors based on their distribution around CHIP-seq peaks.
Calculate centrality indexes used for the identification of the most important nodes in a network. Suite of algorithms dedicated to network nodes centrality analysis, computing several centralities for undirected, directed and weighted networks. The results of the topological analysis can be integrated with data set from lab experiments, like expression or phosphorylation levels for each protein represented in the network.
CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file.
Genetic mutation database for rare diseases that enables to search, sort and filter genetic variants from clinically diagnosed individuals worldwide and make symptoms-based queries.
A gradient boosting algorithm for cell-type-specific enhancer-target prediction.
A very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini index, optimized specifically for the metagenomic classification problem. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.
Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
Assembling Centromeres with Long Error-Prone Reads | An algorithm for centromere assembly using long error-prone reads | Scripts for analyses and figures for centroFlye manuscript | centroFlye is an algorithm for centromere assembly using long error-prone reads. Currently it supports assembly of a human centromere X. Here we show how to apply it for the centromere X of the CHM13hTERT human cell line | Results_and_several_Appendices.ipynb replicates Results and Appendices: Analysis of centromeric reads that do not map to centroFlye assembly, Hanging index test, and Breakpoint test
Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).
CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.
Tool for decomposition centromeric assemblies and long reads into monomers
Set of human and fly genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Genes have been considered as centrosomal on the basis of different kinds of evidences including high-throughput proteomics assays, annotations in public databases and orthology relationships to centrosomal genes in closely related species (e.g. mouse).
CEPS is an open access MATLAB Graphical User Interface (GUI) for the analysis of complexity and entropy in physiological signals.
CEPZ is a predictor for identifing DNase I hypersensitive sites.
Graphical, event-driven tool for copy number abnormalities/allelic-imbalance coupled analysis of whole-exome sequencing data. By using case-control matched exome data, it performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection.
content extraction, recognition, and construction system (CERC) is a web-based summarization and visualization tool, CERC (https://newton.isye.gatech.edu/CERC1/), for extracting salient information from clinical and biomedical text. The system ranks sentences by relevance and includes features that can facilitate early detection of medical risks in a clinical setting.
Cerebrovascular event risk calculator 2(cvecalculator). TAVR-related (transcatheter aortic valve replacement) CVE (Cerebrovascular events) can be estimated using this deep learning-based predictive algorithm.
The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple environmental stresses including cold, heat, drought, and salt stress as well as on the application of ABA.
cerebroViz is an R package that can map spatiotemporal brain data to vector graphic diagrams of the human brain.
An open, complete CAD/CAM system with smart software.
ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.
CERES is a cryo-EM re-refinement system for continuous improvement of deposited models.
Fast sequence motif identification algorithm that utilizes suffix arrays to efficiently find optimal motifs in large sequence sets (such as tens of thousands of sequences identified by chromatin or RNA immunopreciptation experiments). It uses rank-order statistics and accounts for quantitative information for each sequence.
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) is a R package that simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs.
An R package for identification and analysis of ceRNA-miRNA triplets.
CeRNASeek is an R package for identification and analysis of ceRNA regulation. It årovides several functions to identify and analyse miRNA sponge, including popular methods for identifying miRNA sponge interactions, two types of global ceRNA regulation prediction methods and four types of context-specific prediction methods, which are based on miRNA-messenger RNA regulation alone, or by integrating heterogeneous data, respectively. In addition, For predictive ceRNA relationship pairs, this package provides several downstream analysis algorithms, including regulatory network analysis and functional annotation analysis, as well as survival prognosis analysis based on expression of ceRNA ternary pair.
ceRNAshiny, an interactive R/Shiny application, which integrates widely used computational methods and databases to provide and visualize the construction and analysis of ceRNA network, including differential gene analysis and functional annotation.
Decentralized healthcare training certificate management system using blockchain and smart contracts.
Cerulean is a hybrid assembly using high throughput short and long reads
Cis expression structural alteration mapping
CeTF is an R package to Coexpression for Transcription Factors using Regulatory Impact Factors (RIF) and Partial Correlation and Information (PCIT) analysis. The package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm.
The CEToolbox application is a calculator for capillary electrophoresis. It aims to provide several information on the separation of compounds like the hydrodynamic injection, the volume of the capillary, the injection plug length or the quantity of injected analyte. The application works with any type of CE system.
Tool for looking up metabolites in different databases (Kegg, HMDB, LipidMaps, Metlin and MINE) from experimental masses obtained by mass spectrometry.
Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.
Accessible Web Application for Rapid Re-Analysis of Cystic Fibrosis Pathogen RNA Sequencing Studies.
Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing | Analysis of cfDNA data with UMIs (consensus generation, SNV calling, annotation and evaluation of fragment length profiles) | Detection of genomic alterations with error-corrected cfDNA sequencing | Several recent studies have demonstrated the ability of cfDNA sequencing to provide early prognostication, better molecular profiling and monitoring of disease dynamics with many applications in genomic-driven oncology
An explainable deep learning model for annotating the transcriptional roles of cis-regulatory modules based on epigenetic codes.
Cross-fusion of network and attributes based on attention mechanism for protein function prediction.
The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.
CFBI(+) is a tool for collaborative video object segmentation by (multi-scale) foreground-background integration.
cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls.
cfDNApipe(cell free DNA Pipeline) is an integrated pipeline for analyzing cell-free DNA WGBS/WGS data. It contains many cfDNA quality control and statistical algorithms. It is a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data.
Definition and quantification of multiple haplotypes in a mixed sample.
CFM is a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation.
CFM-ID (Competitive Fragmentation Modeling) is a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra data.
CFO is an R package that implements calibration-free odds type Bayesian designs for dose finding in phase I clinical trials, leveraging historical data to identify the maximum tolerated dose (MTD) efficiently and safely. The package includes variants for various scenarios, such as drug-combination trials and late-onset toxicity.
Cell-free multi-omics database for diseases.
Software tool for the sensitive detection of somatic mutations from cell-free DNA.
CFSP is a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification.
An interactive desktop platform for drawing gene structure and protein architecture
With current sequencing technologies, it is feasible to generate a lot of reads for a given genome. However, the assembly usually ends up in a set of contigs with gaps between them. If the sequences of one (or several) related genome(s) are already known, this information can be used to estimate the order and orientation of the contigs towards each other. This helps in the finishing phase of a sequencing project since it eases the design of specific primer sequences to fill the gaps.
A collection of software packages for the statistical performance assessment of CGM systems.
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions. CG-TARGET is a collection of R scripts to be used for the purpose of predicting gene-set targets from chemical-genetic interaction profiles.
A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data..
Tools for viewing, manipulating and converting data from Complete Genomics.
Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.
CGATCPred is a convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals.
Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.
Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data.
Metallocage construction and binding affinity calculations
Provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism.
Comprehensive guide designer (CGD) is a python based on-target scoring method for CRISPRi, CRISPRa, Cas9, Cas9 (non-canonical) and Cas12a sequences.They are consortium of scores such as CGDi, CGDa, CGD9, CGD9NG and CGD12a, which are based on ENLOR(ELastic Net Logistic Regression) weights.
Interactive visualisation of the sequence-dependent ground state, or free energy minimizing, configuration of a DNA double helical fragment as predicted by the cgDNA model.
This toolbox provides direct access to cBioPortal cancer genomics data from within the MATLAB environment.
An R package for analysis of case-control studies in genetic epidemiology.
CGeNArate is a sequence-dependent coarse-grained model for DNA molecular dynamics simulations, allowing for accurate atomistic resolution with reduced computational effort. The software enables simulations of very long segments of B-DNA for biotechnological and chromatin studies.
The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRNA microarray and matched clinical data. The analyse tool allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.
Contains functions and classes that are needed by arrayCGH packages.
Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
Provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters.
This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.
Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).
Combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas.
Dimension Reduction for Array CGH Data with Minimal Information Loss.
Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. CGI relies on existing knowledge collected from several resources and on computational methods that annotate the alterations in a tumor according to distinct levels of evidence.
H2020-EU.3.1.6. - Health care provision and integrated care
CGINet is graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph containing three types of nodes: chemicals, genes, and pathways.
cGLMM is a R method for privacy-preserving construction of generalized linear mixed model for biomedical computation.
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Precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
cgMLST@Taiwan is a web service platform for Vibrio cholerae cgMLST profiling and global strain tracking.
The cgmquantify software resource enables comprehensive analysis of continuous glucose monitor data with clinically validated metrics and easy to implement visualizations.
Pathogen detection within species from nanopore metagenomic sequencing data.
Continuous Glucose Monitoring Time Series Data Analysis (CGMTSA) is an R package for continuous glucose monitoring time series data analysis.
A visual interface to the cgNA+ sequence-dependent statistical mechanics model of double-stranded nucleic acids.
A novel end-to-end three-stage channel and position attention (CPA) module integrated graph reasoning convolutional neural network (CGNet) for retinal OCTA vessel segmentation.
Cancer Gene and Pathway Explorer (CGPE) provides a highly integrated bioinformatics webserver for investigating, analyzing, and visualizing the TCGA and GEO gene expression data. CGPE provides key interactive and customizable analysis portal
Database for candidate genes for QTL for milk production traits in cattle
CGRdb2 is a Python package connecting to a PostgreSQL database that enables native searches for molecules and reactions without complicated SQL syntax.
Coarse-grained statistical potentials with residue separation for RNA structure evaluation.
A web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.
CGRphylo is an R pipeline that uses Chaos Game Representation (CGR) to analyze SARS-CoV-2 lineages, strains, and recombinants. It offers a computationally efficient, alignment-free method for phylogenetic analysis and offers an R pipeline for visualization.
Clinic and genetic risk score (CGRS) calculator is a web application for calculating the assessing the prognosis of gastric cancer (GC) patients.
CGSEA is a flexible tool for evaluating the associations of chemicals with complex diseases. CGSEA for scanning the candidate chemicals associated with complex diseases or traits. CGSEA only need genome-wide summary level data, such as transcriptome-wide association studies (TWAS) and mRNA expression profiles.
A web service for integrative cancer genome and pharmacogenomic data analysis.
The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots. The server uses BLAST to compare the primary sequence of up to three genomes or sequence sets, aiding in the identification of conserved genome segments, instances of horizontal transfer or visualization of genome segments from newly obtained sequence reads.
CH-Bin - metagenomic binning using convex-hull distance metric
Manual-curated database regrouping published results referenced in Pubmed.
CHAI is an R package that aggregates results from multiple scRNAseq clustering methods to identify cell types. It offers two methods (CHAI-AvgSim and CHAI-SNF) and provides a framework for incorporating new clustering algorithms.
chainchecker is an application to visualise and explore transmission chains for Ebola virus disease.
Improves genome alignment specificity and sensitivity.
Universal tool for standardized relative quantification in real-time PCR.
ChAlPred is a web server for prediction of allergenicity of chemical compounds.
Chamaeleo is a robust library for DNA storage coding using different codec methods for DNA storage. This kit is mainly developed and operated by Synthetic Platform of BGI-Research, for a detailed list of authors, see authors.md. It provides you a chance to use the classical DNA encoding and decoding methods to save files into DNA sequences or load them from DNA sequences.
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.
A framework for rapid evaluation of deep neural networks for patch-based histopathology classification.
ChanFAD is a functional annotation database for ion channels.
Changes one feature name by an other name (the feature name can be found on the 3rd column).
Change the chromosome name or gene name of a singla fasta, gff or sam file. For this tool, it can not treat mutiple-chromosome, gene files.
Changes the name of tag of a list of transcripts.
Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to UNIX pipeline philosophy. Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. The database also works as an API to downstream tools like the Chanjo Coverage Report generator.
A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.
Draw a chaos game representation plot for a nucleotide sequence.
The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.
CHAPAO (Compressing Alignments using Hierarchical and Probabilistic Approach) is a novel reference-based technique for compressing MSA files.
Chaplin (Case-control haplotype inference package.) is a software program for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study.
Geometrical approach to identify differentially expressed genes.
Identifies genomic duplications or deletions from gene expression data.
CharID (Chromatin Accessible Region Interaction Detector), a two-step model that combines neural network and ensemble learning to predict OCR-mediated loops.
This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.
CharPlant (Chromatin Accessible Regions for Plant) is a de novo OCRs prediction tool based on deep learning model. It can take complete DNA sequences or scaffolds as input, and output the outline of OCRs in a .Bed format file rely on sequence features. To our knowledge, this is the first tool to de novo predict potential open chromatin regions from DNA sequence and assay data. The result of OCR (Open Chromatin Region) assay technologies such as DNase-seq and ATAC-seq represents the open state of a tissue at a given time and does not cover all the chromatin accessible information of this species. To predict the potential open regions of different tissues at different times in the whole sequence can help to understand gene transcription and regulation from a global perspective.
Curated database of biochemically characterized proteins. The initial data set was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.
CHARTS is a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq datasets. CHARTS is a web application, and associated backened analysis pipeline, for exploring publicly available single-cell RNA-seq data from human tumors.
Chaste (Cooper et al., 2020) is an open-source, general-purpose simulation package for modelling soft tissues and discrete cell populations that can be used with MPI. This tool allows using different modelling frameworks on a given problem, enabling users to select the most appropriate one for their research and to better understand the limitations of each one of them. Chaste has been used for a wide range of projects, such as intestinal (Dunn et al., 2013) or colonic crypt (Dunn et al., 2012) studies.
The chaste_codegen module takes CellML models as input, via cellmlmanip to read and manipulate them, then uses templating to generate C++ code.
Text mining approach to organize and evaluate scientific literature on cancer.
Tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.
A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations.
CHDGKB (A knowledgebase of non-syndromic congenital heart disease genetic variations) is a manually curated database of genetic variations associated with non syndromic congenital heart disease. CHDGKB contains a comprehensive information of genetic variations for 370 subtypes of human congenital heart disease reported in PubMed from 1998, which would provide an exhaustive and summary of current status of non-syndromic CHD genetic research that can contribute to better interpret the human variants for illustrating NS-CHD causing variants.
ChIP-exo Analysis Pipeline (ChEAP) that executes the one-step process, starting from trimming and aligning raw sequencing reads to visualization of ChIP-exo results.
Dictionary of molecular entities focused on small chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
checkCIF reports on the consistency and integrity of crystal structure determinations reported in CIF format.
A Microsoft Windows-based software application for checking biotechnology Sequence Listings for compliance with 37 Code of Federal Regulations (CFR) 1.821 – 1.825 for both ‘old rules’ (October 1990) and ‘new rules’ (July 1998).
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Rapid assessment of genome bin quality using machine learning. CheckM2 uses two distinct machine learning models to predict genome completeness. The 'general' gradient boost model is able to generalize well and is intended to be used on organisms not well represented in GenBank or RefSeq (roughly, when an organism is novel at the level of order, class or phylum). The 'specific' neural network model is more accurate when predicting completeness of organisms more closely related to the reference training set (roughly, when an organism belongs to a known species, genus or family). CheckM2 uses a cosine similarity calculation to automatically determine the appropriate completeness model for each input genome, but you can also force the use of a particular completeness model, or get the prediction outputs for both. There is only one contamination model (based on gradient boost) which is applied regardless of taxonomic novelty and works well across all cases.
CheckMyBlob is a machine learning system that detects and validates ligands in X-ray electron density maps. Upload your files or type a PDB code to try it out!.
When sequencing several libraries simultaneously, the selection of compatible combinations of indexes is critical for ensuring that the sequencer will be able to decipher the short, sample-specific barcodes added to each fragment. However, researchers have few tools to help them choose optimal indexes. Here, we present checkMyIndex, an online R/Shiny application that facilitates the selection of the right indexes as a function of the experimental constraints.
CheckMySequence is a Python package for the automated detection of register-shift errors in cryo-EM models.
CheckSumStats is an R package for the identification of errors and analytical issues in the results and metadata of genome-wide association studies (GWAS)
Report STOP codons and ORF statistics of a protein.
CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.
CHEER is a hierarchical model, which can learn the species masking feature via deep learning classifier, for new RNA virus taxonomy classification.
Cheetah is a simple to use Python library to support the development of analysis workflows and real-time cybergenetic control platforms that combine microscopy imaging and environmental control. The toolkit relies on a U-Net convolutional neural network to perform cell segmentation and uses this with additional functions that can label, track and generate control signals based on this information.
Web server to model protein complexes using tandem cross-linking mass spectrometry data.
Chem4Word makes it easier to insert and modify chemical information, such as labels, formulas, and 2D depictions, within Microsoft Word. Additionally, it enables the creation of inline “chemical zones,” the rendering of print-ready visual depictions of chemical structures, and the ability to store and expose chemical information in a semantically rich manner.
The package provides a comprehensive collection of tools for processing files with chemical structures and associated data.
Chembench is a free portal that enables researchers to mine available chemical and biological data. Chembench can help researchers rationally design or select new compounds or compound libraries with significantly enhanced hit rates in screening experiments.
An integrative platform to navigate the biology, structure and chemical inhibition of human proteins.
ChemBioServer is an an advanced web server pipeline for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing.
Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
BLAST search against biological molecules (e.g. mAbs) stored in ChEMBL database.
BLAST search against protein targets stored in ChEMBL database.
Search against small molecules stored in ChEMBL NTD database.
Search against small molecules stored in ChEMBL database.
ChemChains is a logical network simulation and analysis suite.
A logical network simulation and analysis suite. The driving force behind the development of this tool was to be able to study and visualize the complex dynamics of biological signal transduction networks. It considers the approach of using Boolean modeling technique. The most prominent feature of that is that it allows users to interact with the model in a continuous manner.
Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks. Instructions for installation and explanation of the ChemChaste package may be found in ChemChaste_Documentation.pdf.
Analyzing potential interaction effects of chemical mixtures.
Engine for metabolite annotation in mass spectrometry.
Used for drawing accurate, chemically-aware structures for use in database queries, preparation of publication-quality graphics, and entry for modeling and other programs that require an electronic description of molecules and reactions.
ChemFate predicts daily chemical environmental concentrations for four classes of chemicals in nine environmental compartments (e.g., air, freshwater, coastal seawater, natural soil, urban soil, agricultural soil with and without applied biosolids). ChemFate comprises four different models:.
An integrated online platform developed for the screening and prediction of potential frequent drug hitters, thus improving the efficiency of drug R&D in colloidal aggregate, firefly luciferase reporter enzyme inhibition, fluorescence, chemical reactivity, and promiscuity. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.
Firefly luciferase (FLuc) is one of the highly favored detection techniques in HTS. However, FLuc inhibitors can cause negative interference in detection, which may result in false positive signals in HTS assays. In order to prescreen FLuc inhibitor thus avoid such unnecessary false positives, we build a reliable prediction model based on a large data set. ChemFLuc is a public webserver which could be useful to flag FLuc inhibitors in large dataset.
ChemFLuo is a web-server for structure analysis and identification of fluorescent compounds. Fluorescent detection methods are indispensable tools for chemical biology. However, the undesirable effect induced by fluorescent compound interference has produced many false positive results, thus hampering the efficiency of drug development. In order to prescreen potential fluorescent interferences, we build a reliable prediction model based on a large data set. ChemFluo is a public webserver which could be useful to flag blue and green fluorescent compounds in large dataset.
ChemFOnt (the Chemical Functional Ontology) is a hierarchical, OWL-compatible ontology describing the functions and actions of more than 341,000 biologically important chemicals.
Fast cheminformatics fingerprint search, at your fingertips. Chemfp is a set of command-line tools and a Python library for fingerprint generation and high-performance similarity search. There are two ways to try out chemfp. From the download page page you can request an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license
ChemFREE is a web platform for evaluating the eco-environmental risk of chemicals, enabling users to input SMILES strings and obtain assessment outputs. The platform incorporates in silico models to address the limitations of traditional risk assessment methods.
A tool for chemical genomics analysis and phenotypic profiling.
ChemGenerator is a web server for generating potential ligands for specific targets.
A tool tuned for navigation in biologically relevant chemical space.
Match either a single name of a chemical compound or a whole list of names against reference databases, even when the notations are different. This matching is solely done on the name (string) basis of chemical compounds without identifying the exact chemical structure of the molecule described.
ChemHub is a comprehensive database for selecting biosynthetic target molecules based on compound functions.
Grain protein function prediction based on self-attention mechanism and bidirectional LSTM.
The Chemical Checker (CC) is a resource that provides processed, harmonized and integrated bioactivity data on 800,000 small molecules. The CC divides data into five levels of increasing complexity, ranging from the chemical properties of compounds to their clinical outcomes. In between, it considers targets, off-targets, perturbed biological networks and several cell-based assays such as gene expression, growth inhibition and morphological profilings. In the CC, bioactivity data are expressed in a vector format, which naturally extends the notion of chemical similarity between compounds to similarities between bioactivity signatures of different kinds.
This service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier.
The Chemical Probes Portal is a resource that supports the selection and use of chemical probes in biomedical research. It provides information, guidelines, and tools to ensure the quality and robustness of research using these reagents.
An expert review-based public resource to empower chemical probe assessment, selection and use.
ChemicalToolbox is a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model.
Chemistry42 is a software platform for de novo small molecule design and optimization that integrates Artificial Intelligence (AI) techniques with computational and medicinal chemistry methodologies. Chemistry42 efficiently generates novel molecular structures with optimized properties validated in both in vitro and in vivo studies and is available through licensing or collaboration.
Webserver to easily browse, navigate and mine chemical space. The first version features more than 8000 approved, in development, and rejected drugs, as well as over 47 000 environmental chemicals.
ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.
This package provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. This package aims to make a subset of these utilities available from within R.
Cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization.
Web server to design chemistry-driven focused libraries.
A server to predict chemokines and their receptors.
Chemoproteogenomics is a platform that integrates chemoproteomics, whole exome, and RNA-seq data to reveal the landscape of cysteine genetic variation, utilizing a customized two-stage FDR controlled proteomic search and a user-friendly FragPipe interface.
ChemOS is a portable, modular and versatile software package, which supplies the structured layers indis-pensable for operating autonomous laboratories. Additionally, it enables remote control oflaboratories, provides access to distributed computing resources, and comprises state-of-the-art machine learning methods.
Chemotion is a repository for chemistry research data that provides solutions for current challenges to store research data in a feasible manner, allowing the conservation of domain specific information in a machine readable format. A main advantage of the repository Chemotion is the comprehensive functionality, which offers options to collect, prepare and reuse data using discipline specific methods and data processing tools. For selected analytical data, automated procedures are implemented to facilitate the curation of the data. Chemotion provides functions to facilitate the publishing process of data and the citation of the deposited data
Open Source electronic lab notebook for chemists in academia.
Mapping between chemical perturbation and transcriptional response for non-cancer cells
ChemPix: an offline, hand-drawn hydrocarbon structure recognition tool using deep learning.
Machine learning package for chemical property prediction.
ChemProps is a RESTful API enabled database for composite polymer name standardization.
Ressource of annotated and predicted chemical-protein interactions.
This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. It provides a browser-based pipelining which requires no programming skills.
ChemScanner, a software that can be used for the extraction of chemical information from ChemDraw binary (CDX) or ChemDraw XML-based (CDXML) files and to retrieve the ChemDraw scheme from DOC, DOCX or XML documents. This can facilitate the reuse of chemical information embedded into diverse documents used as standard storage and communication instrument in chemical sciences.
ChemSchematicResolver IS A Toolkit to Decode 2D Chemical Diagrams with Labels and R-Groups into Annotated Chemical Named Entities.
Chemsearch is a cross-platform server application used to create, browse, and search a chemical compounds library.
ChemSpectra is a web-based spectra editor for analytical data. This web service provides NMR/IR/MS processing for jcamp/RAW/mzML files.
Various search options for searching the ChemSpider database.
ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads common chemical file formats using the Open Babel chemistry library. Spotlight can then index and search chemical data: molecular weights, formulas, SMILES, InChI, fingerprints, etc.
ChemStor is an open-source, automated computational system that can guarantee (mathematically verify a system is correct with respect to its specification), with regard to prescribed constraints, safe storage and disposal of chemicals used in academic, industrial, and domestic settings. ChemStor borrows concepts from formal methods - a branch of computer science capable of mathematically proving a specification or software is correct - to safely store or dispose of chemicals. If two or more chemicals can be combined in the same cabinet without forming possibly dangerous combinations of chemicals (while observing cabinet/shelf space constraints), then ChemStor determines that the storage configuration is safe.
ChemT is an open-source software for building chemical compound libraries, based on a specific chemical template. The compound libraries generated can then be evaluated, using several Virtual Screening tools like molecular docking or QSAR modelling tools.
ChemTables is a dataset for semantic classificationon tables in chemical patents.
A curated database of molecular tastants.
ChemTB is a tool for identification of active molecules against Mycobacterium tuberculosis through machine learning.
ChemVox is an interactive Amazon Alexa skill that uses speech recognition to perform quantum chemistry calculations. This new application interfaces Alexa with cloud computing and returns the results through a capable device. ChemVox paves the way to making computational chemistry routinely accessible to the wider community.
Improving annotation propagation on molecular networks through random walks.
CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.
CHEmical Shift Projection Analysis (CHESPA) and CHEmical Shift Covariance Analysis (CHESCA) can help reveal pathways of allosteric transitions in biological macromolecules by identifying changes in correlated Nuclear Magnetic Resonance (NMR) chemical shifts. CHESCA-SPARKY and CHESPA-SPARKY are plugins for the NMR analysis software NMRFAM-SPARKY
CheSPI (Chemical shift Secondary structure Population Inference) is a tool for a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder.
An R package and shiny app for processing, plotting, and interactive exploratory data analysis of full-length scRNA-seq as SingleCellExperiments
chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
Chewie Nomenclature Server (chewie-NS) is a web server that allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potential confidentiality issues and the need to compare results.
Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays.
CHFinder is a tool to characterize genes coding for a key part of the jawed vertebrate adaptive immune system immunoglobulins.
CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes.
Versatile and flexible pipeline for ChIA-PET data analysis.
ChIA-PIPE is a fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loop.
Quality control pipeline for ChIP-seq data using a comprehensive set of quality control metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The framework allows assessing quality of samples with sharp or broad enrichment profiles, whereas previously proposed metrics were not taking this into account. It provides a reference compendium of quality control metrics and trained machine learning models for scoring samples.
Robust detection of DNA looping interactions in Capture Hi-C data.
A pipeline for analysing Capture Hi-C data.
CHiCANE is a data processing and interaction calling toolkit for analysis and meaningful interpretation of CHi-C assays.
Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.
Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron–electron resonance (DEER).
Comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform | Visualization Tool for Protein Validation in Chimera Platform
This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.
Identifies chimaeric transcripts in RNA-Seq data
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences. It involves the different series of steps that operate to flag chimeric 16S rRNA sequences.To run it, you need NAST-formatted sequences generated by the included NAST-iEr utility.
Structure visualization for researchers, educators, and developers. Tutorials can be viewed in any browser, but those with click-to-execute links should be viewed from within ChimeraX for the links to work. To view a web page from within ChimeraX, start ChimeraX and use the command open URL (substituting in the actual URL), or navigate here using the ChimeraX menu: Help... Tutorials. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
Knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project, OMIM, PubMed and the Mitelman database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. It can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments.
Identifying the oncogenic potential of gene fusions exploiting miRNAs
Computation, analysis and visualization of global RNA networks. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and provides an interactive graph-based visualization for data exploration and interpretation. ChimericFragments detects true RNA-RNA interactions with high precision and is compatible with several widely used experimental procedures such as RIL-seq, LIGR-seq or CLASH. ||| HOMEPAGE BROKEN!
Chromatin Interaction Neural Network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences
Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.
ChIP-AP (Chromatin ImmunoPrecipitation Sequencing Analysis Pipeline) is an integrated ChIP-Seq analysis pipeline.
ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.
ChIP-Atlas is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.
ChIP-BIT2 is a software tool to detect weak binding events using a Bayesian integration approach.
ChIP-GPT is a large language model fine-tuned to extract metadata from biomedical databases, particularly focusing on chromatin immunoprecipitation (ChIP) targets and cell lines. It demonstrates high accuracy in extracting data even from records with errors and is adaptable to different databases.
Inferring active transcription factor modules to predict functional regulatory elements.
ChIP-Hub is an integrative web-based/Shiny application for exploring plant regulome.
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites.
The ChIP-seq web server provides access to a set of useful tools performing common ChIP-seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interoperability with other resources, in particular the motif discovery programs from the Signal Search Analysis (SSA) server.
Population size estimation for quality control of ChIP-Seq datasets | If you are not redirected automatically, follow the link
Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator).
The encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes.
R package that can be incorporated into the normalization workflow for chip-chip data, chromatin immunoprecipitation (ChIP) with microarray technology (chip).
Detects differentially bound sharp binding sites across multiple conditions considering matching control.
Web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.
ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.
Package with a quality control pipeline for ChIP-exo/nexus data.
CHIPIN is an R package that provides a normalization procedure to compare signals between ChIP-seq samples in different conditions; experiments should be performed using the same antibody.
Extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.
Combining data from ChIP-seq and ChIP-chip.
ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences.
The package includes functions to retrieve the sequences around the peak, obtain enriched GO terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other TF binding sites supplied by users. New functions have been added for finding the peaks with bi-directional promoters with summary statistics, for summarizing the occurrence of motifs in peaks and for adding other IDs to annotated peaks or enrichedGO.
CHIPS (CHromatin enrIchment ProceSsor) is an Snakemake analysis pipeline in to streamline the processing of ChIP-seq, ATAC-seq, and DNase-seq data.
This package implements functions to retrieve the nearest genes around the peak, annotate the genomic region of the peak, statistical methods for estimating the significance of overlap among ChIP peak data sets, and incorporate GEO database to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses.
R package for ChIP peak Annotation, Comparison, and Visualization.
ChipSeg is an automatic tool to segment bacteria and mammalian cells cultured in microfluidic devices. ChipSeg is a computational tool to segment bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy.
Tools for helping process short read data for chipseq experiments.
Identify protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but it is flexible enough to handle other types of experiments as well.
Chromatin Immuno-Precipitation followed by Sequencing is used to determine the binding sites of any protein of interest, such as transcription factors or histones with or without a specific modification, at a genome scale. The many steps of the protocol can introduce biases that make ChIP-Seq more qualitative than quantitative.
A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.
Combine all tasks required for analysis and quantitation of micro-array data – both DNA or protein arrays. It’s image processing routines may be also applied to automated evaluation and quantiation of microscopic images.
Free, open source software for analyzing high-throughput data such as NGS. It is available as a ready-to-run virtual machine (VM) containing a large collection of up-to-date analysis tools and reference data, such as Ensembl genomes indexed for aligners. The tools can be used on command line, or via an intuitive client GUI.
ChIPuana is a snakemake-based workflow for the analysis of ChIP-seq data from the raw fastq files to the differential analysis of transcription factor binding or histone modification marking.
Random access-enabling lossless and lossy compression method for ChIP-seq data.
This tool takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.
A basecaller for Oxford Nanopore Technologies' sequencers.
An allele-specific method for testing the association between molecular quantitative traits and phenotype-genotype interaction.
ChiTaH, a fast and accurate method for the discovery of known human chimeras or fusion genes using DNA-Seq or RNA-Seq data generated using NGS technologies
The improved database of Chimeric Transcripts and RNA-seq data. The comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.
ChloroDBPFinder is an R package that utilizes machine learning to recognize chlorinated disinfection byproducts (Cl-DBPs) from nontargeted LC-HRMS analysis. The tool provides a solution for identifying Cl-containing compounds in water samples and is freely available on GitHub.
Prediction of presence of chloroplast transit peptides and their cleavage sites in plant proteins.
Chloroplot is a web application for versatile plotting of organelle genomes.
CHM-eval, aka Syndip, is a benchmark dataset for evaluating the accuracy of small variant callers. It is constructed from the PacBio assemblies of two independent CHM cell lines using procedures largely orthogonal to the methodology used for short-read variant calling, which makes it more comprehensive and less biased in comparison to existing benchmark datasets.
Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater.
An R package for exploratory data analysis and interactive visualization of pain patient body map data.
CHOmics is a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
Analysis of X-ray fluorescence spectrum to yield curves for f' and f", as well as energies for MAD and SAD experiments.
CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.
Valen Group (Computational Biology Unit)
CHOPCHOP is a versatile tool for selecting target sites for CRISPR (Cas9, Cas9 nickase, Cas13, Cpf1/CasX) or TALEN-directed mutagenesis. The latest release of CHOPCHOP (version 3) includes many new features and visualization options, supporting over 200 genomes with whole-gene targeting and versatile search modes. The tool now enables precise RNA targeting with Cas13, supporting alternative transcript isoforms and predicting RNA accessibility using ViennaRNA's RNAfold. The update also introduces new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. For larger queries or handling unsupported genomes, a command-line version is available with additional functionalities. CHOPCHOP v3 is user-friendly and well-equipped to support diverse targeting applications, facilitating effective experimental design.
Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.
Implementation of classes and methods for large-scale SNP association studies.
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs.
Chord is an R package to remove single cells Doublets by integrating tools. Chord uses the AdBoost algorithm to integrate different methods for stable and accurate doublets filtered results.
Open-source algorithm for automatic choroid segmentation of OCT volume reconstructions
Chorus2 is a tool for design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization.
Predicts two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.
The Chromosome 7 database is a community-curated project which contains the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data.
ChrNet (Chromosome-based 1D-CNN network) is a tool for re-trainable chromosome-based 1D convolutional neural network for predicting immune cell types.
We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds.
Shiny-based framework for interactive analysis, visualization and integration of genomic data.
Image correction software for chromatic shifts in fluorescence microscopic images.
Chromas is a low-cost chromatogram file editor with search, vector sequence detection and multi-format sequence export functions, plus powerful batch processing.
An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
Chromatin Dynamics tool Multiscale Complex Genomics (MuG) VM
Interactive R/Shiny App for plotting chromatography profiles.
Fast and scalable breeding program simulator.
Analyzing spatial contact of chromosomes from Hi-C data.
A Dirichlet-Multinomial Mixture Model For Clustering Heterogeneous Epigenetic Data.
R package for drawing the schemes of karyotype(s) in the linear and circular fashion that can visualize cytogenetic marsk on the chromosomes. This tool has its own input data format that can be imported from the GenomicRanges data structure. This package can visualize the data in the BED file format.
ChromeBat is a bio-inspired approach to genome reconstruction.
ChromeGCN is a graph convolutional network for epigenetic state prediction using both sequence and 3D genome data.
An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot).
This package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map, that can be used to interactively identify probes and genes of interest.
ChromHMM is software for learning and characterizing chromatin states.
Displays the nodes and edges of the chromatin network using a real-time force model.
R package for interactive visualization of multi-omics data and annotation of chromosomes.
Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.
Tool for finding haplotypes in sequence data. Each individual is "painted" as a combination of all other sequences. It can output a range of features, including: Sample haplotypes, Expectation of the number of recombination events, and a range of related features. It can be used to generate PCA from dense data, for creating data summaries for fine STRUCTURE, and for dating admixture events.
Chromosight is an algorithm inspired from computer vision that can detect patterns in Hi-C maps. Chromosight has greater sensitivity than existing methods, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals.
R package for multimodal visualization of microarray data, DNA copy number alterations, cross-platform and cross-species comparisons,and genomic non-expression data obtained from public databases onto chromosomes.
ChromoZoom is a web-based genome browser currently hosting tracks for the yeast and human genomes.
Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.
ChromSCape is a user-friendly interactive Shiny/R application distributed as a Bioconductor package, that processes single-cell epigenomic data to assist the biological interpretation of chromatin landscapes within cell populations. ChromSCape analyses the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets.
This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.
Flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP-seq data.
Inferring transcription-factor-associated accessibility from single-cell epigenomic data.
Analysis of Heterogeneous Genomic Samples Using Image Normalization and Machine Learning.
Chronogram is an R package designed for data curation and analysis of infection and vaccination cohort studies. It allows for the integration of diverse data sources like PCR, sequencing, and symptom diaries into a tidy-like data structure to facilitate biological hypothesis testing.
High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture.
A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs
Chronos is an algorithm for inferring gene fitness effects from CRISPR knockout experiments. Chronos is competitive with or superior to the other CRISPR algorithms we tested given readcounts from only one late time point, but it will perform even better with multiple late time points if your experiment has them.
Chronumental is a tool for creating a "time-tree" (where distance on the tree represents time) from a phylogenetic divergence-tree (where distance on the tree reflects a number of genetic substitutions).
Chrysalis is a computational method that uncovers tissue compartments in spatial transcriptomics data using archetypal analysis without external reference data. It offers a unique visualisation approach for characterising tissue and identifying distinct cellular niches.
Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.
ChunkChromosome is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices.
Clinical-Inspired Network for Automated Skin Lesion Recognition.
Cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data.
CiberAMP is an R package that uses differential expression analyses to stablish accurate correlations between specific SCNVs and changes in expression in the genes affected by them.
deconvBenchmarking is a software package designed for benchmarking cell-type deconvolution methods. It implements a heterogeneous simulation strategy to generate more realistic bulk expression values and provides a user-friendly interface for assessing the performance of different deconvolution techniques.
Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.
CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq. It is a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.
Cross-platform training In CLinical Outcome PredictionS (ciclops) is a pipeline for building clinical outcome prediction models on training dataset and transfer learning on validation datasets.
CIDACS-RL is a indexing search and scoring-based record linkage system for huge datasets with high accuracy and scalability.
Genome-based transcript reconstruction and quantification from RNA-seq reads. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms
Classification of Intrinsically Disordered Ensemble Regions.
A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.
R package CIDER: Meta-Clustering for Single-Cell Data Integration and Evaluation
The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease.
CIEVAD is a collection of Nextflow workflows designed to facilitate rapid and on-demand deployment of end-to-end testing of genomic variant detection. It allows for the generation of synthetic test data and the evaluation of variant sets against that data.
Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them.
A package for reading, writing, visualizing, and manipulating CIFTI files in R.
Database and interactive platform for insect-associated trichomycete fungi.
An Ultrasensitive Chemical Isotope Labeling Assisted Pseudo-MRM Platform to Accelerate Exposomic Suspect Screening. Exposome is the future of next-generation environmental health to establish the association between environmental exposure and diseases. However, due to low concentrations of exposure chemicals, exposome has been hampered by lacking an effective analytical platform to characterize its composition. In this study, by combining the benefit of chemical isotope labeling and pseudo-multiple reaction monitoring (CIL-pseudo-MRM), we have developed one highly sensitive and high-throughput platform (CIL-ExPMRM) by isotope labeling urinary exposure biomarkers. Dansyl chloride (DnsCl), N< i>-methylphenylethylamine (MPEA), and their isotope-labeled forms were used to derivatize polar hydroxyl and carboxyl compounds, respectively ||| HOMEPAGE MISSING! ||| CORRECT NAME OF TOOL COULD ALSO BE 'MRM'
A freely available open-source software for the analysis of mucociliary activity in respiratory cells.
Integrated database for ciliopathy genes and ciliopathies.
CiliaQ is a simple, open-source ImageJ plugin for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images.
CilioGenics is an open-source database and method for predicting ciliary genes, combining data from single-cell RNA-seq, comparative genomics, and other sources to provide a CilioGenics score for each human gene.
This tool separates junction reads based on their linear or circular origin. Only non-ambiguous junction reads are used to compare the relative linear and circular transcript abundance. Together with the circ fraction (circ/(circ+lin)), a 95% confidence interval is provided.
CIMAP is an open-source Python toolbox for analyzing muscle activation patterns during cyclical movements using agglomerative hierarchical clustering. It offers a complete analysis framework and is freely available on GitHub.
Web-based tool for drug synergy analysis in small- and large-scale datasets.
CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds.
CimpleG is a simple package to find single-CpG based signatures for use in classification and deconvolution.
A speckle-tracking strain-based artificial neural network model to differentiate cardiomyopathy type. Click on the different areas to enter strain values.
CIMtools is a ChemoInformatics Modeling tools distributive. It Include ISIDA Fragmentor python wrapper and RDtool atom-to-atom mapper python wrapper.
The package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar. It calculates the chromosome instability index to quantitatively characterize genome-wide DNA copy number alterations. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses at the chromosome and cytoband level.
Compressed indexes for fast retrieval of FASTQ files.
Real-time tools for analysis of dynamic diamond anvil cell experiment data.
An R package for chromosomal instability analysis.
CINS combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie them.
Flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.
CIPHER-SC is the latest version of CIPHER, is a complete end-to-end prediction algorithm based on a context-aware network including single-cell data. CIPHER-SC is able to perform Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network with Single-Cell Data.
Cluster Identity Predictor (CIPR) is a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments. CIPR provides a graphical user interface to quickly score gene expression profiles of unknown cell clusters against mouse or human references, or a custom dataset provided by the user. CIPR can be easily integrated into the current pipelines to facilitate scRNAseq data analysis. During the analysis of single cell RNA sequencing (scRNAseq) data, annotating the biological identity of cell clusters is an important step before downstream analyses and it remains technically challenging.
Project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software.
CIR-Net is a method for Automatic Classification of Human Chromosome based on Inception-ResNet Architecture.
A pseudo-Siamese framework for circRNA-RBP binding sites prediction integrating BiLSTM and soft attention mechanism.
circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools to find circular forms of genes associated with specific molecular functions, biological processes or cellular components or predict their targeted microRNAs. This resource will enable researchers to rapidly identify circular RNAs relevant for their specific research question.
A unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs | circMeta is a unified computational framework for circRNA analyses. circMeta mainly includes three function modules: (i) provide a comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu and SINEs, competition score for forming circulation and RNA editing in back-spliced flanking introns (ii) develop a two-stage DE approach of circRNAs based on splicing junction reads (iii) develop a Bayesian hierarchical model for DE analysis of circRNAs based the ratio of circular reads to linear reads in spliced sites. circMeta mainly consists of four modules: circClass, circFeature, circJuncDE, circCLRDE | A unified computational framework for genomic feature annotation, differential expression analysis of circular RNAs
Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. March 31, 2018, the CircR2Disease has been updated. Circular RNAs (circRNAs) are widely expressed in diverse eukaryotic species and are characterized by covalently closed RNA loops through backsplicing events. They are known to function as miRNA sponges, regulators of alternative splicing, transcription factors and protein-coding templates for translation. To date, dysregulation of circRNAs have been associated with a group of diseases, i.e. various cancer. Here, CircR2Disease curated a database for experimentally supported associations between circRNAs and diseases, providing a platform for investigating mechanism of the disease-related circRNAs.
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model | Contextual_Regression_for_CircRNA | Contextual Regression for CircRNA
Pipeline for circRNA identification, transcript prediction, and abundance estimation.
circad is a comprehensive manually curated resource of circular RNA associated with diseases. Circular RNAs (circRNAs) are unique transcript isoforms characterised by back splicing of exon ends to form a covalently closed loop or circular conformation.
Integrating circadian genomics, transcriptomics, proteomics and metabolomics.
A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data.
Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection.
CircAST (CircRNAs with Alternative Spliced Transcripts) is a computational tool for circular RNA full-length assembly and quantification using RNA-Seq data with the back-spliced events detected by upstream circRNA identification tools, such as UROBORUS, CIRI2, or CIRCexplorer2.
circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This database contains 1,007,087 highly reliable circRNAs, of which over 81.3% have been assembled into full-length sequences. We profile their expression pattern, conservation, and functional annotation. We describe a novel multiple conservation score, co-expression, and regulatory networks for circRNA annotation and prioritization.
Explore public circRNA datasets and download tools to discover circRNAs in RNA-seq data.
Python code for Predicting the Back-Splicing Sites for Circular RNA Formation by Cross-Validation and Convolutional Neural Networks
CircDBG is an Algorithm of Circular RNA Detection by de Bruijn graph.
An online transcriptome platform for human circRNA expressions in cancers.
CIRCexplorer3 is a CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression. It is a computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq.
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements. CircFusion is a new software tool to detect linear fusions and f-circRNAs from RNA-seq data, both in samples where the fusion breakpoint is known and in a discovery mode.
An annotation algorithm circGPA that identifies prospective links between circRNAs and annotation terms. The algorithm is deterministic and based on generating polynomials.
circHiC is a Python library, built upon the widely used Matplotlib library, to display Hi-C-like data in circular strips together with the possibility to overlay genomic data (plots and heat maps). Tools are light and fast, aiming to facilitate the exploration and understanding of bacterial chromosome structuring data.
An R Package to Explore Circular RNA Impact on Gene Expression and Pathways. The goal of circIMPACT is to detect the molecular pathways associated with the expression levels of certain circRNAs.
A method for identifying genome-wide off-target cleavage sites of CRISPR–Cas9.
An integrated resource and analysis platform for human eccDNAs.
Tool to identify extrachromosomal circular DNA from ATAC-Seq data.
circLGB is a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing adenosine to inosine (A-to-I) deamination, A-to-I density and the internal ribosome entry site.
Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.
An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs.
CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions.
Database to integrate, analyze and visualize human disease-related circRNA transcriptome.
CircMiner is Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme. It is a sensitive and fast computational tool for detecting circular RNAs (circRNAs) from RNA-Seq data.
CircNet 2.0 provides a practical and user-friendly platform on which researchers can explore novel cancer biomarkers and circRNAs related to the pathogenesis, diagnosis, and therapy of malignant and other diseases.
Interactive web application for visualizing interaction networks of circular RNAs.
A GHMM-based tool for accurate prediction of coding regions in circRNA.
CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods.
Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.
Circos visualization of whole-genome sequence variations stored in VCF files .
CircParser is simple and fast pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumable host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using genome annotation file.
Identification of Plant CircRNAs with a CNN-BiGRU-GLT Model.
CircPlant is a tool for the exploration of plant circRNAs, their potential role as competing endogenous RNAs (ceRNAs), as well as function annotation. In addition to high efficiency and usability, CircPlant is confirmed to have robust high sensitivity and accuracy in detecting plant circRNAs, by analyzing simulated and real RNA-Seq datasets from Arabidopsis thaliana and Oryza sativa.
Web-based platform for design of specific circular RNA primers.
Circr is a computational tool for the prediction of miRNA:circRNA associations. It combines publicly available algorithms for de novo prediction of miRNA binding sites on target sequences with experimentally validated miRNA-AGO and miRNA:RNA sites in different organisms.
circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.
circRB is a tool for identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture.
circRIP: An accurate tool for identifying circRNA-RBP interaction.
circRNAprofiler is an R-based framework that only requires an R installation and offers 15 modules for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis. The pipeline used by circRNAprofiler is highly automated and customizable. Furthermore, circRNAprofiler includes additional functions for data visualization which facilitate the interpretation of the results.
A database for different circRNAs found in fluids.
CIRCScan is machine learning framework used for predicting circRNAs expression in a cell/tissue specific manner by machine learning based on epigenetic features.
CircSeqAlignTk is an R package designed for end-to-end analysis of RNA-seq data from circular genomes, particularly useful for studying organisms like viroids. It offers a user-friendly interface with both command-line and GUI options, and includes features for generating synthetic sequencing data.
circRNA-binding site identification based on self-supervised learning.
Software for computational circRNA analyses.
Fast simulation of Gaussian random fields via the Fast Fourier Transform
Circulant Embedding method for generating stationary Gaussian field
Compute descriptive and inferential statistics for circular or directional data.
Web application for creating circular sequence logos for DNA (or RNA) motifs. By virtue of the circular layout, it not only displays nucleotide stacks like the traditional sequence logo, but also depicts intra-motif dependencies using linked arches.
circularMT is a tool for creating customizable, publication-quality images of linear and circular mitochondrial genome maps. It allows users to visualize gene and noncoding feature complement, their order, and strand orientation, and is implemented in C# with binaries, source code, and user guides available on GitHub.
Stack-based RNA 3D structural alignment tool for circular matching.
A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans.
circVAR database is genome-wide archive of genetic variants for human circular RNAs Circular RNAs (circRNAs), the 3' and 5' ends of which are covalently linked, are a kind of widely distributed and abundant RNAs found in eukaryotic organisms in recent years. They could play as sponges for regulating microRNAs and RNA binding proteins. Our circVAR database aims to provide resources for circRNA-related genetic variants in healthy and diseased populations.
A large-scale Dataset for Clinically-Interpretable lung nodule Radiomics and malignancy prediction.
CIRI-vis is a tool for visualizing alignments of BSJ & RO merged reads and estimating the related abundance of isoforms according to the output of CIRI-full or CIRI-AS.
CirPred is a structure modeling and linker design system for circularly permuted proteins. It is a protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling.
CirRNAPL is a web server for the identification of circRNA based on extreme learning machine.
Shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks.
CISA has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools.
CisCross web service that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana gene
An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining.
CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.
R package that uses web browsers to visualize and manage protein-protein interaction networks.
cisRED is a database system for genome-scale computational discovery of regulatory elements.
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.
CIST (Confidence Intervals for SAGE Tags )is a Windows program for the analysis of gene expression data generated using SAGE (Serial Analysis of Gene Expression).
cisTEM (computational imaging system for transmission electron microscopy) is a complete software solution for processing cryo-electron microscopy images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
cis-regulatory topic modeling on single-cell ATAC-seq data. cisTopic v3: Faster topic modelling based on WarpLDA (see vignettes for details).
A web-based application with an analysis platform for CHIP-chip/seq and gene expression microarray data.
cit is a software package that provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators.
Citation.js is a format-independent, modular bibliography tool for the browser and command line.
The Contraceptive and Infertility Target DataBase. The CITDBase is a tool that provides a gateway for reproductive tissue-specific genes and proteins for research and the discovery of new contraceptive/infertility targets.
CITE-sort is an artificial-cell-type aware surface marker clustering method for CITE-seq data. CITE-sort conducts auto-gating with CITE-seq ADT data using recursive Gaussian Mixture Model. It is robust against artificial cell types that stem from multiplets. CITE-sort also provides concrete explanations of its internal decision process by constructing a biologically meaningful sort tree. See our paper for more details.
A manually curated database of cell-cell interactions in human.
Interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.
Combine literature search with text mining tools for biology.
CITL (Causal inference with time-lagged information) that infer the time-lagged causality of genes using scRNA-seq data
Citrullia is a program for fast and easy semi-automatic (manual) validation of citrullinated peptides.
Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers.
The Citrus Pan-genome Database provides assembled citrus genomes and resequencing data for cultivated citrus, enabling genomic research and facilitating breeding efforts. It includes resources for four ancestral taxa and information on interspecific introgressions and gene specializations.
An open access and integrated systems biology portal for the Huanglongbing (HLB) disease complex. user interface for the citrusgreening site https://citrusgreening.org/. Repo for code behind Psyllid Expression Network https://pen.sgn.cornell.edu. This site uses cookies to provide logins and other features. Please accept the use of cookies by clicking Accept. The citrus hosts infected by Huanglongbing or yellow dragon disease. The Asian citrus psyllid is a sap-sucking, hemipteran bug in the family Psyllidae. The new v2.0 genome is online!. Search genomic sequences and annotations. Having trouble viewing events on the calendar?
CitrusKB is a Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages.
Platform that provides experimentally supported signatures of cancer immunotherapy and analysis tools based on bulk and scRNA-seq data.
CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants.
Transcriptomic architecture of nuclei in the marmoset CNS. A companion Callithrix jacchus Primate Cell Atlas (CjPCA)
Composite Kernel Association Test (CKAT) is a R package for flexible and robust kernel machine based approach to jointly test the genetic main effect and gene-treatment interaction effect for a set of single-nucleotide polymorphisms (SNPs) in pharmacogenetics (PGx) assessments embedded within randomized clinical trials.
A predictive models for chronic kidney disease after radical or partial nephrectomy in renal cell cancer using early postoperative serum creatinine levels. An easy-to-operate web-based calculator for predicting the progression of chronic kidney disease.
Clinical Knowledge Graph (CKG) is a Python project that allows you to analyse proteomics and clinical data, and integrate and mine knowledge from multiple biomedical databases widely used nowadays.
A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer. Dark Kinase Knowledgebase Application. CKI - Dark Kinase Knaowledgebase App.
Checkpoint Therapeutic Targets and Modulators Database (CKTTD) for Cancer Immunotherapy is a comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. Immune checkpoints are regulators of the immune system which prevents the immune system from attacking cells indiscriminately.
CladeOScope is a tool for elucidating functional interactions via a clade co-evolution prism. CladeOScope is a bioinformatic method for the prediction of functional interactions between human genes based on their phylogenetic profile.
A tool for investigating the impact of labelled ligand affinity in competition experiments.
Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
High-performance Nanopore long-read variant calling in family trios with Trio-to-Trio deep neural networks.
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP.
CLAIRE stands for Constrained Large Deformation Diffeomorphic Image Registration. It is a C/C++ software package for velocity-based diffeomorphic image registration in three dimensions.
Contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity.
CLAM is an analytical framework for detecting co-regulated gene modules by integrating multi-omics data and known molecular interactions.
clampFISH 2.0, a method that uses an inverted padlock design to efficiently detect many RNA species and exponentially amplify their signals at once, while also reducing the time and cost compared with the prior clampFISH method.
ClaMSA is tool that uses machine learning to classify sequences that are related to each other via a tree. It takes as input a tree and a multiple sequence alignment (MSA) of sequences and outputs probabilities that the MSA belongs to given classes.
Constructing consensus trees and supertrees from multiple source trees
Classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal peptide, the number of cysteine residues and the associated functional annotations.
A web-server for automatic classification of proteins with special reference to multi-domain proteins.
A web portal for interactive exploration of the cardiovascular cellular landscape in health and disease.
Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations.
CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures (CLARITE) is as a tool to efficiently clean environmental data, perform regression analysis, and visualize results on a single platform through user-guided automation. It exists as both an R package and a Python package. Though CLARITE focuses on EWAS, it is intended to also improve the QC process for phenotypes and clinical lab measures for a variety of downstream analyses, including phenome-wide association studies and gene-environment interaction studies.
Clarity: An R package for Comparing SimiLARITY Matrices and comparing heterogeneous data using dissimilarity.
Shiny app for interactive visualisation of the bovine physical-genetic map.
Classification method based on a supervised sequence classification using discriminative k-mers.
Clarke EGA quantifies the accuracy of glucose estimates generated by meters as compared to reference
A Web Server to Identify In Vivo RNA-RNA Interactions from CLASH Data.
A fast and flexible fragment chainer that supports linear and sum-of-pair gap costs and uses highly time-efficient index structure, i.e., Johnson priority queues and range trees padded with Johnson priority queues. Chaining of short match fragments helps to quickly and accurately identify region of synteny that may not be found using common local alignment heuristics alone.
CMIP performs a series of analysis centered in the obtention of molecular interaction potentials using classic formalisms: Electrostatic interactions through coulombic potentials with several dielectric options or Poisson-Boltzmann equation Van de Waals potentials computed from the Lennard-Jones expression Electrostatic Solvation energy evaluated from PB potentials Hydrophobic Solvation from surface analysis with a variety of alternative scales.
Classical Molecular Interaction Potentials (CMIP)
The effect of uncertainty in patient classification on diagnostic performance estimations.
classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes.
Classifyber is a robust streamline-based linear classifier for white matter bundle segmentation.
ClassifyCNV is a command-line tool that implements the 2019 ACMG guidelines to evaluate the pathogenicity of germline duplications and deletions.
The software formalises a framework for classification in R with four stages: data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, although specialised variables for functions can be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes.
ClassifyTE is a stacking-based machine learning framework for hierarchical classification of transposable.
Automated structural analysis of cross-linking data.
An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data.
CLBTope: Conformational and linear B-cell epitope prediction
CLC-Pred (Cell Line Cytotoxicity Predictor) 2.0 is a web-service for in silico prediction of cytotoxic effect of chemical and natural compounds in non-transformed and cancer cell lines based on structural formula. CLC-Pred provides a prediction of the cytotoxicity of a compound to assess the relevance of the substance's inclusion in experimental screening.
De novo assembly algorithm of CLC Assembly Cell for both short and long reads.
Convert a cas file to sam or bam format.
Extract a consensus sequence from a read mapping. It operates on a cas file produced by the reference assembly programs.
Find positions where the reads indicate a consistent difference from the reference sequences. Optionally, consensus sequences can be written to a fasta file.
Convert CLC find_variations output into a snpEff compliant tabular format.
Map some reads to some reference sequences.
Print some information about a sequence file.
De novo and reference assembly SNP and small indel detection and annotation.
CLCL is a software for discovering non-coding RNA elements in fly’s 3’UTRs by structural clustering
Multispecies design of CRISPR/Cas9 libraries.
cLDLA is a Nextflow workflow for performing combined linkage disequilibrium and linkage analysis (cLDLA) to identify the genetic basis of complex traits. It requires a VCF file and phenotype file as input and includes workflows for SNP-based heritability estimation and result visualization.
CLEAN is a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score). The score is derived by correlating the clustering structure as a whole with functional categories of interest.
Use adapters definition file ADAPTER.txt and remove the adapters from the input read files. The program writes out the cleansed reads and the rejected reads. Nucleotides are also removed based on quality thresholds from the 5' and 3'.
clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads.It can trim bad quality regions, adaptors, vectors and regular expressions and also filters out reads that do not meet a minimum quality criteria.
CleanBSequences is a R package that cleans biological sequences massively, quickly, without errors and without internet connection. Biological sequences cleaning is performed by aligning the forward and / or revers primers or ends of cloning vectors with the sequences to be cleaned. After the alignment, new subsequences are generated without biological fragment not desired by the user.
Cleaner: R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays.
Public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
CleanEx database of gene expression profiles
Clean a transcript file so that it is useable for S-MART.
This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.
ClearCNV - CNV analysis in the presence of ambiguity and noise
A pipeline for using degradome data to find cleaved small RNA targets.
In-silico cleavage of polypeptide sequences.
A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.
CLEP is A Hybrid Data- and Knowledge-Driven Framework for Generating Patient Representations. CLEP is a framework that contains novel methods for generating patient representations from any patient level data and its corresponding prior knowledge encoded in a knowledge graph. The framework is depicted in the graphic below.
clevRvis provides an extensive set of visualization techniques for clonal evolution. Three types of plots are available: 1) shark plots (basic trees, showing the phylogeny and optionally the cancer cell fraction CCF); 2) dolphin plots (advanced visualization, showing the phylogeny and the development of CCFs over time); 3) plaice plots (novel visualization, showing the phylogeny, the development of CCFs and the development of remaining healthy alleles, influenced by bi-allelic events, over time). Moreover, the tool provides algorithms for fully automatic interpolation of time points and estimation of therapy effect to approximate a tumor's development in the presence of few measured time points, as well as exploring alternative trees.
Clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.
Computational tool for helping users identify new members of a pathway of interest, as well as the RNA expression datasets in which that pathway is relevant.
CLICK web server is a topology independent method of comparison of biomolecular 3D structures.
Click-ExM is a tool, which integrates click labeling into Expansion microscopy (ExM) to enable a ‘one-stop-shop’ method for nanoscale imaging of various types of biomolecule. By click labeling with biotin and staining with fluorescently labeled streptavidin, a large range of biomolecules can be imaged by the standard ExM procedure normally used for proteins.
Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc.
CLIJx-Assistant is an intuitive user interface for building custom GPU-accelerated image processing workflows using CLIJ2 in Fiji. It visualizes workflows as image date flow graphs while building them. It suggests what to do next and generates scripts and human readable protocols to facilitate reproducible bio-image analysis.
Cell line integrated molecular authentication.
Cell Line Integrated Molecular Authentication database and Identification tool. It represents a reference for validated molecular authentication of human cell lines independently from the platforms used.
ClimMobTools is an R package providing tools for data analysis and project management within the ClimMob platform, enabling experimental citizen science in agriculture. It supports decentralized, large-N trials using the tricot approach.
CLIN-IK-LINKS is a web-based platform that enables users to create, modify and delete mappings as well as to define and execute workflows. The CLIN-IK-LINKS platform allows the composition and execution of clinical data transformation workflows to convert EHR data into EHR and/or semantic web standards.
CLIN_SKAT is a package within the R programming language to (i) first extract clinically relevant variants (rare and common), followed by (ii) gene-based association analysis by grouping the selected variants.
Comprehensive information system for data stewardship in clinical trials, registries and other clinical/scientific databases. It is web-based application accessible via internet browser.
ClineHelpR is an R package for genomic cline outlier detection and visualization. ClineHelpR allows you to plot BGC (Bayesian Genomic Cline) output.
ClineHelpR is a R package that allows you to plot BGC (Bayesian Genomic Cline) output. After we ran BGC, we realized it wasn't easy to plot the BGC results, so we put together this package in the process of figuring it out.
Candidate Cancer-Related lncRNA Prioritization via Integrating Multiple Biological Networks. Identification and characterization of lncRNAs in cancer with a view to their application in improving diagnosis and therapy remains a major challenge that requires new and innovative approaches. We have developed an integrative framework termed "CLING", aimed to prioritize candidate cancer-related lncRNAs based on their associations with known cancer lncRNAs. CLING focuses on joint optimization and prioritization of all candidates for each cancer type by integrating lncRNA topological properties and multiple lncRNA-centric networks. Validation analyses revealed that CLING is more effective than prioritization based on a single lncRNA network. Reliable AUC (Area Under Curve) scores were obtained across 10 cancer types, ranging from 0.85 to 0.94. Several novel lncRNAs predicted in the top 10 candidates for various cancer types have been confirmed by recent biological experiments
ClinGen defines the clinical relevance of genes and variants for medical and research use, developing standards for data sharing and curation. The resource provides curated data on gene-disease relationships, pathogenicity of genetic variation, dosage sensitivity, and actionability of gene-disease interventions, available through a web portal.
ClinGen Variant Curation Interface is a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.
The tool enables to assess the pathogenity of Mendelian germline sequence variants.
An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies. Clinica is command-line driven and written in Python. It uses the Nipype system for pipelining and combines widely-used software packages for neuroimaging data analysis (ANTs, FreeSurfer, FSL, MRtrix, PETPVC, SPM), machine learning (Scikit-learn) and the BIDS standard for data organization.
Trajectory forecasting of clinical events using Transformer and Generative Adversarial Networks.
Recurrent Deep Network Models for Clinical NLP Tasks | Sentence detection for clinical notes | Training and evaluation expects .labels/.txt file pairs where .labels is a file with lines of tokens in space separated format as shown below, and .txt is the plain text of the document | [segment] [start index] [end index] [tag] [is_identifier] [token text]
Clinical-Longformer is a clinical knowledge enriched version of Longformer that was further pre-trained using MIMIC-III clinical notes.
Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.
Easy access to results of publications and genetic or drug information in other databases that are relevant to a clinical trials.
Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis.
Automatic generation of gene cluster comparison figures. Gene cluster comparison figure generator. A d3 chart for generating gene cluster comparison figures. clinker is a pipeline for easily generating publication-quality gene cluster comparison figures. Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file. clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.
Tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus. The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result. Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.
Takes variants as input and queries NCBI eutilities to generate ClinVar Variation Report scoring metrics. The overall goal is to generate annotations of use for given batches of variants to inform clinical interpretation. The metrics include: Clinotator Raw Score, Average Clinical Assertion Age, Clinotator Predicted Significance and eclassification Recommendation.
An integrated and user-friendly pipeline for quality control, filtering and trimming of Sanger and NGS sequencing data for hundred to thousands of samples/patients in a single run in clinical research.
ClinSV is a tool for clinical grade structural and copy number variant detection from whole genome sequencing data.
Python package for the analysis of trajectories in clinical data
A freely accessible, public archive of reports of relationships among medically important variants and phenotypes hosted by the NCBI. It integrates and cross-references data from multiple databases at NCBI. In addition to dbSNP and dbVar, it depends on MedGen to represent phenotype, Gene to represent genes, and on human RefSeqs to represent the location of sequence variation. Each record represents the submitter, the variation and the phenotype.
CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.
CliP is a tool for subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model.
A new method and implementation named ClipCrop for detecting SVs with single-base resolution
Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.
This tool is for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path.
p-value-free FDR control on high-throughput data from two conditions. A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions.
Clipplotr is a self-contained command-line tool written in R to facilitate comparative visualisation of CLIP data. It plots multiple CLIP tracks across a gene or region of interest with a range of normalisation and smoothing options. It can also optionally plot:.
Nextflow pipeline for comprehensive CLIP data analysis. CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry.
ClipSV (Structural variation detection with clipped reads) is a tool for improving structural variation detection by read extension, spliced alignment and tree-based decision rules. ClipSV was developed to detect structural variations by read extension, spliced alignment and local assembly. It primarily depends on clipped reads from short-read sequencing platform. ClipSV was optimized to discover INDELS (5bp-50bp) and structural variations (>=50bp) in human genomes.
Automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.
“Cliquely” is a tool that discovers protein-protein interaction networks by identifying proteins that are functionally linked to each other.
A Comparative Effectiveness Study of Newborn Screening Methods for Four Lysosomal Storage Disorders. CLIR - Collaborative Laboratory Integrated Reports.
this work is to segment the cytoplasm and the nucleus of the CLL microscopic blood images
Chronic Lemphocytic Leukemia Cell Segmentation Using Watershed and optimal Thresholding
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. Improving residue-residue contacts prediction. Welcome to use clmDCA for protein contact prediction. COLORS is more effcient than PSICOV, mfDCA and plmDCA.
Contrastive Learning framework for Metagenome Binning (CLMB) is a framework for metagenomic binning. The basic idea of the CLMB module is that, since the noise of real dataset is hard to calculate, we add simulated noise to the data and force the training to be robustto them. By effectively tacking the noise in the metagenomics data using the contrastive deep learning framework, it is possible to group pairs of contigs that originate from the same type of bacterial together while dividing contigs from different species to different bins.
An R Package for Linear Mixed Effects Models under Inequality Constraints. The R package CLME implements a linear mixed effects model where the regression coefficients are subject to linear order constraints. Inference is based on bootstrap methodology. Constrained Inference for Linear Mixed Effects Models. Estimation and inference for linear models where some or all of the fixed-effects coefficients are subject to order restrictions. This package uses the robust residual bootstrap methodology for inference, and can handle some structure in the residual variance matrix.
A deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types.
Clockor2 is a client-side web application for conducting root-to-tip regression to assess the degree to which molecular data behave in a clock-like fashion. It allows users to quickly fit local and global molecular clocks and is freely available online.
clogitRV is tool for conditional logistic regression with a robust variance estimator.
This tool fits binomial distributions to counts obtained from NGS data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.
ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues
Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles.
ClonalOrigin is a tool for recombination detection in bacteria. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
Reconstructing the evolutionary history of a B cell lineage with minimum spanning tree and genotype abundances.
Examining the Spatial Clonal Architecture of Tumors.
Automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. CLoNe - Clustering based on local density neighborhoods. CLoNe is a clustering algorithm with highly general applicability. Based on the Density Peaks algorithm from Rodriguez and Laio (Science, 2014), it improves on it by requiring a single parameter, 'pdc', that is intuitive and easy to use. 'pdc' can be incremeted if there are too many clusters, and decremented if there are not enough. Integer values between 1 and 10 are usually enough, with many values leading to the same results in most cases.
Clone Mapper is an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans.
GUI for the sub-tasks of processing raw NGS data by wrapping available implementations of various algorithms.
a tool for identifying homologous immunoglobulin and T cell receptor sequences in large databases. ClonoMatch is an open source full-stack web service for an immunoglobulin Clonotype matching database. There are multiple steps for setting up ClonoMatch on your own system and it is recommended that the instructions for each step be read thoroughly before beginning. If you are familiar with the technologies involved these instructions will probably be straight forward, but there are a couple of steps that are custom to ClonoMatch and essential to getting the app working. ClonoMatch is webservice that allows users to input V3J clonotypes to search for similar B cell or T cell receptor sequences derived from adaptive immune repertoire sequencing (AIRR-seq). Single Clonotype Search Search Multiple Clonotypes From File.
The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
cLoops2: full stack analysis tool for chromatin interactions.
A framework for closed-loop neurofeedback for real-time EEG decoding.
A platform for closed-loop intracranial stimulation in humans. Targeted interrogation of brain networks through invasive brain stimulation has become an increasingly important research tool as well as a therapeutic modality. The majority of work with this emerging capability has been focused on open-loop approaches. Closed-loop techniques, however, could improve neuromodulatory therapies and research investigations by optimizing stimulation approaches using neurally informed, personalized targets. Specifically, closed-loop direct electrical stimulation tests in humans performed during semi-chronic electrode implantation in patients with refractory epilepsy could help deepen our understanding of basic research questions as well as the mechanisms and treatment solutions for many neuropsychiatric diseases. However, implementing closed-loop systems is challenging
Closha 2.0 is a cloud computing service designed for analyzing massive genomic datasets, providing a user-friendly platform for researchers of all skill levels. It supports Python, R, and shell script programming and executes tools in independent containers for stable and reproducible workflows.
A curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases, mutation and links to external databases.
a web tool for the development of quantitative structure-activity relationship models in drug discovery. The Cloud 3D-QSAR Server is developed to help running 3D-QSAR jobs by submitting molecular structures and pKi values on web pages which is much more convenient than by command line. This server use Open3DQSAR as the QSAR software and Open Babel to process structure stuff.
assembly of synthetic long reads using de Bruijn graphs | SPAdes Genome Assembler. Contribute to ablab/spades development by creating an account on GitHub | You can’t perform that action at this time | You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session
an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation. Last updated: July 31, 2020. Please check our preprint on biorxiv and our published paper on Bioinformatics. Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google. Fortsæt til Google Cloud Platform. Skriv den tekst, du hører eller ser. To be able use CloudASM, you need to create an account on https://cloud.google.com/ and set up how you want to be billed (e.g. with a credit card). As of January 2020, GCP offers $300 in credits for opening an account -- which is enough to test this pipeline.
CloudBridge provides a consistent layer of abstraction over different Infrastructure-as-a-Service cloud providers, reducing or eliminating the need to write conditional code for each cloud.
CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.
CLOUDe is a suite of machine learning methods for predicting evolutionary targets of gene deletion events from expression data.
CloudReg is a tool for cross-modal, nonlinear, image registration between arbitrary image volumes.
Isoform assembly using bulk barcoded RNA sequencing data.
a clustering-oriented de novo assembler for Illumina sequences. Clover is a clustering-oriented de novo assembler for Illumina sequences, which bases on the de Bruijn graph method and utilizes a novel k-mer clustering approach from the overlap-based concept to improve the robustness with respect to sequencing error especially using large k-mers.Clover achieves a superior assembly quality in terms of corrected N50 and E-size.
An Efficient DNA Clustering algorithm based on Tree Structure.
Data analysis in the life sciences often suffers from reproducibility, standardization and accessibility issues and these problems become even more severe with the escalating volume and complexity of data. While best-practice data analysis workflows try to tackle these challenges, many existing workflows still grapple with scalability issues, limited portability due to tight coupling with the execution environment and accessibility constraints arising from the absence of user-friendly interfaces. To overcome these issues, we created CloWM, a comprehensive cloud-based workflow management platform that allows the generic transformation of command-line driven workflows into user-friendly web-based services. CloWM offers the seamless integration of (1) scientific workflows written in the Nextflow DSL, (2) robust data storage, (3) a highly scalable compute layer for data-intensive analysis tasks and (4) a user-friendly interface.
CLPred is a tool for sequence-based protein crystallization predictor using bidirectional recurrent neural network with long short-term memory (BLSTM). BLSTM to capture the long-range interaction patterns between k-mers amino acids.
Pruning Networks With Cross-Layer Ranking & k-Reciprocal Nearest Filters.
Continual Learning Benchmark for Remote Sensing Image Scene Classification. This is a database designed for the new task named Continual/Lifelong learning for remote sensing image scene classification. The existing remote sensing image scene classification datasets use static benchmarks and lack the standard to divide the datasets into several sequential learning training batches, which largely limits the development of Continual/Lifelong learning in remote sensing image scene classification. The proposed CLRS data set consists of 15,000 remote sensing images divided into 25 scene classes, namely, airport, bare-land, beach, bridge, commercial, desert, farmland, forest, golf-course, highway, industrial, meadow, mountain, overpass, park, parking, playground, port, railway, railway-station, residential, river, runway, stadium, and storage-tank. Each class has 600 images, and the image size is 256x256. The resolution of the images ranges from 0.26 m to 8.85 m.
Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.
Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.
a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries. Choose the library format of your file.
CLUE (Constrained LUmping for differential Equations) is a tool for exact maximal reduction of kinetic models by constrained lumping of differential equations.
Clustering Markov Packager Across K- was developed in order to aid users analyse the results of STRUCTURE-like programs. The main pipeline offers a full pipeline for the summation and graphical representation of the results previously obtained by the user using a STRUCTURE-like program.
Cluster matching and permutation program with integer linear programming.
Accurate Clustering-based Ensemble Method to Predict Motor Imagery Tasks from Multi-channel EEG Data.
ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.
For analyzing and comparing accessory genomic elements (AGEs) between genomes.
Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris. Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.
Finds the best global alignment for a set of input sequences (nucleic acid or protein).
ClustAll is an R package designed for unsupervised patient stratification using clinical data. It facilitates the identification of multiple robust stratifications, even with complex clinical data like missing values and correlated data types.
Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.
Multiple sequence alignment using guide trees and HMM profile-profile techniques.
Align two or more protein sequences on the UniProt web site using ClustalOmega.
JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.
Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV).
General purpose global multiple sequence alignment program for DNA or proteins.
Phylogenetic tree generation from an alignment using neighbor-joining or UPGMA.
ClustalW is a general purpose multiple sequence alignment program for DNA or proteins
This package implements several techniques for the comparison and visualisation of relationships between different clustering results. These relationships are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection: the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness.
clusTCR is a Python interface for rapid clustering of large sets of CDR3 sequences. It is a two-step clustering approach that combines the speed of the Faiss Clustering Library with the accuracy of Markov Clustering Algorithm.
A interactive web-based tool to facilitate effective and intuitive SARS-CoV-2 geographic data exploration and visualization across the USA.
The tool is designed to perform radiomics harmonization on large and heterogeneous datasets, where the risk of over-harmonization is present. Instead of directly applying harmonization based on predefined batch labels, the tool first identifies groups of batches that share similar characteristics through clustering of the radiomics data. It then performs harmonization using these cluster-derived labels. The tool allows the harmonization of radiomics variables using two methods: (1) original ComBat (Rabinovic, 2007) method, where each original batch group is considered for the harmonization process and (2) cluster-based ComBat method, where batch groups with similar radiomics characteristics form clusters and the latter are being considered for the harmonization process.
Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)
Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
A command-line pipeline tool which uses common cluster managers to run bioinformatics analysis pipelines.
The Cluster Randomised Trials Stepped Wedge website provides resources and information related to cluster randomised trials and stepped wedge designs, aiming to promote high-quality research in these methodologies. It offers a collection of links to relevant papers and announcements related to the field.
ClusterApp is an R Shiny application designed to guide cluster studies based on GPS data, streamlining the process of data management and analysis for wildlife researchers. The application facilitates a step-by-step guide and is demonstrated with data on brown bears and gray wolves.
ClusterCAD provides a database and web-based toolkit designed to enable researchers to harness the potential of type I modular polyketide synthases and nonribosomal peptide synthetases for combinatorial biosynthesis.
Cluster DNA sequences using Fourier power spectrum
This package provides functions for running and comparing many different clusterings of single-cell sequencing data.
Simple and flexible bioinformatics pipeline that automates and standardizes bioinformatics analyses on high-performance cluster environments.
Web-based heatmap visualization and analysis tool for high-dimensional biological data.
This program creates clusters by GA tool box
Create a clustering summary tab for cd-hit and CROP.
The ClusteringSuite is the software package that includes the cluster analysis tool.
Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.
ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002).
a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. Source Code and Supplementary Materials for ClusterM. · The relevant files can be found in the [zip] file.
Multi-algorithm clustering app for Cytoscape.
ClusterMatch is a software resource that aligns single-cell RNA sequencing data at the multi-scale cluster level using a stable matching optimization model. It leverages canonical correlation analysis, Louvain clustering, and marker gene sets to improve data integration and cell type annotation.
A knowledge-integrated clustering approach based on expression profiles of gene sets. ClusterMine is a knowledge-integrated clustering approach to cluster samples based on gene expression profile. Two inputs are required to run ClusterMine: (1) a list of gene sets, (2) gene expression data matrix with genes in rows and samples in columns (row names are RefSeq gene symbols). ClusterMine (1) uses piror gene sets that often contain a set of functionally related genes to partition gene expression data into gene-set-wise subdata, (2) perform clustering analysis for each subdata, and (3) combine the clustering results of all subdata into a final clustering as the output.
Efficient parallelization of genomic analyses.
This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.
A nucleus segmentation framework, namely ClusterSeg, to tackle nuclei clusters, which consists of a convolutional-transformer hybrid encoder and a 2.5-path decoder for precise predictions of nuclei instance mask, contours, and clustered-edges.
Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.
ClusterSheep is a GPU/CUDA-accelerated software tool for large-scale clustering of tandem mass spectra from shotgun proteomics.
This package provides tools to assess if clusters have a separation different from random or permuted data. It investigates clusters of two or more groups by first, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.
This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.
The clusterv R package implements a set of functions to assess the reliability of clusters discovered by clustering algorithms. This library is tailored to the analysis of high dimensional data and in particular it is conceived for the analysis of the reliability of clusters discovered using DNA microarray data.
Free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.
An R package for automated single-cell RNA sequencing cluster classification. Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets. clustifyr classifies cells and clusters in single-cell RNA sequencing experiments using reference bulk RNA-seq data sets, sorted microarray expression data, single-cell gene signatures, or lists of marker genes
An R package to build predictive genomic signatures of microbial phenotypes
A scalable version of the clustMMRA pipeline for the identification of genomically co-clustered microRNAs driving cancer subtypes.
In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.
Consensus clustering applied to multi-omic disease subtyping.
On the robustness of graph-based clustering to random network alterations. clust.perturb is an R package designed to test the robustness of graph-based clusters by randomly rewiring a portion of the underlying network and reclustering. Robust clusters “stick together” even after network rewiring, while non-robust clusters do not. Robustness is quantified using maximum Jaccard index.
A cluster-guided short read de novo transcriptome assembly pipeline.
a structure informed clustering strategy for population stratification. This package performs agglomerative hierarchical clustering with the Mahalanobis distance based Genetic Relationship Matrix (GRM) representing the population-level covariance (LD) for the genetic markers. Genome-wide association studies (GWAS) have been extensively used to estimate the signed effects of trait-associated alleles and compute polygenic risk scores.
Dynamic Visualization and Fast Computation for Convex Clustering via Algorithmic Regularization. clustRviz aims to enable fast computation and easy visualization of Convex Clustering solution paths. Note that RcppEigen (which clustRviz internally) triggers many compiler warnings (which cannot be suppressed per CRAN policies). Many of these warnings can be locally suppressed by adding the line CXX11FLAGS+=-Wno-ignored-attributes to your ~/.R/Makevars file. To install an R package from source, you will need suitable development tools installed including a C++ compiler and potentially a Fortran runtime. Details about these toolchains are available on CRAN for Windows and macOS.
Web tool which allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box.
Comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.
cMatch is a simple, lightweight tool to perform quality control of modular synthetic constructs at speed and scale
CMBD (Cancer Metabolic Biomarker knowledge Database) a manually curated cancer metabolic biomarker knowledge database.
Cross-mapping Correction is a set of modern high-throughput technologies which enable deep sequencing of non-coding RNA species on an unprecedented scale. When mapping such small RNAs to the genome, cross-mapping may occur, in which RNA sequences originating from one genomic locus are inadvertently mapped to a different locus. This may give rise to spurious novel RNAs, as well as spurious editing sites in known miRNAs.
CMCompare wbe server uses covariance models to compare infernal RNA family models to identify models with poor specificity and explore the relationship between models.
Risk prediction in cutaneous melanoma patients from their clinico-pathological features. CMcrpred:Risk prediction in cutaneous melanoma patients using clinical featurs
Database of osteogenesis imperfecta and type III collagen variants.
Chinese Millionome Database (CMDB), a database that contains 9.04 million single nucleotide variants (SNV) with allele frequency information derived from low-coverage (0.06×–0.1×) whole-genome sequencing (WGS) data of 141 431 unrelated healthy Chinese individuals.
CMDSR is a novel conditional meta-network framework which helps the SR framework learn how to adapt to changes in the degradation distribution of input.
CMEIAS Color Segmentation is a free, improved computing technology designed to alleviate the laborious task of segmenting foreground objects of interest (e.g., microbes) from background in complex digital micrographs, as commonly encountered when preparing digital images of microbial populations and communities in environmental samples for quantitative image analysis.
Contrast motif finder that finds motifs with differential enrichment between two datasets. It aims to take advantage of multiple high quality binding datasets to identify subtle regulatory signals, such as context-dependent motifs, within bound sequences. It is specifically designed to discriminate between two sets of bound sequences and takes into account false positive sites when updating PWMs and other model parameters.
an accurate imputation tool for single-cell RNA-seq data.
The cmfinder program infers an alignment and consensus secondary structure of an RNA, using unaligned sequences as input.
A script for predicting drug-disease associations via multi-task learning based on collective matrix factorization.
A parallel acceleration tool for classical frequent subgraph mining algorithm. The core idea is to employ parallel techniques to parallelize extension tasks, so as to reduce computation time. On the other hand, multi-node strategy is employed to solve the problem of memory constraints.
An efficient quality score compressor with random access functionality.
cmirC is a database and analysis tool providing insights into clustered miRNAs and their relationship with copy number variations and DNA methylation in cancer. It allows users to explore miRNA expression patterns and identify regulatory mechanisms associated with cancer progression.
CMLC is an R package implementing a novel approach for computing a variant of eigenvector centrality for multilayer networks with inter-layer constraints. The package facilitates the analysis of network relationships across multiple layers and is accompanied by example vignettes and a homepage with installation instructions.
CMM (Coupled Mixed Model) is used to simulnateously conduct genetic analysis for independently collected data sets of different related phenotypes. CMM aims to achieve this goal by inferring all the information enclosed by dashed lines in the following figure.
CMNPD is the comprehensive marine natural products database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various physicochemical and pharmacokinetic properties, standardized biological activity data, systematic taxonomy and geographical distribution of source organisms, and detailed literature citations. It is an integrated platform for structure dereplication (assessment of novelty) of (marine) natural products, discovery of lead compounds, data mining of structure-activity relationships and investigation of chemical ecology.
C-MORE (cellular morphology recognition) is a workflow from bench to data analysis tailored for heterogeneous primary cells using the R package cmoRe.
CMorph is a script tracking algorithm for cell motion and morphology.
CmPI (CELLmicrocosmos 4.2 PathwayIntegration) is a Java-based 3D software which can be used to map 3D pathways - such as metabolic networks, Protein-Protein interaction networks, etc. - onto a virtual cell model. For this purpose, a database is queried in the background using protein/gene identifiers as input. The user can chose between different localization information by using an interactive table or linked bar charts with different categories. Cell environments can be explored in 3D in different navigation modes. Also, stereoscopic rendering is supported.
CELLmicrocosmos 4 PathwayIntegration (CmPI)
The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.
CMRSegTools: an open-source application software designed for the segmentation and quantification of myocardial infarct lesion enabling full access to state-of-the-art segmentation methods and parameters, easy integration of new algorithms and standardised results sharing.
The cms is an R package that uses tabular data from rat epilepsy studies and applies a composite measures scheme (via PCA) to select the most prominent features. Further, variables can be selected to perform cluster analysis on a subset in order to build a composite score. Finally, the cluster distribution is displayed for the subgroups and allows severity assessment between animal models.
A heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment.
Consensus molecular subtyping of colorectal cancer pre-clinical models.
Removes lower scoring overlaps from cmsearch results. This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output.
CMTT-JTracker is a fully test-time adaptive framework for automated cell tracking, designed to balance computational efficiency and accuracy across diverse cell datasets. It combines pre-segmentation and multi-task learning with spatial attention to achieve high tracking performance.
CMTTdb (The Cancer Molecular-Targeted Therapy database) is an integrated database to store relevant information about molecular targeted agents as well as their combinatorial approaches in clinical trials and studies for cancer treatment. It contains the information from public available clinical trials to obtain the clinical agents, their corresponding targets, cancer subtypes, biomarkers, clinical features of the patients, as well as the treatment modalities (monotherapy or combinatorial therapies)
An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping. It enables antiviral drug resistance genotyping, with Human Cytomegalovirus sequencing data.
Contact Map Web Viewer (CMWeb) is an online tool for studying basic properties of residue-residue contact formation and contact clusters. CMWeb can used to visualize contact maps, link contacts and display them in 3D or multiple sequence alignments, predict residue contacts, or calculate various contact statistics.
Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.
CNA2Subpathway is an R package for identification of dysregulated subpathway driven by copy number alterations in cancer.
CNA_origin is a Deep Learning Framework to Predict Tumor Tissue-of-Origin Based on Copy Number Alteration.
CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-controlled situ synthesis of DNA microarrays, and is the highest density and widely used chip preparation technology. In addition, agilent aCGH (array-based Comparative Genomic Hybridization) platform also provides high performance, high resolution chip data. The raw array data were collected from GEO (Gene Expression Omnibus) and TCGA (The Cancer GenomeAtlas) databases. Genomic DNA copy number variations (CNVs), a type of structure variations, is one of the key hallmarks of carcinogenesis.
CNAHap is a tool to estimate tumor allele-specific copy numbers and perform germline haplotyping along segments with imbalanced copy numbers.
Web server for rigidity theory-based thermal unfolding simulations of proteins so to link structure with function.
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
CNAnova is a stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data. It runs from the command line on the Linux platforms and is composed of several modules written in the R programming language.
CNApp is a user-friendly web tool that offers sample- and cohort-level association analyses, allowing a comprehensive and integrative exploration of CNAs with clinical and molecular variables. CNApp generates genome-wide profiles with tumor-purity correctiion, calculates CNA levels by computing broad, focal and global CNA scores (BCS, FCS and GCS, respectively), identifies CNAs associated with clinical features and molecular annotated variables and uses machine learning-based predictions to classify samples by using segmented data from either microarrays or next-generation sequencing. CNApp provides a unique scenario to comprehensively analyze CNAs and integrate them with molecular and clinical features.
An integrated environment for metabolic network analysis.
CNAqc is a package for quality controlling bulk cancer sequencing data to computationally validate clonal and subclonal copy number alterations. It is validated using single-cell data and incorporated into a clinically accredited bioinformatics pipeline.
CNAseg is a novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses the Skellam distribution to compare read depth in tumour and control samples, which allows the use of smaller window sizes for copy number estimation and leads to greater sensitivity in pinpointing breakpoints for small CNAs.
iCNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumours. CNAsim can be used to generate copy number profiles with noise patterns that mimic those of single-cell CNA detection algorithms, and to generate DNA-seq data for sampled cells.
User-guided local and global copy-number segmentation for tumor sequencing data.
CNCA aligns multiple small, closely related annotated genomes, typically viruses, using information from both protein and nucleotide sequences to guarantee no frameshifts. The tool constructs multiple alignments and integrates coding and non-coding sequences.
CNCDatabase(Cornell Non-Coding Cancer driver Database) provides a helpful resource for researchers to explore the pathological role of non-coding alterations and their associations with gene expression in human cancers. This database provides the list of non-coding cancer drivers in gene promoters, enhancers, ncRNAs and CTCF-cohesin insulators published in over 25 studies. It is created from text mining and manual curation to the PubMed articles.
cncRNAdb is a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function.
cnCV is an R package for Consensus Nested Cross-Validation.
Program to detect copy number variation in inbred mouse strains.
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
CNest - Copy Number Methods for Detection and Genome Wide Association Tests
China National GeneBank DataBase (CNGBdb) is a uniﬁed platform built for biological big data sharing and application services to the research community. Based on the big data and cloud computing technologies, it provides data services such as archive, analysis, knowledge search, management authorization, and visualization.
Convolutional neural network based predictor for β-Lactamases (BL) and their classes.
CNN-based survial prediction model combining with prognosis-related cascaded Wx feature selection.
CNN-peaks is a Convolution Neural Network(CNN) based ChIP-Seq peak calling software. ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection.
CNN-PepPred is an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets. Application to peptide-MHC class II binding prediction.
CNN-SVR is a deep learning-based method for CRISPR/Cas9 guide RNA (gRNA) on-target cleavage efficacy prediction. It is composed of two major components: a merged CNN as the front-end for extracting gRNA and epigenetic features as well as an SVR as the back-end for regression and predicting gRNA cleavage efficiency.
Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction.
CNN-Pred is a machine learning tool to accurately predict single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins (DSBs).
A CNN structure for training models for predicting arginine methylation sites based on the One-Hot encoding of peptide sequence.
CNNAthUbi is a tool for ubiquitination site prediction for Arabidopsis Thaliana using convolutional neural networks (CNNs).
CnnCrispr is a deep learning method for sgRNA off-target propensity prediction. It automatically trained the sequence features of sgRNA-DNA pairs with GloVe model, and embeded the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers.
Cnngeno is a high-precision deep learning based strategy for the calling of structural variation genotype. The current hand-crafted features and parametric statistical models used for genotype calling are still greatly influenced by the size of structural variations and the coverage of the next sequencing data.
have ability to extracts both local contexts and long-range interdependencies by combing multi-scale CNN and highway network. The evaluations on common datasets and comparisons with state-of-the-art methods indicate that CNNH_PSS is an useful and efficient tool for protein secondary structure prediction.
Detection of structural variants by encoding long-read alignment information and convolutional neural network.
A CNN-based predictor website for identifying the optimal growth temperatures of prokaryotes using only genomic k-mers distribution.
Robust models for splice site prediction using convolutional neural networks.
A CNN approach for multiple tree classification. It returns a number of clusters of the input phylogenetic trees for different-size sets of trees.
Detect and quantify CNVs in prokaryotic whole-genome sequencing data. After aligning WGS reads to a reference genome, we count the individual reads in a sliding window and normalize these counts for bias introduced by differences in GC content.
This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.
This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.
This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).
CNpare is designed to compare and contrast genome-wide tumour copy number profiles.
Bayesian hierarchical mixture models for batch effects and copy number.
CNGB (China National GeneBank) Nucleotide Sequence Archive (CNSA) is a service that provides online data submitting of data and metadata of projects, samples, experiments and sequencing. The CNSA is a system for archiving global omics data, dedicated to the storage, management and sharing of omics data, promotes the reuse of omics data and the development of life sciences.
Imputation, consistent segmentation, statistical analysis, and visualization of copy number profiles.
CNSsolve (Crystallography & NMR System or CNS) is an X-ray crystallography suite used for refinement, phasing, and molecular replacement
This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.
A multimodal deep-learning-based network for cranial nerves tract segmentation.
PennCNV is a software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays, handling Illumina and Affymetrix data and others with appropriate preparation. The tool is implemented in Snakemake and automates CNV detection and analysis, including quality control and frequency assessment.
A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database.
CNV-JACG is a random forest based framework for assessing the accuracy of CNVs detected base on paired-end whole genome sequencing data.
CNV-PG is an application written in Python, including two parts: CNV predicting (CNV-P) and CNV genotyping (CNV-G). For CNV-P, we trained on a subset of validated CNVs from different CNV callers separately to obtain the corresponding classifier used for the identification of true CNVs. For CNV-G, a genotyper, which is compatible with existing CNV callers and generating a uniform set of high-confidence genotypes.
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
The CNV-clinviewer is a user-friendly web-application for the interactive visualization, genomic exploration and standardized clinical significance interpretation of large copy-number variants (CNVs).
CNV-P: A machine-learning framework for filtering copy number variations.
Program for detecting the integrated copy number veriation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria. The result is a VCF format genotype file which can be used in GWAS/QLT research.
CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.
CNVfilteR is an R/bioconductor package to identify false positives produced by germline NGS CNV detection tools.
This package is intended to facilitate gene-set association with rare CNVs in case-control studies.
Joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.
An open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage.
Multi-ethnic database for identifying copy number variations associated with cancer. View gene-centric CNV profile collected from healthy individuals and multiple cancer types.
CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.
CNV discovery and genotyping from read-depth analysis of personal genome sequencing.
Detecting intergenic copy number variation using off-target exome sequencing data.
A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.
CNVpytor is a Python package for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.
This tool uses NGS data to measure human gene copy number for multiple samples, indentifying SNPs tagging copy number variants and detecting copy number polymorphic genomic regions.
This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.
CNVxplorer is a web server suited for the functional assessment of CNVs in a clinical diagnostic setting. CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs. It provides sequence constraint metrics, impact on regulatory elements and topologically associating domains, as well as expression patterns. Analyses offered cover (a) agreement with patient phenotypes; (b) visualizations of associations among genes, including those mediated by regulatory elements, and transcription factors; (c) enrichment on functional and pathway annotations; and (d) co-occurrence of terms across PubMed publications related to the query CNVs. A flexible evaluation workflow allows dynamic re-interrogation in clinical sessions.
CO-19 PDB 2.0 is a comprehensive database integrating COVID-19 and cancer-related data, providing global auto-notifications and statistical analysis. It organizes 120 datasets into six categories and aims to be a centralized resource for researchers.
Co-AMPpred (composition-based antimicrobial peptide prediction); in silico-aided predictions of antimicrobial peptides by integrating composition-based features
Noise-tolerant Medical Image Classification via mutual Label Correction.
Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria.
Co-Var is a web-server for studying intra-protein or inter-molecular co-evolution.
Algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.
Protein-ligand binding site prediction. First, five individual methods are used to predict the ligand-binding pockets and residues. Then the ligands (from the templates or the user) are the docked into the binding pockets. he ligand-binding poses are refined to make them physically more realistic, using the efficient molecular docking algorithm AutoDock Vina.
coADAPTr is an open-source R package designed for automated data analysis in covalent labeling mass spectrometry, particularly hydroxyl radical protein footprinting (HRPF). It simplifies and accelerates data processing, offering improved fidelity and throughput compared to traditional methods like Excel’s Power Pivot.
A multi-modal co-attention based framework for drug-target interaction annotation.
CoAI (Cost-aware AI) is a framework to enable any kind of AI predictive model (e.g., deep neural networks, tree ensemble models, etc.) to make accurate predictions given a small number of low-cost features.
COALISPR is a Python command-line tool for analyzing high-throughput sequencing data, particularly useful for incorporating negative controls to improve data quality. It enables fast counting of reads and identification of RNA targets in organisms with poorly annotated genomes.
Simulated Annealing Search for Coalescent Trees.
COATi is a statistical, codon-aware pairwise aligner designed to improve sequence alignment accuracy by accounting for indels within codons, addressing limitations of traditional aligners. It is designed to reduce discarded data and provides enhanced sequence alignments for genomic data.
CoaTran is a tool that, given a transmission network and sample times, will simulate a coalescent phylogeny constrained by the transmission network.
A neuroscience-oriented simulation framework for complex behavior and learning.
Prediction and Consequences of Cofragmentation in Metaproteomics | cobia is a computational tool to predict the number of cofragmenting ions in a mass spectrometry experiment, focused on metaproteomics. Specifically, we calculate 'cofragmentation scores' which represent identification and quantification bias using mass spectrometry based metaproteomics
Quantitative analysis of the genomic overlaps.
Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes.
Cobolt is a method developed for modeling multi-omic single-cell sequencing datasets. It provides an integrated analysis of multi-omic data by learning a latent representation shared by the different data modalities. Cobolt jointly models these multiple modalities via a novel application of Multimodal Variational Autoencoder to a hierarchical generative model. It uses a probablity model that is robust to sparse counts and high numbers of features, therefore works for omics such as chromatin accessibility or methylation status.
CoBRA is a comprehensive ChIP/ATAC‐seq analysis tool built using snakemake and Docker which allows for escalable, reproducible, portable and easy-to-use workflows. CoBRA combines the use of several dozen ChIP/ATAC‐seq tools, suites, and packages to create a complete pipeline that takes ChIP/ATAC‐seq analysis from unsupervised analyses, differential peak calling, and downstream pathway analysis. In addition, CoBRA has been outfitted with several recently published tools that allow for better normalziation and CNV correction. The results are compiled in a simple and highly visual report containing the key figures to explain the analysis, and then compiles all of the relevant files, tables, and pictures into an easy to navigate folder.
COBRAC is a fast implementation of convex biclustering with compression
COnstraints-Based Reconstruction and Analysis for Python.
The R package cobrar provides structures and functions for constraint-based metabolic network analysis, e.g. the prediction of metabolic fluxes using fluxes using Flux Balance Analysis (FBA). cobrar is inspired by the former CRAN R package sybil.
CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays scanned with an Agilent scanner.
Identifying conserved protein complexes between species by constructing interolog networks.
A collection of software tools for dealing with co-citation data.
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit.
COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.
CoCoCoNet iis a tool for identifying conserved gene modules and co mparing co -expression networks. CoCoCoNet is a resource for both data and methods, providing gold-standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species.
Web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps.
CoCoMoRP is a tool for predicting community mortality risk due to CoVID-19 using machine learning and development of a prediction tool.
CoCoNat is a novel deep-learning based method for predicting coiled-coil regions, register annotation and oligomenrization state. CoCoNat adopts a sequence encoding based on two state-of-the-art protein language models and a deep-learning architetcure to perform prediction.
Coevolution and Convolutional Neural Network (CoCoNet) is a meyhod used for RNA contact prediction.
CoCoNet is an efficient deep learning tool for viral metagenome binning.
COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download ntural products (NPs). NPs are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed.
Coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.
Feature-based prediction of genome quality indices
Establishing immune-relevant regions for cancer vaccine design.
A tool for quantitative 3D reconstruction of large tissues at cellular resolution.
Package for compositional data analysis for microbiome cross-sectional and longitudinal studies.
A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Codabench, a meta-benchmark platform that is open sourced and community driven for benchmarking algorithms or software agents versus datasets or tasks.
CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers.
Compositional Data Analysis using Kernels (CODAK) is a tool for multivariate statistical learning methodology based on the kernel distance covariance framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status.
Codaloss: direct interaction network inference for compositional data. One essential step in the analysis of microbiome compositional data is inferring the direct interaction network among microbial species. Here, we propose a novel loss function called codaloss for direct microbes interaction network estimation under the sparsity assumptions. We develop an alternating direction optimization algorithm to obtain sparse solution of codaloss as estimator. Compared to other state-of-the-art methods, our model makes less assumptions about the microbial networks and outperforms them in network inference.
COmpositional Data Analysis with Recursive Feature Elimination.
Tool to deoptimize the RNA or DNA sequences based on codon usage. Codon-pair deoptimization involves increasing the frequency of underrepresented codon pairs without changing codon usage or amino acid sequences.
CODECHECK is an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility.
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
This package facilitates reading, preprocessing and manipulating microarray data.
CODER embeddings excellently reflect semantic similarity and relatedness of medical concepts. One can use CODER for embedding-based medical term normalization or to provide features for machine learning. Similar to other pretrained language models, CODER can also be fine-tuned for specific tasks.
Extract CDS, mRNA and translations from feature tables.
Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement.
A normalization and copy number variation calling procedure for whole exome DNA sequencing data. The tool relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model includes terms that specifically remove biases due to GC content, among others. It also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.
A next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.
CoDiFold is a de novo protein structure prediction by coupling contact with distance profile. In CoDiFold, contacts and distance profiles are organically combined into the Rosetta low-resolution energy function to improve the accuracy of energy function. As a result, the correlation between energy and root mean square deviation (RMSD) is improved.
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). CoDiNA categorizes links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks.
Combined DNA Index System (CODIS) is a GUI tool for forensic paternity lawsuit.
CoDNaS Quaternary is a high confidence database of conformational diversity in proteins that present a biologically relevant quaternary structure.
CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RNA structure in its native ensemble. The conformers are taken from the wwPDB and include structures solved by X-Ray Diffraction, Nuclear Magnetic Resonance and cryo-Electron Microscopy. CoDNaS-RNA allows you to quantify the conformational diversity of a given RNA, compare the structures of selected conformers, retrieve site-specific interactions between RNA and bound polynucleotides or proteins, and get more data cross-referenced from external resources like RNAcentral.
Ranking codons and orthologs based on their phylogenetic signal.
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
CodonAdjust is a free software to optimize a codon nucleotide composition mimicking a certain amino acids profile (AA profile). CodonAdjust formulates the optimization of a codon nucleotide composition as a non-convex optimization problem which minimizes the squared error between the desired and the calculated AA profiles. We provide CodonAdjust with four different options, which have various customization in practical scenarios such as selecting or avoiding specific codons.
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
Simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage
Predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein.
A Telemedicine Tool to Improve Awareness and Diagnosis for Patients With Congenital Dyserythropoietic Anemia. Algorithms and recommendations for diagnosis and management of congenital dyserythropoietic anemia (CDA). This website uses cookies to ensure you get the best experience on our website. Learn more. This is a web service dedicated to Congenital Dyseritropoyetic Anemias. Our aim is to provide information to patients and their families, but also to provide doctors with specific tools for this disease. Congenital Dyseritropoyetic Anemias. CoDysAn collaborates with various Associations.
Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integration connectors for different data sources along with ontology mapping techniques.
The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree.
Extracts the gene expression matrix from GEO DataSets (.CEL files) as a AffyBatch object. Additionally, can make the normalization process using two different methods (vsn and rma). The summarization (pass from multi-probe to one gene) uses two different criteria and the process of gene differentially expressed analisys using two methods (sam and acde).
CoExp Webpage is a web platform that enables the exploitation of co-expression networks. CoExp currently offers 109 co-expression models focused on brain transcriptomics with plans to expand its scope. It is a powerful, easy to use and innovative tool for gene set annotation across a variety of brain specific transcriptomicdata sets. CoExp makes co-expression models visually manageable, accessible and easily exploitable to the scientific community.
Comparative co-expression networks construction and visualization.
Structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, it infers three categories of protein functions including gene ontology, enzyme commission and ligand-binding sites from various analogous and homologous function templates.
Identification of Rossmann folds and prediction of FAD, NAD and NADP specificity.
CoffeeProt is an online tool for correlation and functional enrichment of proteome-wide systems genetics.
CoFly is a gene coexpression database for the fruit fly Drosophila melanogaster
Coordinated Gene Activity in Pattern Sets implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
Phytopathogenic fungi and oomycete EST database.
Workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data.
COGENT (COnsistency of Gene Expression NeTworks) is an R package designed to aid the construction of gene co-expression networks without the need for annotation or other external validation data. COGENT can be used to choose between competing co-expression measures (e.g. Pearson vs. Kendall correlation coefficients), as well as to inform score cut-off choice. While designed for gene expression data, COGENT can be applied to other cases where network construction relies on similarity profiling, e.g. microbiome or synthetic lethality data.
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly quality with BUSCOs; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Cogito “COmpare annotated Genomic Intervals TOol” provides a workflow for an unbiased, structured overview and systematic analysis of complex genomic datasets consisting of different data types (e.g. RNA-seq, ChIP-seq) and conditions.
COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures.
Cognac (COre GeNe Alignment Concatenation) is an R package for for generating concatenated gene alignments. The main function identifies shared genes to be used as phylogenetic markers within the input set of genomes. Marker genes are aligned individually with mafft and concatenated into a single alignment for downstream phylogenetic analysis. The algorithm uses mutli-threading and several algorithmic tricks to improve speed and efficiency, which make cognac capable of generating core-gene alignments for thousands of genomes in only a few hours.
A contrastive learning framework to predict disease similarity based on gene network and ontology structure.
Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies.
COGRIM is an R program of Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion.
Collections of Clusters of Orthologous Genes provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes.
Experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital. CogStack is a lightweight distributed, fault tolerant database processing architecture and ecosystem, intended to make NLP processing and preprocessing easier in resource constrained environments. CogStack is a lightweight distributed, fault tolerant database processing architecture, intended to make NLP processing and preprocessing easier in resource constained environments.
CogTale ( Cognitive Treatments Article Library and Evaluation) is an online platform for the evaluation, synthesis and dissemination of evidence from cognitive interventions studies CogTale is a comprehensive database of design (methodological) features and summary results from all relevant trials of cognitive interventions in the field of cognitive ageing.
CoGTEx provides access to system-level and tissue-level coexpression estimations derived from GTEx human data. The resource enables users to explore and download coexpressed genes, facilitating analyses of biological pathways and identification of novel functional gene partners.
COGVIC(Catalogue Of Germline Variants In Cancer). A comprehensive database of germline pathogenic variants in East Asian pan-cancer patients.
This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.
A comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.
CohortFinder is an open-source tool designed to improve machine learning model generalizability in digital pathology and medical imaging by intelligently partitioning data cohorts to avoid bias from batch effects. It is freely available for download at cohortfinder.com.
Package for standardized and reproducible processing, analysis, and integration of clinical proteomics data.
an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation. Contextualization and Evaluation of COI-5P Barcode Data. Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data
The CoilGen Project is a community-based tool for the generation of coil Layouts within the MRI/NMR environment.
Program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
Privacy-enabled infrastructure model for brain imaging. It enables groups of users to run common analyses on their own machines over their own datasets with ease. The results of these analyses are synchronized to the cloud, and undergo aggregate analyses processes using all contributor data.
CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.
COVID-19 Knowledge Extractor (COKE) is a tool and a web portal to extract drug - target protein associations from the CORD-19 corpus of scientific publications on COVID-19.
cola is an R package that provides a general framework for consensus partitioning through a general framework.
ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.
Calculates Area under ROC curve (AUC) for a vector or for each column of a matrix.
A server to build collagen fibril models.
ColFeatures is an automated data extraction and classification of bacterial colonies.
A project and collection of tools for analyzing and comparing next generation sequencing data without the need to first assemble the genome.
CoLiDe is a Combinatorial Library Design tool for probing protein sequence space
A lims system to automate and expedite proteomics data management, processing and analysis.
A born-digital field-to-database solution for collections-based research using collNotes and collBook | collBook: Refine biological field observations | Modernizing Field Collection Techniques | collBook, is the desktop counterpart for the mobile app collNotes. Combined they are a field-to-database solution designed for field biologists to gather and format “born digital” field notes into database ready formats. A mobile application, collNote is being developed for Android and iOS devices to gather Darwin Core formatted field notes. A desktop application, collBook is being developed for Linux, OS X, and Windows to refine those field notes into portal ready Darwin Core files and specimen labels. Field note refinements include: reverse geocoding localities, taxonomic alignments, and creation of customizable labels which can optionally include catalog number barcodes
Implements a generalized version of the CDH test for detecting compound heterozygosity on a genome-wide level, due to usage of generalized linear models it allows flexible analysis of binary and continuous traits with covariates.
A representation learning framework for identification and characterization of protein structural sites.
Merges two reads if they have exactly the same genomic coordinates.
Collateral Missing Value Estimation software can be used to estimate missing values in the correlate.
Collects MGF files and dd_results from an XMass setup_QDD.tcl experiment to a single MGF file.
SingleQ is a database providing single-cell expression quantitative trait loci (sc-eQTLs) across human tissues, facilitating research into gene regulation in specific cellular contexts. The database curates and provides online visualization of sc-eQTL data.
COLMARppm is a web server tool for the accurate and rapid prediction of 1H and 13C NMR chemical shifts of organic molecules and metabolites. It utilizes an empirical prediction strategy to provide predicted chemical shifts for candidate structures and can be directly incorporated into metabolomics workflows.
Finds, summarizes, and plots (if desired) 2-color colocalization from 3D images.
COLOCdb represents the most comprehensive colocalization analysis by integrating publicly available GWASs, 187 multi-omics datasets from 13 types of xQTL and three different colocalization algorithms.
Pipeline for running colocalization tests between GTEx version 8 single-tissue eQTLs or sQTLs and GWAS signals using COLOC.
R package for conducting co-localization analysis on fluorescence microscopy images.
Software framework equipped with a GUI for the statistical analysis of sequences of a genome. It can be equipped with different plugins that actually perform the analysis. The current version is supplied with SIGI-HMM, a tool for the prediction of Genomic Islands.
Web based portal for exploring and analyzing comprehensive organism-specific cross-platform expression compendia of bacterial organisms. The compendia were carefully constructed by collecting, homogenizing and formally annotating publicly available microarray and RNA-seq experiments from Gene Expression Omnibus (GEO), and ArrayExpress.
The dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. The lists of samples for training (train+val) set and testing set are provided in the Zenodo repository. Source code in Github is to train and validate five deep learning models using ColoPola dataset.
ColoPola dataset for colorectal cancer detection
Color Data is a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets. Color Data is the largest public database of its kind, containing aggregated genetic and phenotypic information from 54,000 individuals who took a Color test.
Allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.
ColorCells is a database of expression, classification and functions of lncRNAs in single cells. Single cell RNA sequencing (scRNA-Seq) technology has revealed significant differences in gene expression levels between different cell groups.
A versatile compressor of third generation sequencing reads.
ColorDecontmas is a collection of ImageJ macros (scripts) for performing color deconvolution and analysis of immunohistochemistry (IHC) staining on tissue microarray (TMA) images
R package for quantitative color profiling of digital images with earth mover's distance.
Parses a DOOR report file and writes the information in a gff3 out file.
Colosseum is low-cost, scalable, and automated fluid sampling for fluidics applications.
Colour Deconvolution 2 is a plugin that implements context-based segmentation algorithms for intelligent microscopy. The Colour Deconvolution 2 ImageJ plugin implements stain unmixing with Ruifrok and Johnston’s method described.
This uses PCA to normalise histology images
This function effectively normalizes multi colour images (RGB, multispectral, hyperspectral).
A resource for analysis of colocalization of genomic features.
Collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using a microarray detection platform.
ColTapp is an automated image analysis application for efficient microbial colony growth dynamics quantification.
Dynamic partitioning of search patterns for approximate pattern matching using search schemes.
Distant homology detection method based on sequence profile-profile comparison. It takes a protein sequence or multiple sequence alignment as input and searches for remote homologs in SCOP, PDB and PFAM databases.
Comprehensive metatranscriptomics analysis.
ComBat is a powerful and fast statistical harmonization method developed to mitigate the “batch effect” in gene expression microarray data and was adapted for multi-site dMRI harmonization to reduce scanner/site effect. R library is licensed under Artistic 2.0, while Python and MATLIB is licensed under MIT.
The COMBAT-TB Workbench is an IRIDA based, module workbench for M. tuberculosis bioinformatics. It is designed to be easily deployed on a single server.
COMBATdb is a multi-omics database for the human blood response in SARS-CoV-2 infection generated by the COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium.
Combenefit is a software tool that enables the visualization, analysis and quantification of drug combination effects in terms of synergy and/or antagonism.
Automated method for the prediction of protein function. Users can either submit a sequence or use a uniprot identifier.
Modeling binding specificities of transcription factor pairs with random forests.
Tool will take one or more assemblystats results and combine into a single tabular line file where each result is represented by a single line.
This tool combine MetaPhlAn outputs and HUMANnN outputs
Combinatorial selection of biomarkers to optimize gene signatures in diagnostics and single cell applications.
comboLTR is a new polynomial regression-based framework for modeling anti-cancer effects of drug combinations in various doses and across different cancer cell lines.
Personalized tumor combination therapy optimization using the single-cell transcriptome.
A statistical framework for evaluating drug synergism in patient-derived xenografts.
COMBREX is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.
Combinatorial and Semantic Analysis of Functional Elements (CombSAFE). It is a flexible computational method to identify combinations of static and dynamic functional elements genome-wide, or in a specific genomic region, and how they change across semantically annotated biological conditions.
COMBSecretomics is a computational framework for secretome-related higher-order drug combination analysis. It offers the unique opportunity to study how multidrug treatments (i.e., more than 2 drugs) affect the protein release patterns of inactive/unprovoked and active/provoked cell populations. This molecular based evaluation approach of combination treatments opens for systematic studies associated with the secretome of complex diseases where there are still unmet diagnostic and therapeutic needs.
A COding potential calculation tool based on Multiple fEatures integrates multiple sequence-derived and experiment-based features to identify and characterize novel lncRNAs in RNA sequencing data.
Co-Methylation with genomic CpG Background (CoMeBack) estimates DNA co-methylation, defined as proximal CpG probes with correlated DNAm across individuals. CoMeBack outputs co-methylated regions (CMRs), spanning sets of array probes constructed based on all genomic CpG sites, including those not measured on the array, and without any phenotypic variable inputs.
Significant co-mentions in the scientific literature between diseases, biological functions and clinical signs.
Protein sequence alignment tool designed for protein remote homology detection. It accepts a multiple sequence alignment as input and converts it into the profile to search against a profile database for statistically significant similarities.
GPU-accelerated sensitive and specific homology searches. COMER2, cross-platform software for protein remote homology search. The COMER method based on sequence profile-profile comparison is one of the most sensitive and accurate computational tools developed for protein alignment and homology search. COMER version 2.1 (COMER2) represents one of the fastest implementations of calculations for sensitive protein homology search. High COMER2 performance is achieved by harnessing the power of the Graphics processing unit (GPU). Hence, a GPU is expected to be installed on the system. COMER2, a cross-platform software package for protein remote homology search and alignment.
Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.
A toolkit for composing customizable genetic programs in mammalian cells. COmposable Mammalian Elements of Transcription (COMET) is an ensemble of TFs and promoters that enable the design and tuning of gene expression to an extent not previously possible. COMET currently comprises 44 activating and 12 inhibitory zinc-finger TFs and 83 cognate promoters, combined in a framework that readily accommodates new parts. This system can tune gene expression over three orders of magnitude, provides chemically inducible control of TF activity, and enables single-layer Boolean logic
CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.
Visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.
Assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).
CometAnalyser is an open-source deep-learning tool designed for the analysis of both fluorescent and silver-stained wide-field microscopy images. Once the comets are segmented and classified, several intensity/morphological features are automatically exported as a spreadsheet file.
A network-based methylome approach to investigate the multivariate nature of health and disease.
COMETS Analytics is an online tool for analyzing and meta-analyzing metabolomics data in large research consortia.
ComiR is a web tool for combinatorial microRNA (miRNA) target prediction. Given an messenger RNA (mRNA) in human, mouse, fly or worm genomes, ComiR predicts whether a given mRNA is targeted by a set of miRNAs.
COMMA (COMmunication MApping) is a method to dissect proteins dynamical architectures.
ComMap is a software for protein complexes structural mapping for cross-linking mass spectrometry (CXMS).
This software provides a global similarity overview between all datasets of a large metagenomic project.
ComMet (COMparison of METabolic states) is a method based on genome-scale metabolic models for comparing different metabolic states.
Web server for the identification and analysis of consensus gene modules across multiple methods.
Literature mining for context-specific molecular relations using multimodal representations (COMMODAR). Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations.
A Python package for generic common-nearest-neighbour clustering.
An webserver and R package for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics.
Community Simulator is a Python package for microbial ecology. It is designed for simulating batch culture experiments on complex microbial communities.
Pipeline for multi-omics data integration in metabolic modelling and drug discovery.
Systematic analysis of disease comorbidities.
CompaCt performs automated integrative comparative analysis of large-scale (protein) interaction datasets, identifying groups of interactors (e.g., protein complexes) in parallel in multiple species, allowing systematic identification and comparison of conserved as well as taxon-specific components of protein complexes and other interactions.
Compacta is a fast contig clustering tool for de novo assembled transcriptomes. Compacta is designed to reduce the number of contigs given by the assembler to a smaller set of representative sequences, preserving the information about relative expression given by the reads. Compacta output can then be employed in downstream analyses for contig identification and differential gene expression.
CompAIRR is a command line tool to compare two sets of adaptive immune receptor repertoires and compute their overlap. It can also identify which sequences are present in which repertoires.
Companion is a web server for annotating parasite, fungi, and arthropod genomes using a reference-based method, allowing non-experts to assess output before submission to public databases. The tool has been updated to incorporate novel gene-finding methods and increased reference genome coverage.
Devoted to the characterization of complete chromosome sequences by standardized genometric methods, this website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles.
This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples
Compare taxonomy summary for several taxonomy summary files.
CompareM i a toolbox for comparative genomics.
CompareM2 is a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes. It integrates community-adopted tools to perform genome quality control, annotation, and phylogenetic analyses, generating a portable dynamic report.
compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.
Print all the transcripts from a first file which overlap with the transcripts from a second file.
Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes.
Provide the queries that overlap with a reference, when the query is small.
Provide the queries that overlap with a reference, when the reference is small.
Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
CompariPSSM is a tool that quantifies the similarity between motif-binding determinants using sliding window PSSM-PSSM comparison and a probabilistic framework. It can be used for peptide classification, clustering, and benchmarking experimental motif discovery methods.
COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.
Compartor is toolbox for automatic moment equation generation for stochastic compartment populations: From a set of provided interaction rules, it derives the associated system of ODEs that describes the population statistics. Equations can be exported as Python or Julia code.
Statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
COMPletely Arbitrary Sequence Simulator.
converts Bruker analysis.baf and analysis.yep files to mzXML or mzML
This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.
Systematic retrieval and storage of functional genomics data via a MySQL database.
Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.
This package contains functions to accomplish several tasks. It can download full genome databases from UCSC, import .bed files, annotate these .bed file regions with genes from aforementioned database dumps, interface with DAVID to create functional annotation and GO enrichment charts based on gene lists and visualise and compare these enrichments using either directed acyclic graphs or scatterplots.
Compi is an application development framework for portable computational pipelines.
A metaproteomic analysis method for matching sequences against experimental shotgun proteomics spectra based on the Prolucid search engine.
A computational pipeline "COMPILE" to accelerate identification and annotation of candidate genes in Genome-Wide Association Studies.
Compleasm: a faster and more accurate reimplementation of BUSCO. It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
A computationally scalable method to improve completeness of large-scale protein sequence clustering.
Predicts the interfacial contacts between two potentially interacting protein sequences (heterodimer only) using co-evolution and deep learning techniques. It applies an ultra-deep learning model trained from single-chain proteins to predict contacts for a pair of proteins. This deep learning method greatly outperforms the latest co-evolution methods by learning contact occurrence patterns from solved protein structures.
ComplexFinder is a software package for the analysis of native protein complex fractionation experiments. It finds complexes from Blue-Native and SEC Fractionation analyzed by Liquid Chromatogrpahy coupled to Mass Spectrometry. In principal it works with any separation technique resulting in co-elution signal profiles.
Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
Aided Decision-Making for the Study of Protein Complexes | Abstract Proteins are the chief effectors of cell biology and their functions are typically carried out in the context of multi-protein assemblies; large collections of such interacting protein assemblies are often referred to as interactomes. Knowing the constituents of protein complexes is therefore important for investigating their molecular biology. Many experimental methods are capable of producing data of use for detecting and inferring the existence of physiological protein complexes. Each method has associated pros and cons, affecting the potential quality and utility of the data. Numerous informatic resources exist for the curation, integration, retrieval, and processing of protein interactions data. While each resource may possess different merits, none are definitive and few are wieldy, potentially limiting their effective use by non-experts
A two-dimensional polyacrilamide gel electrophoresis federated database.
CompMap is an allele-specific expression read-counter based on competitive mapping. It compares reads mapped to two references and counts reads for allele-specific expression.
compmerge is a program that tries to solve the same problem as cuffmerge. It is not limited to cufflinks/stringtie models and transcripts, but can work with any GTF file. It merges the spliced transcripts that have a compatible intron structure and merges the monoexonic transcripts based on simple stranded overlap.The output is a GTF file of merged transcripts.
Compo is a software for composite motif discovery using discrete models.
Sequence composition dynamics of genes and genomes.
A tool to visualize and validate quantitative proteomics data from different sources.
Predicting peptide signatures for targeted proteomics.
Open-source java library for computational proteomics.
This software is designed to visualize data, specifically combined scores data, utilizing graph theory and network analysis concepts.
Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties.
CompoundDB4j is an Integrated Drug Resource of Heterogeneous Chemical Databases.
Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP) is a tool for helping to uncover missing heritability in human diseases and other phenotypes.
Web-based collaborative platform for comparing phylogenies.
compreheNGSive is an interactive visualization of the end results of the next-generation sequencing pipeline.
CompRet is a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration.
Facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets.
Comprotein is (or was) a computer program to aid in primary protein structure determination, i.e. protein sequencing.
Calculate the composition of unique words in sequences.
COMPSRA (COMprehensive Platform for Small RNA-seq data AnalySis) Quality Control, Alignment, Annotation, Microbe and Function. They are integrated into a pipeline and each module can also process independently.
Sequential programming model General purpose programming languages + annotations/hints Exploitation of implicit parallelism Automatic on-the-fly creation of a task dependency graph COMPSs workflows portable to HPC and Cloud without change
Jorge Ejarque - Barcelona Supercomputing Center
Rosa M. Badia - Barcelona Supercomputing Center
Community data resource for environmental chemistry.
compuGUT is a simulation tool developed to assist in exploring interactions between intestinal microbiota and their environment.
Illustrates computation of best match scoring with PWM and constructs sequence logo.
Compute Position Weight Matrix (PWM) and display SequenceLogo in terms of frequency
Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences
Compute the coverage of a set with respect to another set.
Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data.
CompuTiX is a flexible open-source library for off-lattice agent based modeling (not only) in biomedical applications including liver tissue microarchitecture reconstruction with deformable cell model (Pesek J. et al, in preparation) and NMR signal modeling (Boulitrop C. et al., in preparation). The main focus of the library is on extensibility, flexibility and transparency of internal state.
ComSeg is a point cloud segmentation framework for image-based spatial transcriptomics that operates directly on single RNA positions without cell shape priors. It is available as an open-source pip package and documented on ReadTheDocs.
ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.
This small GUI program can simplify repeated COMSOL simulations.
Compares two datasets in netCDF or ASCII format.
COMSUC web server for identification of COnsensus Molecular SUbtype of Cancer allows users to identify Consensus Molecular Subtypes (CMS) by integrating multiple clustering results based on multiple platform, multiple omics data and multiple methods. The COMSUC web server has the goal of fusion, clustering and interactive visualization of multi-omics data for patient samples.
CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
Efficiently creating and browsing comutation plots online.
CoMutDB: the landscape of somatic mutation co-occurrence in cancers
Contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. Con-AAE is a deep learning framework based on Pytorch.
Using molecular dynamics trajectories, analyzes inter-residue contacts, creates videos of time-resolved contact maps, and performs correlation, principal component, and cluster analysis, revealing how specific contacts relate to functionally relevant states sampled by molecular dynamics.
Probabilistic framework for the discovery of single nucleotide variants that overlap copy number alterations from next generation sequencing data. This software explicitly integrates information about copy number state of different genomic segments into the inference of single nucleotide variants.
CONAN is a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis.
A versatile tool for the detection of large syndromic copy number variation from whole genome sequencing data
A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
Long non-coding RNA and microRNA landscape of two major domesticated cotton species.
Method to assess the outcome of non-synonymous SNVs using a CONsensus DELeteriousness score that combines various tools.
ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data
ConDiGA is a pipeline for accurate taxonomic annotation of genes from metagenomic data, optimizing the construction of protein sequence databases for metaproteomic analysis. It uses a 'contigs directed' approach and has demonstrated improved performance compared to other methods.
CondiS is a web tool with user-friendly GUI to address the censoring problem in machine learning-based survival analysis.
Analysis of conditional colocalization relationships and hierarchies from three-color microscopy images.
Multi-Objective De Novo Drug Design with Conditional Graph Generative Model.
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
R package for CONdition-Dependent Operon Predictions. It is a tool in R to identify from RNA-seq transcriptome profiles operons expressed in a condition/transcriptome-specific manner, based on a Random Forest classifier.
Simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model.
To simulate a CBCT system by computing the 2D X-ray projection images.
Analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families.
Tool that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data.
inference of biological association networks using Cytoscape. CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices. Find relationships between repeatedly observed items. CoNet is a Cytoscape plugin that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). CoNet - Co-occurrence Network inference. CoNet detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. 12th January 2018: Thanks to Lisa Röttjers, there is now an R implementation of CoNet.
The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.
ConfID is a Python-based computational tool to identify and characterize conformational populations of drug-like molecules sampled through molecular dynamics simulations. ConfID is an analytical method for conformational characterization of small molecules using molecular dynamics trajectories. Conformational generation is a recurrent challenge in early phases of drug design, mostly due to the task of making sense between the number of conformers generated and their relevance for biological purposes.
Various methods for estimating parametric and non-parametric confidence intervals for the AUC.
Confidence intervals for area under the receiver operating curve (AUROC)
ConfocalGN is a user-friendly software that can generate synthetic microscopy stacks from a ground truth (i.e. the observed object) specified as a 3D bitmap or a list of fluorophore coordinates. This software can analyze a real microscope image stack to set the noise parameters and directly generate new images of the object with noise characteristics similar to that of the sample image.
Conformer-RL is an open-source Python package for applying deep reinforcement learning (RL) to the task of generating a diverse set of low-energy conformations for a single molecule. The library features a simple interface to train a deep RL conformer generation model on any covalently bonded molecule or polymer, including most drug-like molecules.
Confortho is a MATLAB script that generates orthogonal views of 3D confocal microscopic image stacks.
A Bayesian method to cluster single-cell RNA sequencing data using Copy Number Alterations.
ConGRI is a contrastive learning scheme based on deep Siamese CNN architecture, which identifies gene regulatory interactions from gene expression images.
R package for integrating numerical omics data that allows multiform graph representations to study molecular interaction networks.
Integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.
Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching event information from single-cell sequencing data to more accurately identify clones and their evolutionary relationships.
ConjuPepDB is a database of drug–peptide conjugates, created with the aim to gather and provide relevant information to the wider scientific community.
Open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions.
ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.
Hetnet Connectivity Search on the Hetionet network
Connectome is an R toolkit to explore cell-cell connectivity patterns based on ligand and receptor data in heterogeneous single-cell datasets.
Tool that enables fast and accurate classification of conopeptides (the main bioactive component of cone snail venom) into superfamilies based on their amino acid sequence. Predictions are made using Hidden Markov Models and generalized profiles.
ConoDictor2 enables fast and accurate classification of conopeptides (the main bioactive component of cone snail venom) into superfamilies based on their amino acid sequence. Predictions are made using Hidden Markov Models and generalized profiles with algorithm improvements for an improved prediction and classification.
ConoMode is a database dedicated to collection of the complex 3D structures of conopeptides binding with their target proteins.
Database specializing in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.
Web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.
Contrastive learning in protein language space predicts interactions between drugs and protein targets.
ConPlot is a web-based application for the visualisation of information derived from residue contact and/or distance inter-residue predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.
A server for Quality Assessment of Protein Model-Structures using Evolutionary Conservation.
CONQUER is an interactive toolbox to understand functional consequences of GWAS hits.
Multi-species estimation of geographical range parameters for preliminary assessment of conservation status following Criterion B of the International Union for Conservation of Nature.
CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
CONREL is a genome browser that allows for the exploration of consensus regulatory elements at different levels of abstraction. The total binding affinity of transcription factors on whole consensus region sequences is here fully exploited to characterize and annotate functional properties of regulatory elements. CONREL can be used to explore genomic loci, genes or genomic regions of interest across different cell lines and tissues.
Create a consensus sequence from a multiple alignment.
Cons creates a consensus sequence from a protein or nucleotide multiple alignment.
Creates a consensus from multiple alignments.
ConsAlifold, a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment.
Create an ambiguous consensus sequence from a multiple alignment.
An online WEB application that scores residue conservation a site on a Multiple Sequence Alignment based on Jensen-Shannon Divergence, introduced by Capra and Singh.
ConSemble is a consensus-based de novo ensemble transcriptome assembly pipeline.
The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling.
An R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. RNA-seq analysis using multiple algorithms. This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation. publication_ruv - RUV integration with edgeR, voom/limma and DESeq2. For more details, contact Ashley Waardenberg: a.waardenberg@gmail.com. Clustering, MultipleComparison, Sequencing, Software, Transcriptomics
Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.
Implementation of four major subtype classifiers for high-grade serous (HGS) ovarian cancer. In addition, it implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human.
Max-Planck-Institute for Molecular Genetics in Berlin
Pipeline to identify ideal consensus regions from homologue sequences for primer design.
This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.
CoNSEnsX+ is a service specifically designed for the investigation of such ensembles for compliance with NMR-derived parameters. In contrast to common structure evaluation tools, all parameters are treated as an average over the ensemble, if are not themselves an ensemble property like order parameters. CoNSEnsX+ is also capable of selecting a sub-ensemble with increased correspondence to a set of user-defined experimental parameters.
Ligand-based virtual screening with consensus queries.
CONSENT (Scalable long read self-correction and assembly polishing with multiple sequence alignment) is a self-correction method for long reads. It works by, first, computing overlaps between the long reads, in order to define an alignment pile (i.e. a set of overlapping reads used for correction) for each read. Each read's alignment pile is then further divided into smaller windows, that are corrected idependently. First, a multiple alignment strategy is used in order to compute consensus. Then, this consensus is further polished with a local de Bruijn graph, in order to get rid of the remaining errors. Additionally to error correction, CONSENT can also perform assembly polishing.
CoNSEPT (Convolutional Neural Network-based Sequence-to-Expression Prediction Tool) is a tool to predict gene expression in various cis and trans contexts. Inputs to CoNSEPT are enhancer sequence, transcription factor levels in one or many trans conditions, TF motifs (PWMs), and any prior knowledge of TF-TF interactions.
Predicts functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue.
ConSIG is a web page which can discovery of molecular signature from OMIC data.
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
Fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure.
CONSORT-NLP is an Artificial Intelligence Tool with Automated Reporting Checklist Generation for Parallel Group Randomized Trials.
CONSORT-TM is a corpus annotated with CONSORT checklist items, and studied baseline sentence classification methods as well as their combinations to recognize a subset of these items.
Prokaryotic genome annotation framework that performs various intrinsic gene predictions, homology searches, predictions of non-coding genes, and complex features and integrates all evidence into a consensus annotation. It achieves high-quality and comprehensive annotations based on rules and priorities, similar to decision-making in manual curation. Parameters controlling the annotation process are configurable by the user.
ConSReg is a Python package for condition specific regulatory network analysis.
ConsRM is a collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.
An Efficient Normalization Method for Relative Quantification in Small- and Large-Scale Omics Experiments in R BioConductor and Python.
Constava calculates conformational states probability and conformational state variability from protein structure ensembles.
Tool for improved taxonomic resolution of environmental fungal ITS sequences.
CONSTAX (CONSensus TAXonomy) is a tool for improved taxonomic resolution of environmental fungal ITS sequences.
constclust is a Python packages for consistent clusters for scRNA-seq. It uses unsupervised clustering to identify distinct cell types is a crucial early step in analyses of scRNA-seq data.
CONSULT is a tool for contamination removal from genomic sequencing reads. Relying on locality-sensitive hashing, CONSULT extracts k-mers from a query set and tests whether they fall within a user-specified hamming distance of k-mers in the reference dataset.
Tool used for estimation of the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences.
A tool provides evolutionary conservation profiles for proteins of known structure in the PDB.
Server for the Identification of Functional Regions in Proteins.
ContactGAN is a tool for protein contact map refinement for Improving structure prediction using Generative Adversarial Networks. ContactGAN takes a predicted protein contact map as input and outputs a new contact map that better captures the residue-residue contacts.
The Container Profiler tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Our implementation leverages facilities provided by the Linux operating system that is integral with Docker containers. Development and testing of the Container Profiler described in this paper was completed using Debian-based Ubuntu Linux.
contamDE-lm is R package for linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples.
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data
ContamLD is a software designed to estimate autosomal contamination in ancient DNA samples.
GATK tool to estimate amount of cross-individual contaminating sequence in a dataset
ContextMap is a very accurate read mapping tool for data from RNA-seq experiments. It can be used to refine mapping provided by other tools or as a standalone program.
Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, this tool can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.
ContigExtender is a tool to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.
Phage-bacterial contig association prediction with a convolutional neural network.
Assigns taxonomy to metagenomic contigs.
A bacterial genomes finishing tool for structural insights on draft genomes
Contiguity is interactive software for the visualization and manipulation of de novo genome assemblies.
A novel, open-source interactive computation and visualization tool for brain connectome data.
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets.
COnTROT (COmprehensive Transcriptomic ORganizational Tool) is a program that will download and organize all expression data in GEO related to a search result, commonly an organism
MATLAB code for a segmentation method using local Gaussian distribution fitting energy.
Active contours driven by local Gaussian distribution
Systematic tracking of dysregulated modules identifies novel genes in cancer.
Protein complex-based analysis of dysregulated cellular processes in cancer.
A tool for copy number variation (CNV) detection from targeted resequencing data such as those from whole-exome capture data.
A tool to identify transcription factor binding sites across species.
Visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes.
Exploiting flux constraints in genome-scale models for the detection of vulnerabilities.
A novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. The result closes the gap between probabilistic and thermodynamic models, demonstrating that statistical learning procedures provide an effective alternative to empirical measurement of thermodynamic parameters for RNA secondary structure prediction.
A Hadoop based genome assembler for assembling large genomes in the clouds.
CONTRAlign (CONditional TRAining for Protein Sequence Alignment)is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization.
A consensus method of tumor trees based on maximum directed partition support problem.
The Antarctic Biodiversity Portal provides distributional data on copepods collected from desalination unit filters at the Mario Zucchelli Research Station, contributing to Antarctic biodiversity research and data integration.
Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
Control the ZEN Blue microscope control software from within a MATLAB script
This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.
CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.
Search for variations that are overrepresented in a population. CNV-based association study between two groups of samples.
ConVarT is a tool for functional inference of human genetic variants. It is an integrated search engine for orthologous variants between humans, mice, and C. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic OrthoVars from mice and C. elegans can give clues about the functional consequence of human genetic variants.
Define coerce methods for microarray data objects.
Inter-conversions between various formats of position-specific scoring matrices (PSSM). The program also performs a statistical analysis of the original matrix to provide different position-specific scores (weight, frequencies, information contents), general statistics (marginal frequencies, total information content), and synthetic descriptions (strict and degenerate consensus).
Convert other genotype calling format into ANNOVAR format.
Automatically convert a GenBank-format file into FASTA format.
Convert a file from a format to another.
Convex-PL^R augments Convex-PL with conformational flexibility for better performance in affinity prediction and virtual screening tasks. It is trained on a more novel dataset that includes cofactors.
COnVIDa is a COVID-19 multidisciplinary data collection and dashboard.
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.
The most simple implementation of the cellular automata game of life
CONY is a Bayesian procedure for detecting copy number variations from sequencing read depths.
An extreme gradient boosting-based tool for robust tissue or cell-of-origin prediction of tumors.
Selecting Representative Samples From Complex Biological Datasets Using K-Medoids Clustering.
CoolBox is a flexible toolkit for visual analysis of genomics data.
coolpup.py is a versatile Python tool to perform pile-up analysis on Hi-C data in .cool format. coolpup.py is particularly well suited performance-wise for analysing huge numbers of potential interactions, since it loads whole chromosomes into memory one by one (or in parallel to speed it up) to extract small submatrices quickly. Having to read everything into memory makes it relatively slow for small numbers of loops, but performance doesn't decrease until you reach a huge number of interactions.
Enabling high-resolution Hi-C analysis in Python.
A fast, web-based tool for returning a subset of mmCIF coordinate data for a PDB entry held in the PDB archive. The server is able to return the specific portions of the structure that are relevant, as specified in your query
Extract the sequences from a list of coordinates.
(Crystallographic Object)-Oriented Toolkit.
Method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.
CoPAP (Co-evolution of Presence-Absence Patterns) webserver allows inference of co-evolving characters (genes, restriction sites, introns, indels, methylation sites) as manifested by co-occurring gains and losses.
Open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. It includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.
COVID Outcome Prediction in the Emergency Department (COPE) is a model for predicting death and need for intensive care in COVID-19 patients
Simulate phenotypes: continuous, dichotomous and survival for common variants from existing genotype data simulated with some other tool. Add the phenotype to generated genotype data prepared with a genetic simulator. The output of cophesim can be used as a direct input for different genome wide association study tools.
Composition based Protein Identification
COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.
Robust and scalable maximum exact match finding.
An ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants.
sRNA target prediction boosted by comparative information.
The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space.
CoPTR is a tool for accurate and robust inference of microbial growth dynamics from metagenomic sequencing.
Text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). It also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. Version 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It searches for indirect relations between genes, pathways, drugs and diseases.
Copulacci is a Python-based model for inferring cell-cell interactions from spatial transcriptomics data, utilizing a Gaussian copula to model dependencies even with low transcript counts. It improves upon existing methods and discovers biologically meaningful ligand-receptor interactions.
Deconvoluting single-cell chromatin accessibility of genetic subclones in cancer.
Network-based visual differential analysis. Clone a network view layout by mapping node column values.
CopyDetective is an algorithm for detection threshold aware CNV calling in matched whole-exome sequencing data. Software is available as an R shiny app.
Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.
Correct trait bias in microbial profiles
A computational approach for the inference of copy-number genotypes from personal genome sequencing data.
This tool extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows extracting uniformly distributed copy number information, and it can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, this tool constitutes a widely applicable alternative to available copy number detection tools.
CORACLE is a web application designed for the analysis of COVID-19 and PASC-related scientific articles, facilitating the identification of research trends through publication networks and MeSH maps.
An algorithm for ordering fingerprinted clones within contigs.
Coral is a tool that can accurately bridge paired-end RNA-seq reads. The core of Coral is a optimization formulation that can capture the most reliable bridging path while also filter out false paths. An efficient dynamic programming algorithm is designed to calculate the top N optimum. Coral implements a consensus approach to select the best solution among the N candidates by taking into account the distribution of fragment length. Coral is modular, can be easily incorporated into existing RNA-seq analysis pipeline.
Coral is a web-based visual analysis tool for creating and characterizing cohorts. Users can interactively create and refine cohorts, which can then be compared, characterized, and inspected down to the level of single items. Coral visualizes the evolution of cohorts and also provides intuitive access to prevalence information.
CoralP is a user-friendly interactive web application for visualizing both quantitative and qualitative data. Qualitative and quantitative features can be represented in branch colors, node colors, and node sizes. Phosphatases can be organized using the published phosphatome tree or as radial or force directed networks. CoralP is simple to use, well documented, and freely available. It is the first and only dedicated tool for phosphatome visualization and is widely applicable to a variety of data types including those generated from proteomic, genomic, epidemiological, and high-throughput screening experiments.
CORAZON( CORrelations Analyses Zipper ONline) is a bioinformatic tool that uses artificial intelligence to cluster genes according to their expression in tissues and also a tool to normalize databases. It is a web server for data normalization and unsupervised clustering based on expression profiles. This tool is composed of 3 unsupervised machine learning algorithms: Mean Shift, K-Means and Hierarchical. Unsupervised learning is the machine learning task of inferring a function to describe the hidden structure from unlabeled data. The inductor analyzes the examples provided and tries to determine if some of them can be grouped in any way, forming clusters.
Biological network alignment and querying.
CoRC (COPASI R Connector) is a high-level R API for Complex Pathway Simulator (Copasi).
The Chordata Olfactory Receptor Database (CORD) build from the annotation data from the command line tool Genome2OR
The amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions. Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax (https://cordax.switchlab.org), that explores amyloid sequence beyond its current boundaries.
A R package for convenient correlation analysis
R package for visualizing multi-omics differential correlation networks.
CORDITE is The Curated CORona Drug InTERactions Database for SARS-CoV-2. CORDITE aggregates all available knowledge on potential drugs for SARS-CoV-2. Since the outbreak in 2019, researchers are trying to find effective drugs against the SARS-CoV-2 virus based on de novo drug design and drug repurposing. The former approach is very time consuming and needs extensive testing in humans, whereas drug repurposing is more promising, as the drugs have already been tested for side effects, etc. At present, there is no treatment for COVID-19 that is clinically effective, but there is a huge amount of data from studies that analyze potential drugs. We developed CORDITE to efficiently combine state-of-the-art knowledge on potential drugs and make it accessible to scientists and clinicians
CoRe is a robustly benchmarked R package for the identification of core fitness genes in genome-wide pooled CRISPR knock-out screens.
Cloud-ORiented Engine for advanced MRI simulations (coreMRI) - high-performance, publicly available MR simulation platform on the cloud.
Core Hunter is a flexible tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general.In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed.
A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data.
CoRec is a method for rapid profiling of cell-specific transcription factor-cofactor complexes. This GitHub repository provides code and related resources for implementing and analyzing CoRec data.
CoreCruncher is a Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. CoreCruncher is a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs.
Flexible and efficient program for core-genome alignment of evolutionary diverse genomes.
A webserver for the determination of core genes from sets of viral and small bacterial genomes.
This package provides methods to identify active transcriptional programs, including methods and classes to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model TF cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary.
Search for a niche associated CORE MICrobiome.
This library is ideal for those seeking an overview of a complex subject while allowing the possibility to "drill down" to specific details. Search results are presented in a dashboard format comprised of panels containing various categories of information ranging from introductory sources to the latest scientific articles.
CORENup is a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel levels are devoted to catching both non periodic and periodic DNA string features.
CoreProfiler is a cgMLST (core genome multilocus sequence typing) software that identifies alleles in bacterial genome assemblies by comparing them to a reference allele scheme. It detects both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach, enabling robust and reproducible strain genotyping.
CoreSimul is a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination
Accurate codon reassignment prediction, applied to mitochondrial genomes.
The COVID-19 Repositioning Explorer (CoREx) is a web resource to allow the visualisation of FDA approved drugs in context of their protein targets, several available interactomes, and protein function.
CorGAT is a tool for the functional annotation of SARS-CoV-2 genomes. It is a collection of Perl script for the alignment of SARS-CoV-2 genomes and the functional annotation of genetic variants.
Measures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.
The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets
CoRINs (Comparator of Residue Interaction Networks) is a web tool for comparing multiple residue interaction networks (RINs) that generates easy to understand results through interactive tables, graphics and downloable text files. CoRINs reports may be useful in the evaluation of protein conformational variation, as an additional tool to validate models from homology modeling, or to assess the putative impacts of a mutation on the protein structure and activity, by identifying its effects on the protein network.
Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project.
Comparative Meta RNA-Seq Data Standardized Analysis Pipeline (CMRP) is a processing frame for the standardized analysis of Meta RNA-Seq raw data from wide-ranged species.
It fits correlation motif model to multiple studies to detect study specific differential expression patterns.
Provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional.
Corna is a Python package that perform Natural Abundance Correction on the output intensity of metabolites, obtained after performing Mass Spectrometry(MS).
Analysis of combinatorial cell-based RNAi screens.
Coverage-dependent RNA-Seq analysis of gene expression data without biological replicates.
A neural network based predictor of residue contacts in proteins.
This tool allows you to do co-expression analysis using either predefined or user-defined groups of micro array experiments.
CORNETO is a Python package that provides a unified framework for knowledge-driven network inference from omics data. It addresses limitations of existing methods by incorporating prior knowledge and allowing for simultaneous network inference across multiple samples.
Imports NYTimes data from github and offers logarithmic plots.
Fit Corona / COVID cases of your own country with this simple script. Data is updated every day.
Corona Exponential Fit For Any Country Using Latest Data
This software fits data available corona for accumulated world infections to an empirical equations, and extrapolated the fitted equation
Study- and Sensor-Based Mobile App Platform Exploring Aspects of the COVID-19 Pandemic.
CoronaCentral is a tool for analyzing the vast coronavirus literature with CoronaCentral.
Coronapp is a web application to annotate and monitor SARS-CoV-2 mutations. It is able to easily proces user‐provided SARS‐CoV‐2 genomic sequences and visualizing the current worldwide status of SARS‐CoV‐2 mutations. The webtool allows users to highlight mutations and categorize them by frequency, country, genomic location and effect on protein sequences, and to monitor their presence in the population over time.
CoronaSPAdes – a novel assembler for RNA viral species recovery in general and coronaviruses in particular.
CoronaVIR is a Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates.
Coronavirus Network Explorer is an exploratory tool to connect SARS-CoV-2 viral proteins to selected biological processes, diseases, and pathways. It is a tool for mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function.
Coronavirus tracker created to visually analyze the spread of COVID-19.
Live statistics and coronavirus news tracking the number of confirmed cases, recovered patients, and death toll by country due to the COVID 19 coronavirus.
CoronaViz is a browser-based tool for visualizing multilayer spatiotemporal epidemiological data using animated geocircles. The tool is open-source and designed to improve the understanding of complex data for both experts and the general public.
CoronaVR is a Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2. It is a comprehensive web resource for SARS-CoV-2 study.
CoroNet is a Deep Convolutional Neural Network model to automatically detect Covid-19 infection from chest X-ray images. The deep model called CoroNet has been trained and tested on a dataset prepared by collecting Covid-19 and other chest pneumonia X-ray images from two different publically available databases.
CorrAdjust is a Python module that corrects for confounding variables when computing correlations between transcriptomic features, enhancing biological relevance and interpretability. It's available through GitHub with accompanying documentation and tutorials.
Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis.
A R pipeline to correlate drug distribution with tumor tissue-types in mass spectrometry imaging (MSI) data.
The command corrects a DNA sequencing error of cell barcoding containing RT primer sets for Quartz-Seq2 which one of a high throughput single-cell RNA-sequencing.
YASS is a program designed to enhance the sensitivity of DNA similarity searches. It utilizes an indexing approach and is available as a web interface and command-line tool.
Correlation AnalyzeR is a tool for functional predictions from gene co-expression correlations.
A Python package to calculate, visualize and analyze dynamical correlations of proteins. correlationplus contains three main scripts that you can use to calculate, visualize and analyze dynamical correlations of proteins. These correlations can be dynamical cross-correlations, linear mutual information or generalized correlations. You can use elastic network models or your your molecular dynamics trajectories for these visualizations and analyses.
CorRelator is a tool for easy TEM and FLM correlation for On-The-Fly processing. CorRelator is an interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy. CorRelator supports both on-the-fly and post-acquisition two dimensional (2D) cryo-correlation. The on-the-fly correlation integrates image registration, transformation and correlation between EM and FM. The output is ready for SerialEM automated data collection at transformed fluorescent targets of interest (TOIs) on registered EM images. To get started and gain supports, visit Wiki for more details.
Correlia is an open-source ImageJ/FIJI plug-in for the registration of 2D multi-modal microscopy data-sets. The software is developed at ProVIS - Centre for Correlative Microscopy and is specifically designed for the needs of chemical microscopy involving various micrographs as well as chemical maps at different resolutions and field-of-views.
CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.
Multivariate correlation estimation and statistical inference.
corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.
Command-line software program to go from a de novo transcriptome assembly to gene-level counts. This software takes a set of reads that have been multi-mapped to the transcriptome and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq.
Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph
corto (correlation tool) is a lightweight R package for Gene Network Inference and Master Regulator Analysis. corto package provides a pipeline to infer networks between "centroid" and "target" variables in a dataset, using a combination of Spearman correlation and Data Processing Inequality (DPI).
Database which provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
Helmholtz Zentrum München-German Research Center for Environmental Health
Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.
Comparative Sequencing Analysis Platform.
Cosine score-based iterative normalization of biologically diverse samples.
Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria are provided.
COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.
COSGAP provides containerized statistical genetics analysis pipelines, facilitating reproducible and standardized genetic data analysis across diverse environments. It utilizes established software tools packaged into Singularity containers with helper scripts for tasks such as genome-wide association studies and gene-set enrichment analysis.
COSGAP: COntainerized Statistical Genetics Analysis Pipelines
COSIFER (COnSensus Interaction Network InFErence Service) is a Python package for the consensus inference of molecular interaction networks. Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources. COSIFER runs multiple selected inference algorithms on your expression data and returns a consensus interaction network.
Time distributed data analysis by Cosinor.Online application. Tools for estimating and predicting the cosinor model version 1.1 from CRAN. cosinor is a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients. cosinor: Tools for estimating and predicting the cosinor model. Molcan, L. (2019). Time distributed data analysis by Cosinor. Online application. bioRxiv, 805960. Preprint available at BioRxiv, doi: https://doi.org/10.1101/805960. Cosinor Online, cosinor on the web, is a simple web-based application evaluating the presence of 24-h periodicity. Loading data is easy, just copy and paste columns from an Excel file to the web form
R package for mixed-effects cosinor models. The cosinoRmixedeffects package can be implemented for the estimation and prediction of the a mixed-effects cosinor model for longitudinal periodic data.
CosinorPy is a Python implementation of cosinor-based methods for rhythmicity detection and analysis. CosinorPy merges and extends the functionalities of existing cosinor packages. It supports the analysis of rhythmic data using single- or multi-component cosinor models, automatic selection of the best model, population-mean cosinor regression, and differential rhythmicity assessment.
COSMAS is a software toolkit for cardiac optical mapping data analysis.
Web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data.
Import Cosmed FitMate metabolic data text files into MATLAB.
Catalogue Of Somatic Mutations In Cancer (COSMIC) - resource for exploring the impact of somatic mutations in human cancer.
Tool for the preprocessing of liquid/gas chromatography mass spectrometry (LCMS/GCMS) data, focusing on metabolomics or lipidomics applications. To improve the detection of low abundant signals, it generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately.
COSMOPharm is a Python-based tool that utilizes COSMO-SAC to predict the thermodynamic compatibility of drugs and polymers in amorphous solid dispersions. It facilitates the selection of optimal polymeric carriers to enhance drug bioavailability by calculating solubility and miscibility.
COSMOS is the advanced software package for PC that integrates modeling, crystallography and NMR spectroscopy.
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets. COSMOS leverages extensive prior knowledge of signaling pathways, metabolic networks, and gene regulation with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. This pipeline can provide mechanistic explanations for experimental observations across multiple omic data sets.
Package that implements the COSNet classification algorithm, which predicts node labels in partially labeled graphs where few positives are available for the class being predicted.
COSORE is a community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data.
Server for the analysis, comparison and ranking of docking models based on inter-residue contacts.
Cost-IS is a software instrument designed to estimate the cost of implementation strategies, particularly for digital health innovations. It facilitates data collection and comparison of costs across different case studies.
CoSTA: Unsupervised convolutional neural network learning for spatial transcriptomics analysis.
An accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis.
CoStat is an easy-to-use program for data manipulation and statistical analysis.
A scRNA-seq data analysis based on gene co-expression.
Colon Transcriptome Explorer (CoTrEx). This web-based resource provides exhaustive visualization and analysis of transcriptome-wide gene expression profiles of normal colon tissue from BarcUVa-Seq and GTEx.
A consensus-based decision tool for initiating antitubercular therapy in ocular tuberculosis.
CottonMD is a curated and integrated multi-omics resource for cotton. In this database, we integrated and analyzed datasets from genomics, epigenomics, transcriptomics, metabolomics and phenomics, and offer multiple tools for users to make it easy to utilize datasets.
Framework for identifying co-factors associated with uniquely-bound genomic regions.
Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny.
Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression count data, identifies characteristic genes driving cluster memberships, and provides a visual summary of the cluster memberships.
countfitteR is a tool for efficient selection of count distributions to assess DNA damage.
This function calculates the Color (C) score for ABCD calculation of skin lesions.
Function for Counting Colors in a Skin Lesion
The code counts the facets and the vertices of the spanning tree polytope of a graph.
Counting spanning trees and flacets of a graph
Calculate the number of reads(annotations) overlapping for each transcript.
Count GC percent for each read against a genome.
Compare characteristic features of count data sets.
Coupled co-clustering-based unsupervised transfer learning algorithm (coupleCoC) for the integrative analysis of multimodal single-cell data. coupleCoC builds upon the information theoretic co-clustering framework. In co-clustering, both the cells and the genomic features are simultaneously clustered. Clustering similar genomic features reduces the noise in single-cell data and facilitates transfer of knowledge across single-cell datasets.
the Coronavirus Antibody Database (CoV-AbDab) is a database containing the oV-AbDab contains data on over published and patented antibodies and nanobodies known to bind to at least one betacoronavirus.
CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.
CoV-GLUE is a web appplication for tracking SARS-CoV-2 genomic variation.
A web tool implements a mechanistic model of human signaling for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways known to be involved in the infection by SARS-CoV-2, which are updated with the curated versions released by the COVID-19 Disease Map curation project .
CoV-Seq is a suite of tools and datasets for analysis and visualization of genomes of SARS-CoV-2, the virus that causes COVID-19. Sequences are collected from four major repositories: GISAID, NCBI, EMBL and CNGB.
Cov19VaxKB: COVID-19 Vaccine Knowledge Base.
A web server for screening TCR CDR3 from TCR immune repertoire of COVID-19 patients and their recognized SARS-CoV-2 epitopes.
Stable clustering of SARS-CoV-2 sequences from phylogenetic trees.
Visualization and Analysis Tool of Bacterial Next Generation Sequencing (NGS) Data for Postgenomics Life Scientists.
CoV2ID provides a complete, quality checked and regularly updated list of oligonucleotides for SARS-CoV-2. The database evaluates available therapeutic and detection protocols according to the virus genetic diversity.
CoV2K is a knowledge base of SARS-CoV-2 sequence mutations, variants, and their effects; it is available for exploration as a graph that can be queried through a RESTful API addressing single entities or paths through their relationships.
CoV3D is a web r resource for structures of coronavirus proteins and their recognition by antibodies and other molecules. It contains high resolution coronavirus protein structures.
A fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool.
A toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data.
Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification.
CovalentDock Cloud web server allows one to perform covalent docking experiments and analysis online. Input is the structure of both the ligand and the receptor.
CovalentInDB (Covalent Inhibitor Database) is a web-accessible resource for covalent inhibitors and related targets.
Complementary and Alternative Medicine Clinical Trials Database for COVID-19 Disease (CoVAM) is a user-friendly database which gives update on registered clinical trials of complementary and alternative medicine on COVID-19 disease.
A collection of MATLAB functions implementing common covariance NMR processing methods
Covasim is a stochastic agent-based simulator designed to be used for COVID-19 (novel coronavirus, SARS-CoV-2) epidemic analyses. These include projections of indicators such as numbers of infections and peak hospital demand. Covasim can also be used to explore the potential impact of different interventions, including social distancing, school closures, testing, contact tracing, quarantine, and vaccination.
curated CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains.
CoVdb is a database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale.
Interactive SARS-CoV-2 pan proteome evolution tracker.
Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.
CoVEffect is an interactive web interface for deep learning-assisted scientific text annotation with effects of SARS-CoV-2 mutations and variants.
It is developed to simultaneously compare up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. It has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.
Comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses.
Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file.
This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome.
CoVerifi is a COVID-19 news verification system. It is a web application which combines both the power of machine learning and the power of human feedback to assess the credibility of news. By allowing users the ability to “vote” on news content, the CoVerifi platform enables the release of labelled data as open source, which will enable further research on preventing the spread of COVID-19-related misinformation.
Read coverage calculator for metagenomics
CoVex is an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drug candidates. Thus, CoVex is a resource to understand molecular mechanisms of pathogenicity and to prioritize candidate therapeutics.
This database enables systematic analysis and interpretation of this large-scale dataset by providing a comprehensive view of various features such as affinity, neutralization, in vivo protection and effector functions for each antibody.
COVID-19 antibody therapeutics tracker is a global online database of antibody therapeutics for the prevention and treatment of COVID-19.
OncoMX has been expanded to include COVID-19 biomarkers.
Covid-19.bioreproducibility.org is a web resource for SARS-CoV-2-related structural models. Structural biologists have already determined hundreds of experimental X‐ray, cryo‐EM, and NMR structures of proteins and nucleic acids related to this coronavirus, and this number is still growing. The system can help biomedical researchers, who may not necessarily be experts in structural biology, navigate through the flood of structural models. It aggregates expert‐verified information about SARS‐CoV‐2‐related macromolecular models. In this article,
COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking.
COVID-19-CT-CXR is a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset.
Very basic data analysis and visualization on the spread of the COVID-19 virus in Italy
COVID-19 Data Portal is a tool for accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.
COVID-19 Knowledge Graph is a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology.
he SARS-CoV-2 mutation browser is easy, efficient, and user friendly that only deals with novel coronavirus and display the viral genome variation around the globe on a single platform for the convenience of the researchers and virologists. The browser features comprehensive integration of a genomic sequence of SARS-CoV-2along with their metadata information from NGDC, NCBI, and GISAID. Furthermore, it is open access mutation browser that displays the region and gene-wise (5UTR, ORFab, S, E, M, N, 3UTR) distribution of mutation data of particular virus isolate and also provides position and statistics of mutations. Moreover, viral primer sequence information is also displayed on the same page “primer infopedia”.
The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.
COVID-19 preVIEW is a tool for semantic search to explore COVID-19 research preprints.
COVID-19 Scenarios is an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2. This tool is based on the SIR model that simulates a COVID19 outbreak. The primary purpose of the tool is to explore the dynamics of COVID19 cases and the associated strain on the health care system in the near future.
COVID-19 SignSyma is a tool foor fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model.
COVID-19 TestNorm is a tool to normalize COVID-19 testing names to LOINC codes. Large observational data networks that leverage routine clinical practice data in electronic health records (EHRs) are critical resources for research on coronavirus disease 2019 (COVID-19). Data normalization is a key challenge for the secondary use of EHRs for COVID-19 research across institutions. In this study, we addressed the challenge of automating the normalization of COVID-19 diagnostic tests, which are critical data elements, but for which controlled terminology terms were published after clinical implementation. We developed a simple but effective rule-based tool called COVID-19 TestNorm to automatically normalize local COVID-19 testing names to standard LOINC (Logical Observation Identifiers Names and Codes) codes. COVID-19 TestNorm was developed and evaluated using 568 test names collected from 8 healthcare systems
Dashboard showing recent developments of the COVID-19 virus pandemic. The latest open data on the COVID-19 spread are regularly downloaded and displayed in a map, summary tables, key figures and plots.
A database for tracking the contribution of genomics and precision health to the COVID-19 pandemic response.
Visualises linked human biological data related to SARS-CoV-2 in the form of a knowledge graph, using a range of publicly available data. Includes gene, protein, gene ontology, reaction, pathway, homology, protein domain, phenotype/disease, and GWAS data and the interactions between them. KnetMiner scores and ranks genes to give the most relevant results relating to your query search.
COVID-19 Living OVerview of Evidence (COVID-19 L·OVE) is a public repository and classification platform for COVID-19 articles.
The online platform to query gene expression differences between severe and mild COVID-19 patients in these datasets.
Phenotype data dictionary for COVID-19 patients within the COVID-19 Host Genetics Initiative, employed in several clinical studies around the hospitals and labs of the network.
the COVID-19 Seroprevalence Studies Hub, known as COVID-19 SeroHub, is an online dashboard intended to help researchers and policymakers monitor studies of Severe Acute Respiratory
Covid-19RiskPrediction is a MATLAB script for COVID-19 Patient/Non-Patient Risk Prediction using AI.
COVID-ABS is an agent-based model of COVID-19 epidemic to simulate health and economic effects of social distancing interventions. COVID-ABS is a SEIR (Susceptible-Exposed-Infected-Recovered) agent-based model that aims to simulate the pandemic dynamics using a society of agents emulating people, business and government.
COVID-Align is an accurate online alignment of hCoV-19 genomes using a profile HMM.
COVID-CT-Mask-Net is a model for prediction COVID-19 from CT Scans Using Regional Features.
COVID-DeepPredictor is a recurrent neural network to predict SARS-CoV-2 and other pathogenic viruses.
This graphic interface displays the covid time series (cases, deaths, vaccinations and much more) in many selectable manners.
A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data.
COVID-KOP (COVID linked in Knowledge Oriented Pathways) is a biomedical reasoning system combining the knowledge existing in the ROBOKOP knowledge graph and data collected about the COVID-19 pandemic.
Deep Convolutional Neural Network for Severity Assessment of COVID-19 Cases from Chest X-ray Images.
The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters.
A clinical decision support system for COVID-19 detection.
COVID-Predictor is a Machine Learning model to Predict Novel Coronavirus.
A webserver for the analysis of SARS-CoV-2 sequencing data.
COVID-SGIS is a smart tool for dynamic monitoring and temporal forecasting of Covid-19.
COVID Term is constructed by Institute of Medical Information, Chinese Academy of Medical Sciences and consists of the bilingual preferred terms, abbreviations, synonyms and some definitions and sources for concepts related with COVID-19 in disease, viruses, clinical manifestation, infected population, epidemic prevention and control, psychological assistance et. al.
COVID-TRACK is a Python based web-application that provides a platform for tracking testing, incidence, hospitalizations, and deaths related to COVID-19 along with various derived quantities. Our application makes the comparison across states in the USA and countries in the world easy to explore, with useful transformation options including per capita, log scale, and/or moving averages.
The application allows an analysis of COVID 19 cases in the country of interest as well as a curve fit for the next few days
Linear, exponential, logistic, Gompertz, Gauss, Fourier models fitted to epidemiological data from the COVID-19 outbreak.
COVID-19 Drug interactions is a comprehensive, up-to-date, evidence-based COVID19 drug-drug interaction resource.
COVID-19 drug repurposing system for In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19.
The example trains a Machine Learning Model to forecast the number of covid-19 cases given the number of cases in previous days.
COVID-19 Corona Forecasting using Machine Learning
MATLAB script for generating an animation displaying the spread of COVID-19 India and save it as Vid file.
Shows the actual numbers of people affected with the corona virus COVID-19. Data obtained from https://corona.lmao.ninja/
Script for visualizing COVID-19 infections in the European Union
This model was created based off of fitVirus. This is a data-driven model that obtains up to date data and predicts the spread of COVID-19.
Virus propagation simulator in MATLAB/Simulink
COVID-19 Propagation Simulator (Simulink)
COVID19 Realtime tracking simulation for Indian states
Using Text Analytics in MATLAB to explore research articles related to COVID-19 and other coronaviruses.
Agent-based Transmission model of COVID-19
This code will generate an animation displaying the spread of COVID-19 and save it as a video file. Data is obtained and processed from HDX.
Population-based Forward-time Simulator for the Outbreak of COVID-19
The package covid19census provides functions to extract COVID-19 cases, deaths, hospitalizations and test of U.S. and Italy at the county and regional level, respectively, and then combines them with other population metrics (age, sex, prevalence of chronic conditions, income indexes, access to health services and many others).
Matlab tool to download and plot Covid-19 data
Database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale.
Covid19Risk.ai is an open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19.
This simulation shows how COVID-19 Spread World wide
COVIDanno, COVID-19 annotation in human, which is an integrated RNA-seq database of SARS-CoV-2-infected in vitro models.
COVIDC is an expert system to diagnose COVID-19 and predict its severity using chest CT scans.
CovidCTNet is an open-source deep learning approach to diagnose covid-19 using small cohort of CT images.
COVIDep provides an up-to-date set of B-cell and T-cell epitopes that can serve as potential vaccine targets for SARS-CoV-2. The identified epitopes are experimentally-derived from the 2003 SARS virus and have a close genetic match with the available SARS-CoV-2 sequences. COVIDep is flexible and user-friendly, comprising an intuitive graphical interface and interactive visualizations.
Covidex is an ultrafast and accurate tool for virus subtyping.
CovidExpress is an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes.
CovidGraph, developed by the HealthECCO community, is a platform designed to foster research and data exploration to fight COVID-19.
COVIDHunter is an accurate and flexible COVID-19 outbreak simulation model that forecasts the strength of future mitigation measures and the numbers of cases, hospitalizations, and deaths for a given day, while considering the potential effect of environmental conditions.
COVID-19 resource compendium (COVIDium) that would facilitate the researchers to find suitable DBs and tools for their research studies.
CovidMine is an InterMine dedicated to COVID-19 / SARS-CoV-2 data which integrates confirmed Covid-19 cases, deaths, Sars-CoV-2 reference genome and nucleotide sequences from isolates deposited in Genbank
CovidMulti-Net is a parallel-dilated multi-scale feature fusion architecture for the identification of COVID-19 cases from chest X-ray Images.
CovidNLP is a Web Application for Distilling Systemic Implications of COVID-19 Pandemic with Natural Language Processing
A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity.
Web interface that can process SARS-CoV-2 genome sequences in plain fasta text format or provided through identity codes from the Global Initiative on Sharing Avian Influenza Data (GISAID) or GenBank.
Database for mining protein dysregulation in patients with COVID-19.
Machine Learning-Assisted COVID-19 Prognosis Prediction on Patient's Clinical Information.
COVIDrugNet is a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19.
This website uses natural language processing (NLP) to power search on a set of research papers related to COVID-19.
A web app and R Package for assessing asymptomatic COVID-19 testing strategies.
CovidSim is a web application for a SEIR simulation model for the COVID-19 pandemic and is applied to a hypothetical European country of 10 million population.
Real-time prediction of COVID-19 spread based on time-series modelling.
COVIDStrategyCalculator is a standalone GUI to assess SARS-CoV2 testing- and quarantine strategies for incoming travelers, contact person management and de-isolation. The COVIDStrategyCalculator (CSC) calculates the residual risk, risk reduction and test efficacy for arbitrary testing and quarantine strategies. Where risk is defined as the probability that an individual, who is released from quarantine/isolation, is- or may become infectious and potentially spread the disease.
CovidXrayNet is a tool for optimizing data augmentation and CNN hyperparameters for improved COVID-19 detection from CXR. CovidXrayNet model improves the detection rate of coronavirus 2019 (COVID-19), form Chest X-Ray (CXR), by means of optimizing the data augmentation pipeline and Convolutional Neural Network (CNN) hyperparameters.
COVIEdb is a database for potential immune epitopes of coronaviruses.
Database of SARS-COV-2, SARS-COV, MERS-CoV, HCoV-229E and HCoV-OC43, etc.7 human pathogenic coronaviruses RNAs and host proteins interactions, which are critical for viral infection.
COVision is an interactive dashboard called which includes the Agent based Models (ABM) and classical compartmental models i.e. Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) approaches.
CoVizu is an open source project to develop a public interface to visualize and explore global diversity of SARS-CoV-2 genomes in near real time.
A Transfer Learning Framework for Automatic COVID-19 Detection From Crowd-Sourced Cough Sounds.
An R package for coverage based normalization of Hi-C and capture Hi-C data.
CovPDB, a database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank
CovPepDock is a web application for covalent flexible peptide docking in Rosetta.
CoVpipe2 is a bioinformatics workflow developed by the Robert Koch Institute to accurately reconstruct SARS-CoV-2 genomes from short-read sequencing data, addressing common challenges like primer clipping and mixed samples. It's written in Nextflow and freely accessible under the GPL3 license.
CovRadar is a tool for molecular surveillance of the Corona spike protein. The spike protein contains the receptor binding domain (RBD) that is used as a target for most vaccine candidates.
Automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modelling of metabolic interaction networks.
This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.
A Subsampling Method with Balanced Genetic Diversity for Large-Scale SARS-CoV-2 Genome Data Sets.
CoV-Spectrum is an interactive tool to analyze and discover variants of SARS-CoV-2.
Convert the coverage track from a BAM file into a BED file
Coverage analysis from BAM files supporting target regions in BED or GFF formats
Data integration into SIB Literature services, an application ontology (COVoc) and a triage service named COVTriage
CovXNet is a multi-dilation convolutional neural network for automatic COVID-19 and other pneumonia detection from chest X-ray images with transferable multi-receptive feature optimization. With the recent outbreak of COVID-19, fast diagnostic testing has become one of the major challenges due to the critical shortage of test kit.
An efficient cloud-based genomics workflow for scalable identification of Sars-Cov-2.
Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software.
Multi-snpnet-Cox (mrcox) Efficient Group-Sparse Lasso solver for multi-response Cox model.
Cox-nnet is an artificial neural network method for prognosis prediction of high-throughput omics data.
CoxBase is an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence.
A Knockoff Filter for High-Dimensional Mediation Analysis with a Survival Outcome in Epigenetic Studies.
The Coxmos (Cox MultiBlock Survival) R package is an end-to-end pipeline designed for the study of survival analysis for high dimensional data. Updating classical methods and adding new ones based on sPLS technologies. Furthermore, includes multiblock functions to work with multiple sets of information to improve survival accuracy.
CoxPhLb is an R Package for Analyzing Length Biased Data under Cox Model.
COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.
The COmpositional Zero-Inflated Network Estimation (COZINE) method for inference of microbial networks which addresses these critical aspects of the data while maintaining computational scalability. COZINE relies on the multivariate Hurdle model to infer a sparse set of conditional dependencies which reflect not only relationships among the continuous values, but also among binary indicators of presence or absence and between the binary and continuous representations of the data.
CP-Hunter is a web-based data processing platform for the automatic analysis of mass spectra of chlorinated paraffins and their transformation products. It facilitates untargeted analysis and data evaluation performed locally without data transfer to external servers.
Web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.
Consensus Pathway Analysis (CPA) is a web-based platform for consensus pathway analysis and interactive visualization.
Web-based CpACpP platform and the package containing the prebuilt models
Curated Protein Aggregation Database (CPAD) is an integrated database which contains information related to amyloidogenic proteins, Aggregation prone regions, aggregation kinetics and structure of proteins relevant to aggregation. Authors are encouraged to deposit any information related to above topics to our server.
The evolutionary history of topological variations in the CPA/AT transporters. Structural models, topology information and other details are presented in a searchable database, CPAfold
CPAG can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.
CPAT (Coding-Potential Assessment Tool) is a logistic regression model-based classifier that can accurately and quickly distinguish protein-coding and noncoding RNAs using pure linguistic features calculated from the RNA sequences. CPAT takes as input the nucleotides sequences or genomic coordinates of RNAs and outputs the probabilities p (0 ≤ p ≤ 1), which measure the likelihood of protein coding.
A Bayesian meta-analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus.
Coding Potential Calculator (CPC) is a support vector machine-based classifier to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features.
Coding Potential Calculator. Fast and accurate coding potential calculator based on sequence intrinsic features.
Interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways.
Cancer Personalized Drug Recommendation (CPDR). A R Package of personalized drugs for patients with cancer by reversing individual disease signatures.
CPDSeqer is a tool for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data.
CPE-SLDI is a model for predicting coding potential. It uses oversampling technology and increase the number of positive instances and alleviate the problem of local data imbalance, and propose a coding potential prediction method, CPE-SLDI, which constructs a prediction model by combining various sequence-derived features based on the augmented data.
CpelTdm is a julia package designed to perform DNA methylation differential analysis. The package has several advantages when compared to traditional DNA methylation differential analysis packages. CpelTdm not only detects mean methylation level differences between groups, but it can also detect significant differences in methylation entropy as well as in the probability distribution of methylation.
A data analysis pipeline for shotgun mass-spectrometry proteomics.
CpG Transformer for imputation of single-cell methylomes.
CPGAVAS (Chloroplast Genome Annotation, Visualization, Analysis, and GenBank Submission) is a web server which allows accurate genome annotation, the generation of circular chloroplast genome maps, the provision of useful analysis results of the annotated genome, the creation of files that can be submitted to GenBank directly.
CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant species belonging to spermatophytes. The database also allows comparison of gene length and location of different genes among plant species belonging to same or different families.
CpGmotifs is a tool to discover DNA motifs associated to CpG methylation events.
Identify and plot CpG islands in nucleotide sequence(s).
Identification of potential CpG islands.
Identify and report CpG-rich regions in nucleotide sequence(s).
An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph.
Analysis and visualization of junction sites of chloroplast genomes.
Resource of manually curated lysine acetylated substrates with their sites.
Compendium of protein lysine acetylation (CPLA)
CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors.
A visualized contig plotting application for analysis of short read alignment of nucleotide sequences
A Continuous Profile Models Matlab toolbox for alignment and normalization of time series data
A database of Chinese patent medicine and compound prescription.
Parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
CPMKG is a condition-based knowledge graph for precision medicine that uses conditional events as the basic data structure to provide suggestions for personalized disease treatment and prevention. It integrates a large language model to provide textual interpretations of the graph data.
Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.
Curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. It is built and maintained with open source tools.
CPPA (Cancer Proteome and Phosphoproteome Atlas), a web tool to mine abnormalities of the proteome and phosphoproteome in cancer based on published data sets.
A method for constructing cell-cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.
This tool computes a Persistent Phylogeny from a binary character matrix.
Template-based predictor of RNA secondary structure. It takes a template RNA secondary structure(s) and a query RNA sequence(s) and generates secondary structure of the query sequence(s) using the provided structure(s) as a template(s). Biological reliability of the generated structures is evaluated in form of z-scores.
CPPsite is a Database of Cell Penetrating Peptides. It contains cell penetrating peptides (CPPs) alongwith their secondary & tertiary structure. This database maintains experimentally validated CPPs (linear & cyclic; modified & non-natural residues) and wide range of cargos (nucleic acids, proteins, nanoparticles, PNA) delivered in cells using these peptides.
CPPsite is a database of experimentally validated Cell Penetrating Peptides (10-30 amino acids).
Identify prognostic genes (biomarkers) and use them to predict prognosis of cancer patients.
CPred is a prediction tool for circular permutations (CP) in proteins.
CPRiL is a webserver for exploring functional compound-protein relationships that are extracted automatically from PubMed literature.
A web based interactive platform for online proteomics, phosphoproteomics, and genomics data analysis.
CPSign is an open-source software tool for quantitative structure-activity relationship (QSAR) modeling utilizing conformal and probabilistic prediction. It supports several chemical descriptors and modeling methods, including SVM, with features for visualizing results and deploying models as REST services.
Computational platform update for the analysis of small RNA sequencing data.
Consecutive Positions Scoring Matrix (CPSSM) is a pattern matching algorithm for genomic patterns related to protein motifs.
This software provides easy access to cancer data from the National Cancer Institute’s CPTAC program, which characterizes and studies the proteogenomic landscape of tumors. We implement the software as a Python package called cptac, but you can seamlessly use it in an R environment with the help of the reticulate package (demonstrated in Tutorial 6). Our package is installed in one step with pip:.
Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads.
This package implements two methods to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. These methods require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs.
cpxDeepMSA is a deep cascade algorithm to generate high-quality protein complex multiple sequence alignment with high quality, significant depth, a wide range of sequence sources, and strong generalization ability.
Cluster Quality based Non-Reductional (CQNR) generates new samples proportional to the distribution of samples of the minority classes, without eliminating any sample of the minority class as noise.| Effector protein predictor based on 3D structure (EPP3D) is based on the CQNR and predicts the type of effector protein from a PDB-file of unknown proteins.
The Crop EST Database is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. A view of these information give the summarized numbers about genomic data of species listed in the adjacent table.
Compositionally-Restricted Attention-Based Network for Materials Property Prediction.
CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.
For questions, comments, remarks on the algorithm or the article
CracTools is a set of pipelines allowing to perform diverse RNA-Seq analysis such as chimeras detection, splicing variant detection, SNPs calling, and such.
CRAFT is a tool for Compact Representations of large-scale Alignment-Free genomic/metagenomic sequences daTabase and fast sequence comparisons between sequencing data/long genomic sequences and the compact database.CRAFT parses the input genomic/metagenomic sequences, counts the co-occurrences of adjacent k-mer pairs, learns the embeddings, searches against archived repositories by the dissimilarity between the input and the archived sequences in the embedding space, and finally reports the best matches in various ways.
New program for ab initio gene prediction based on a conditional random field model with semi-Markov structure that is trained with an online large-margin algorithm related to multiclass SVMs. Our experiments on benchmark vertebrate datasets and on regions from the ENCODE project show significant improvements in prediction accuracy over published gene predictors that use intrinsic features only, particularly at the gene level and on genes with long introns.
Craig plot is an interactive navigation in the substituent bioisosteric space. Craig plot allows interactive navigation in the substituent property space defined by Hansch pi hydrophobicity constant and Hammett sigma parameter.
Part of the crambled-seg pipeline. It allows to interactively explore the cellularity, depth of coverage and clonality of tumour samples that have gone for whole-genome sequencing. In particular, it allows the user to assess the competing solutions for such data that can arise from using different packages.
CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals
The Cranfield Genome Browser (CRAMER) is a lightweight, highly customizable web-based genome browser supporting multiple visualization instances. CRAMER is a customisable, JavaScript and Jade based genome browser for interactive exploration of genomic data. Data is visualized in the browser, meaning CRAMER can be installed on any website and show data from a wide range of online, ftp links or local sources. CRAMER works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3, BAM or delimited text files, and can be customised to parse and display any data source as required.
Framework technology comprising file format and toolkit in which highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use are combined.
Takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.
Web-based resource for cancer-related analysis of genomic variants (single base substitutions and indels). It provides scoring, sorting, filtering, and interactive visualizations to assist with identification of important variants.
CrazyQuant is a spot-finding tool. This JAVA-based applet allows the loading and quantitation of your cDNA microarray images and membranes.
Identification of circRNA-RBP interaction sites using an ensemble neural network approach.
CRC64 is the source code for an improved CRC-64 routine for hashing protein sequences. This CRC function has been extensively tested on real sequences and articially generated sequences.
Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.
CRCView is a web-based microarray data analysis and visualization system. CRCView is powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm
CREAMMIST is an integrated cancer drug sensitivity database for in vitro pharmacogenomics analysis, providing an integrative dose-response curve across five widely used cancer cell-line drug-response datasets (CCLE, GDSC1, GDSC2, CTRP1, CTRP2).
Creates a FAIR digital object in the openDS format
Preprocess ChIP-seq aligned reads before calling FindPeaks: Filter out dulpicates from the SAMPLE (optional) and create a CONTROL dataset w/o duplicates with the same number of reads as in the SAMPLE. Only eland, sam and bam files are accepted.
Created metal artifact of Computed Tomography
MLPA is a digital twin framework for personalized cancer simulation and treatment optimization. It integrates electronic health records and genomic data using stochastic cellular automata to model tumor progression and pharmacological responses.
CREDO is a tool that simplifies the creation of reproducible Docker containers for bioinformatics applications, addressing challenges related to inconsistencies and lack of standardization in bioinformatics pipelines. It generates Dockerfiles incorporating heterogeneous packages, facilitating easy image creation and promoting open science practices.
CREMA is an online tool which automatically infers regulatory networks from chromatin accessibility (ATAC/DNase-seq) or enhancer mark (ChIP-seq) data. CREMA directly processes raw data of a set of samples (FASTQ files), identifies cis-regulatory elements (CREs) , infers key transcription factors driving the observed chromatin state changes across the experimental conditions, and makes detailed predictions regarding their regulatory roles.
CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.
Shiny app for transcription factor cataloguing.
CReSCENT (CanceR Single Cell ExpressioN Toolkit) is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data for tumour specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology. CReSCENT uses public data sets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.
A tool for detecting eccDNA from Nanopore reads
Consistency-regularized region-growing network (CRGNet) for semantic segmentation of VHR remote sensing images using point-level annotations. The key idea of CRGNet is to iteratively select unlabeled pixels with high confidence to expand the annotated area from the original sparse points
CRHP Finder is a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data.
The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, expression of key immunomodulators, and tumor infiltrating lymphocyte (TIL) spatial maps.
Used for genetic linkage analysis of diploid species. This version has been upgraded to handle large pedigrees with large numbers of markers on modern hardware.
This tool provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.
Crimp allows to align clusters across multiple clusterings, based on their matrices of membership coefficients (Q-matrices). This is frequently done to post-process outputs from programs like Structure (Pritchard et al. 2000). Crimp can be used as a much faster and typically more accurate alternative to CLUMPP (Jakobsson & Rosenberg 2007).
Crimson (cardiovascular integrated modelling & simulation) is an advanced simulation environment for subject-specific hemodynamic analysis. Crimson is integrating best-in-class open source-solutions for parallel flow solvers, fluid-structure interactions, GUI-based boundary condition specification, data assimilation, medical image processing, mesh generation, transitional hemodynamics, and much more.
CrinetCeRna Interaction NETwork) is a computational R tool to infer genome-wide competing endogenous RNA (ceRNA) interactions and groups.
Computational Resources for predicting protein-macromolecular interactions
Complete Reconstruction of Immunoglobulin V-D-J Sequences from RNA-seq
CRIS_single-sample is a computational R workflow to replicate the training, testing and biological validation of a multi-label classifier (ML2CRIS) for colorectal cancer intrinsic subtyping.
Identifies rare and common variants in pooled sequencing data
CRiSP (Cystine-Rich peptide Structure Prediction) is an accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning.
CRISP-view is a database of functional genetic screens spanning multiple phenotypes.
A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications. Software used to design guide RNA sequences for CRISPR/Cas9 genome editing. Steps to install crispRdesignR (tested in R version 3.4.4):. This software aims to provide all scientifically pertinent information when designing guide RNA sequences for Cas9 genome editing. The DAK1.fasta and DAK1_short.txt file contains a DNA sequence native to the DAK1 gene that can be copied and pasted into crispRdesignR or uploaded as a file (in the GUI version)
CRISP: a deep learning architecture for GC × GC–TOFMS contour ROI identification, simulation and analysis in imaging metabolomics
CrisPam is a web tool that detects SNP-derived PAMs for allele-specific targeting by the CRISPR/Cas system. The algorithm scans the generation of each reported PAM for a given DNA sequence and its variations. A successful result is such that at least one PAM is generated by a SNP. Thus, the PAM shall be part of the variant allele only and the Cas protein will therefore be able to exclusively bind the variant allele for gene-editing, while the wildtype allele remains unchanged.
crispat is a Python package designed to facilitate the choice of a suitable guide assignment strategy for single-cell CRISPR screens. It offers 11 different assignment methods and provides a means for their comparison.
Design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
CRISPRCasFinder is a program that detects CRISPRs and Cas genes in user-submitted sequence data, providing information on CRISPR orientation and Cas gene types. It is used to identify phage defence loci in bacterial genomes.
CRISPR-CBEI is a web-based designing tool for Cytosine Base Editor mediated gene Inactivation
A web server for designing focused CRISPR screening experiments.
A convenient, integrated toolkit to expedite all experimental designs and analyses of mutations for CRISPR/Cas9/Cpf1-based genome editing in plants and other organisms.
CRISPR-GEM is a machine learning model that predicts the downstream effects of CRISPR gene editing by constructing a synthetic gene regulatory network. It identifies optimal CRISPR target genes by modulating experimental group GRNs to motivate transcriptomic shifts toward a target group phenotype.
An online tool for designing highly efficient sgRNAs targeting cell surface proteins
protein-centric CRISPR guide design for targeted proteome engineering. A protein-centric CRISPR gRNA design tool for TArgeted Protein Engineering. Existing CRIPSR gRNA design tools target protein-coding regions within genomic loci and non-specifically target the entire input region of DNA. Current tools fail to consider proteomic-based applications, so CRISPR-TAPE has been developed to reduce the substantial time burden associated with manual curation of gRNA libraries and empower the proteomics community. Hello, welcome to CRISPR-TAPE, a protein-centric gRNA design tool.
Web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins.
Cross-platform graphical analysis tool for high-throughput CRISPR-based genome editing evaluation.
Web-based tool to generate single guide RNAs targeting transposable elements.
CRISPRbase is a comprehensive database curating the outcome and evaluating off-target effects of base editors on various cell types and tissues in dozens of species
CRISPRbuilder-TB is a tool that reconstructs the whole CRISPR locus from a Mycobacterium tuberculosis complex genome, by using Whole Genome Sequencing (WGS) data. This allows to deduce the real spoligotype, to detect mutants of spacers and direct repeats, insertion of mobile elements, and duplications. The Cas locus is reconstructed too. This is a semi automatic approach that leads to a set of contigs to assemble manually. Depending on the number, length, and quality of SRAs, the number of contigs can range from 1-2 patterns, in the best case scenario where the good quality of sequences allows a quasi-automatic reconstruction of the CRISPR cut in mobile element positions, to several contigs difficult to process, for too short or polluted reads.
Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes.
CRISPRCasStack is a toolkit capable of accurately identifying Cas proteins and comprehensively predicting CRISPR-Cas-related components, with the goal of accurately identifying potential Cas proteins that cannot currently be identified based on homology through a machine learning-based approach.
CRISPRCasTyper is a automated software tool with improved capabilities for identifying and typing CRISPR arrays and cas loci across prokaryotic sequences.
A R/Python package and an interactive web application, for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in this tool as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.
CRISPRepi is a platform that consolidates extensive sequencing data from RNA-seq, ChIP-seq, Bisulfite-seq, and ATAC-seq datasets related to CRISPR-based epigenome editing. It allows users to analyze editing outcomes and assess off-target effects.
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. CRISPResso2 can be used to analyze genome editing outcomes using cleaving nucleases (e.g. Cas9 or Cpf1) or noncleaving nucleases (e.g. base editors).
Detects this family of direct repeats found in the DNA of many bacteria and archaea.
CRISPRidentify is a tool to search for CRISPR arrays which utilises machine learning approach for distinguishing false candidates from true CRISPRS. CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, CRISPRidentify approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as an intuitive measure of the likelihood that a given genomic region is a CRISPR array.
CRISPR-oriented web-tool to dissect the key molecular events during the co-evolution of CRISPR and anti-CRISPR mechanisms.
CRISPRLand, relies on an unexploited observation about the nature of the repair process: the landscape of the DNA repair is highly sparse in the (Walsh–Hadamard) spectral domain. This observation enables our framework to address key shortcomings that limit the interpretability and scaling of current deep-learning-based DNA repair models. In particular. ur proposed framework is based on a divide-and-conquer strategy that uses a fast peeling algorithm to learn the DNA repair models. CRISPRLand captures lower-degree features around the cut site, which enrich for short insertions and deletions as well as higher-degree microhomology patterns that enrich for longer deletions.
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems.
Prediction of CRISPR RNA by repeat conservation.
CRISPRnano is a javascript-based program that was developed for rapid deep sequencing based genotyping of nuclease edited cell clones.
CRISPRon is a web application for CRISPR Cas9 on-target predictions. It enhances CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning.
Webservers for CRISPR Cas9 on- and off-target predictions.
Flexible and efficient tool for single guide RNA (sgRNAs) on-target activity prediction in CRISPR/Cas9 systems.
CRISPRpred(SEQ) is a method for sgRNA on-target activity prediction that leverages only traditional machine learning techniques and hand-crafted features extracted from sgRNA sequences. We compare the results of CRISPRpred(SEQ) with that of DeepCRISPR, the current state-of-the-art, which uses a deep learning pipeline.
CRISPRroots: CRISPR–Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites.
The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not.
Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.
crisprSQL is a SQL-based database for CRISPR/Cas9 off-target cleavage assays. It is a one-stop source for epigenetically annotated, base-pair resolved cleavage frequency distributions. This hand-curated dataset can act as an insight into state-of-the-art technologies driving transgenics, inform guide RNA design for genome engineering, and serve as a shared, transparent basis for modelling off-target DNA cleavage of CRISPR/Cas. Attached gene IDs make the high-resolution data usable for informing knockout screens, functional genomics and transcriptomics research.
CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.
CRISPRtracrRNA: an end-to-end standalone bioinformatic tool for tracrRNA predictions. In order to robustly predict the new tracrRNA candidates, CRISPRtracrRNA combines different sources of evidence.
Provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies.
A Python package for visualizing and analyzing CRISPR sequences.
Discrete simulation tool for designing pooled genetic screens.
Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST | CRISPy-web now detects potential amino acid changes introducable by CRISPR-BEST
CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. This tool focuses on generating guide RNA sequences for Yeast and Bacterial species used in bioenergy research.
crisscrosslinkeR is an R package for identification and visualization of protein–RNA and protein–protein interactions from crosslinking mass spectrometry.
CRIT (CircRNA Regulator Identification Tool) is a pipeline based on a non-negative matrix factorization method to integrate various omics information and to identify regulating RBPs.
CRITTERBASE, a publicly accessible data warehouse and interactive portal that currently hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data for 18,644 samples and 3,664 benthic taxa (2,824 of which at species level).
Faster implementation specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.
CRMarker is a manually curated comprehensive resource of both long noncoding and circular cancer RNA markers.
Simulate operating characteristics of the Bayesian CRM.
Scripts for predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features.
cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.
CRNPRED is a program that predicts secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO) of a native protein structure from its amino acid sequence.
CRNT4SBML is a Python package for the detection of bistability in biochemical reaction networks.
A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification.
A a user-centred tool to convert results from crosslinking mass spectrometry experiments | Convert data formats from chemical cross-linking mass spectrometry (XL-MS) | The CroCo cross-link converter — CroCo documentation | CroCo converts multiple data format from cross-linking mass spectrometry software tools to xTable format (in csv format) | The CroCo cross-link converter ¶ | CroCo converts multiple data format from cross-linking mass spectrometry software tools to xTable format (in csv format). It is distributed as graphical programme to be run from an executable and as a Python module to be integrated into workflows
CroCoDeEL is a tool that detects cross-sample (aka well-to-well) contamination in shotgun metagenomic data. It accurately identifies contaminated samples but also pinpoints contamination sources and estimates contamination rates. CroCoDeEL relies only on species abundance tables and does not need negative controls.
Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models.
Cronos, an analytical pipeline written in R. Cronos' inputs are a microbial composition table (e.g., OTU table), their phylogenetic relations as a tree, and the associated metadata.
A clustering tool which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).
CROP (Correlation-based Removal Of multiPlicities) is a visual post-processing tool that removes redundant features from untargeted metabolomic data sets. It is based on a grouping of highly correlated features within a defined retention time window avoiding the condition of specific m/z difference making it a second-tier strategy for multiplicities reduction. Graphical representation of correlation network for better understanding of the clusters composition and parameter tuning is provided.
CRISPR Off-Target-Predictor (CROP) is a CRISPR/Cas9 guide selection program based on mapping guide variants.
Coordinated Panel Visualization for Biological Networks Analysis | CroP – Coordinated Panels Visualization | The Computational Design and Visualization Lab focuses on multidisciplinary research bringing together Computer Science, Graphic Design and New Media Art | CroP is a visualization tool aimed at highlighting patterns of data in networks integrated with temporal data and analyzing their behaviors over time through dynamic visualization models in a coordinated multiple views layout
Integrated platform of crop gene-phenotype associations.
cropCSM is a web tool for identifying safe and potent herbicides.
Comprehensive visual platform for crop gene family mining and analysis. The platform encompasses six important crops (rice, wheat, maize, barley, sorghum and foxtail millet) and one model plant (Arabidopsis), as well as genomics, transcriptomics and proteomics data for gene family mining and analysis, covering a total of 314 611 genes and 4399 types of domains. CropGF provides a search system that allows for the identification of gene families and their members in a single crop or multiple crops.
A data portal to access the compendium of data on crop protein subcellular locations.
ARC Centre of Excellence in Plant Energy Biology
A dynamic, open and global database on crop pollination
Prediction of human and virus protein-protein interactions using cross-attention-based neural networks.
This tool produces plots enabling the discovery of cross-contamination of samples across the full selection of barcodes used in a sequencing plate. It also filters false barcodes from each batch and retains only the 'real' barcodes.
Analysis and Visualization of Complex XL-MS Driven Protein Interaction Networks
CS-MIL is a cross-scale multi-instance learning algorithm for pathological image diagnosis that integrates information across multiple scales. The implementation is publicly available via GitHub, utilizing Docker containers for execution and providing documented installation pathways.
Developed for analysis of genetic fingerprints such as RFLP, RAPD and AFLP.
CROssBAR is a comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations. The purpose of the CROssBAR project is to address the limitations related to data diversity and connectivity in biological data resources, which hamper their real-world applications to biomedical problems. Within CROssBAR, we developed a comprehensive computational resource by linking various biomedical resources, generating relation predictions using machine/deep learning, and developing information rich knowledge graphs that incorporate available and predicted biomedical relationships with the aim of providing aid to biomedical researchers to further understand disease mechanisms and to discover/develop new drugs.
Crossbow is a cloud-computing software tool that combines the aligner BOWTIE, the SNP caller SoapSNP and an accurate genotyper.
Open-source web tool for high-throughput screen data analysis.
Interactive R package to predict cross-reactivity risk using immunopeptidomics databases.
A tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.
CrossICC is a R package for iterative consensus clustering of cross-platform gene expression data without adjusting batch effect. CrossICC utilizes an iterative strategy to derive the optimal gene set and cluster number from consensus similarity matrix generated by consensus clustering and it is able to deal with multiple cross platform datasets so that requires no between-dataset normalizations. This package also provides abundant functions for visualization and identifying subtypes of cancer. Specially, many cancer-related analysis methods are embedded to facilitate the clinical translation of the identified cancer subtypes.
Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.
A medical image segmentation framework with a double-branch encoder and a typical decoder
An R Package for Network Visualization of Grouped Nodes.
The crosslinkWGCNA web tool provides a user-friendly interface to the popular Weighted Gene Co-expression Network Analysis (WGCNA) R package. Users are able to upload their data sets and subsequently apply the standard workflow steps using a project-based structure and an easy to navigate interface. Along the way, the tool provides multiple familiar visualizations such as the hierarchically clustered genes with color-coded clusters, a similar tree for the samples and sample traits, module-trait correlations, and more. In addition, the tool allows for integrating multiple WGCNA projects using a correlation-based approach. Both data and visualizations can be exported
An efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.
Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. This input is used for subsequent surrogate variable analysis (models unaccounted sources of variation) and differential expression analysis.
Joint distribution for number of crossings and longest run in independent Bernoulli observations. The R package crossrun. The R package crossrun computes the joint distribution of the number of crossings and the longest run in a sequence of independent Bernoulli observations. The main intended application is statistical process control where the joint distribution may be used for systematic investigation, and possibly refinement, of existing rules for distinguishing between signal and noise. While the crossrun vignette is written to assist in practical use, this article gives a hands-on explanation of why the procedures works. The article also includes a discussion of limitations of the present version of crossrun together with an outline of ongoing work to meet these limitations.
Repository and statistical tools for directly determined PTM crosstalk based on long peptides measured by mass spectrometry. Focus on histone proteins.
CrossTalkeR is a R framework for network analysis and visualisation of Ligand-Receptor networks. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis.
Software-assisted identification of cross-linked peptides.
Repository of spatial transcriptomics. CROST encompasses high-quality samples and houses 182 spatial transcriptomic datasets from diverse species, organs, and diseases, comprising 1033 sub-datasets and 48 043 tumor-related spatially variable genes (SVGs). Additionally, it encompasses a standardized spatial transcriptome data processing pipeline, integrates single-cell RNA sequencing deconvolution spatial transcriptomics data, and evaluates correlation, colocalization, intercellular communication, and biological function annotation analyses.
Automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes.
Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.
Predicting circRNA-disease associations using graph convolutional network based on heterogeneous network.
Knowledge base of cancer risk prediction models for systematic comparison and personalized applications.
CRRNN2 is a multi-task deep learning method for concurrent prediction of protein structural properties.
Microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).
An R Package for Cancer Rule-Set Optimization (CRSO) in order to inferring the combinations of alterations that cooperate to drive tumor formation in individual patients.
An R package to calculate attained power and construct the power distribution for cross-sectional stepped-wedge and parallel cluster randomized trials.
A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis. It runs with data from human (hg19), mouse (mm9) or drosophila (dm3).
A versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data.
CrustyBase is an interactive online database for crustacean transcriptomes. CrustyBase provides an environment for navigating and visualising crustacean transcriptome datasets. Users can search existing transcriptomes or import new datasets of their own.
Visualization platform for comparative genomics analyses in Brassicaceae species.
Cross-platform suite of analysis tools for interpreting protein mass spectrometry data.
Whole Exome Sequencing Data Analyze System. Tool for annotating, interpreting and reporting genetic variants.
The COVID-19 Real World Data Infrastructure (CRWDi) is a U.S. government resource linking and harmonizing real-world data to study the impact of COVID-19, particularly in immunocompromised patient populations. The dataset contains data on 5.2 million people and is freely available to approved researchers.
COVID-19 Real World Data Infrastructure (CRWDi)
A web server for identifying circRNA-RBP variable-length binding sites based on stacked generalization ensemble deep learning network.
Creates a density map from atomic coordinates, automatically including the density of solvent.
cryoID is a python-based program that determines the unique identity of the protein(s) in unknown near-atomic resolution cryoEM density maps from a pool of candidate protein sequences.
CryoDataBot is an automated pipeline designed to streamline dataset generation for cryogenic electron microscopy (cryoEM)-based atomic model building. It supports large-scale AI training and benchmarking by providing standardized tools for data retrieval, preprocessing, labeling, and quality control. CryoDataBot enables flexible configurations for diverse biomolecular structures, improves modeling reproducibility, and facilitates retraining of AI models such as U-Net and CryoREAD. It is open-source and optimized for structural biology applications in RNA and protein modeling.
CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction.
Ontology to describe data and workflows in Cryo Electron Microscopy
Ais is a segmentation suite for cryo-electron tomography data designed to be fast, intuitive, and accessible. It offers comprehensive annotation, segmentation, and rendering functionality and is available on GitHub.
Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning.
A program for rapidly solving high-resolution 3D structures of proteins and drug targets from cryo-electron microscopy data.
Transformer model for picking protein particles from cryo-EM micrographs.
CryoVR is a virtual reality training tool designed at Purdue University to familiarize users with cryoEM equipment, such as microscopes and sample preparation equipment, through a safe and accessible, virtual environment.
CryProcessor is a python-written tool for searching and extracting Cry toxins from illumina sequence data or from the protein fasta files. It includes several parts: an hmm-based scanning for potential Cry toxins, obtaining information about the domains, extracting Cry toxins with 3 domains only and comparing found toxins with Bt nomenclature.
Integrated database of proteome and immunopeptidome-derived non-canonical cancer proteins.
Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.
Cryptosporidium genome resources CryptoDB
CryptoGenotyper is a bioinformatics tool for rapid Cryptosporidium identification. The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram files that correspond to two of its characteristic gene markers: SSU rRNA and gp60.
Integrated crystallization analysis that builds on support-vector regression (SVR) models to facilitate computational protein crystallization prediction, analysis, and design.
Predict the X-ray solution scattering curve of a known structure, given the atomic coordinates in a PDB file, and fit to an experimental scattering curve.
CrystalExplorer is a native cross-platform program with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density.
The site-symmetry induced representations of layer groups on the Bilbao Crystallographic Server.
crystIT is a Python tool for calculating various complexity measures of crystal structures based on a standardized CIF-file.
CS-CO is a hybrid self-supervised visual representation learning method tailored for H&E-stained histopathological images.
Its modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny. It will allow simulations to take such information into account and some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites.
Protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as input.
Chemical Shift to 3D Structure is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.
Aan improved bioinformatics tool for identifying DNA 6 mA modifications via Chou's 5-step rule | An improved machine-learning based prediction tool for identifying DNA 6mA modifications | csDMA was implemented in python 2.7
Identification and dynamic quantification of regulatory elements using total RNA. Software for motif discovery and next-gen sequencing analysis. Sequencing the 5' end of cap-protected RNAs enables the identification of Transcription Start Sites (TSS) at nucleotide resolution.
Comparative Structural Alignment (CSA) is a webserver for computing and comparing protein structure alignments. Different scoring schemes are used to compute score-optimal alignments. Input is two PDB files.
a web service for the complete process of ChIP-Seq analysis. BACKGROUND:Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA. At present, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces. Although some web services with graphical interfaces have been developed for ChIP-seq analysis, these sites cannot provide a comprehensive analysis of ChIP-seq from raw data to downstream analysis. RESULTS:In this study, we develop a web service for the whole process of ChIP-Seq Analysis (CSA), which covers mapping, quality control, peak calling, and downstream analysis. In addition, CSA provides a customization function for users to define their own workflows.
Matlab codes for diffusion MRI CSA-ODF computation and Hough tractography.
CSA-QBI and Hough Tractography for Diffusion MRI
Statistical tools for ChIP-seq data analysis. Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.
A contig scaffolding tool using algebraic rearrangements.
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
CSBFinder-S is a tool for the discovery and ranking of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder-S incorporates efficient algorithms that identify CSBs in large genomic datasets. The discovered CSBs are ranked according to a probabilistic score and clustered to families according to their gene content similarity.
Web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes’ loci.
Predicts the oncogenic status (disease-driver or neutral) of somatic point mutations in the coding and non-coding regions of the cancer genome. Enter a mutation or list of mutations (one per line) into the form below using the format chromosome,position,reference,mutant (see Help for more details). Mutations uploaded from a file should use the VCF format with a minimum of five columns (chromosome, position, id, reference, mutant).
CScape-somatic is a web tool for distinguishing driver and passenger point mutations in the cancer genome.
Predicts individual component's chemical structure in a mixture, utilizing an iterative dynamic programming algorithm, and a database organized from a large collection of natural products.
Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.
CscoreTool-M infers 3D sub-compartment probabilities within cell population.
A chromatin state interface for Chinese Spring bread wheat.
Software for taking care of all algorithmic complexities and numerical workload of the CSD-ISM, including hardware synchronization and image reconstruction.
The Carbohydrate Structure Database is a free curated repository storing various data on glycans of bacterial, fungal and plant origins.
CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species.
CSDeconv maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach
Differential gene coexpression analysis based on the Conserved, Specific, and Differentiated (CSD) method
Cell type-Specific Enrichment Analysis DataBase (CSEA-DB) is a reference database for GWAS trait-associated cell type-specificity.
This tool filters sequencing artifacts (reads with all but 3 identical bases).
This tool clips adapters from the 3'end of the sequences in a FASTA/FASTQ file.
This tool collapses identical sequences in a FASTA file into a single sequence.
Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
Creates quality statistics report for the given Solexa/FASTQ library.
Rename the sequence identifiers in a FASTQ/A file.
Reverse-complement each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed.
Trim (cut bases from) sequences in a FASTA/Q file.
Split a FASTQ or FASTA file into several files, using barcodes as the split criteria.
Continuous-State Hidden Markov Models Transcription Factors(TF) (CSHMM-TF) is a method which integrates probabilistic modeling of single cell RNA-seq data with the ability to assign TFs to specific activation points in the model. TFs are assumed to influence the emission probabilities for cells assigned to later time points allowing us to identify not just the TFs controlling each path but also their order of activation.
Prediction of Secondary Structure from Backbone Chemical Shifts and Sequence. Uses Bidirectional Long Short Term Memory and NMR Chemical Shifts.
CSM (Cutoff Scanning Matrix) is a novel structure-based protein function prediction and structural classification method. CSM generates feature vectors that represent distance patterns between protein residues. These feature vectors are then used as evidence for classification.
Graph-based antibody-antigen binding affinity prediction and docking scoring function.
Web server for assessing and comparing protein–small molecule affinities.
A computational approach to rapid identification of therapeutic peptides.
CSM-Potential is a resource for the study areas of a protein surface that are likely to mediate protein-protein and protein-ligand interactions.
A novel in-silico protein toxicity classifier, which relies solely on the protein primary sequence.
CSM-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function.
Consensus method for prediction of catalytic residues.
The software for interactive evaluation of mass spectrometric imaging heterogeneity.
Supervised clustering of high-dimensional data using regularized mixture modeling.
Common Substring Network (CSN) is an algorithm that infers gene networks. The algorithm enables inferring novel regulatory relations among genes based only on the genomic sequence of a given organism and partial homolog/ortholog-based functional annotation. It can specifically infer the functional annotation of genes with unknown homology.
CSNAP is a computational approach for compound target identification based on network similarity graphs. Query and reference compounds are populated on the network connectivity map and a graph-based neighbor counting method is applied to rank the consensus targets among the neighborhood of each query ligand. The CSNAP approach can facilitate high-throughput target discovery and off-target prediction for any compound set identified from phenotype-based or cell-based chemical screens.
An effective ensemble learning framework for accurate identification of multi-species coding short open reading frames.
A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening. A fast and efficient multi-spectrum anlayzer for 2-D NMR Fragment Screening based on SMOTE-ENN machine-learning discriminator. - rubbs14/CSP-Analyzer.
fast program for haplotype-aware consequence calling which can take into account known phase.
A framework for summarizing chromatin state annotations within and identifying differential annotations across groups of samples.
Client Service Receipt Inventory as a standardised tool for measurement of socio-economic costs in the rare genetic disease population (CSRI-Ra).
Search a protein structure for likely catalytic sites.
Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.
Assignment of secondary structure to coarse-grained RNA tertiary structures.
Cell State Transition Expression Atlas. Organize, analyze and visualize the time-course gene expression data during cell differentiation, cellular reprogramming and trans-differentiation in human and mouse. In particular, it defines gene signatures for uncharacterized stages during cell state transitions.
CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.
A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
A computed Cell State trajectory inference method for time-series single-cell RNA sequencing data.
cSupB is a tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes. VARI-cSupB is an application of the succinct colored de Bruijn graph constructed by VARI-merge. It overcomes the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, VARI-cSupB provides a novel method that utilizes complete topological information and efficiently detects variants for highly similar samples, which can be validated by simulated datasets. Moreover, VARI-cSupB can adapt to a complex cycle structure.
A web resource for biomarker interactions in cancer outcomes.
Collaborative Spanish Variant Server (CSVS) is a crowdsourcing initiative to provide information about the genomic variability of the Spanish population to the scientific/medical community. It is useful for filtering polymorphisms and local variations in the process of prioritizing candidate disease genes. Submissions from WES or WGS are accepted.
CSynth is a physics based interactive visualisation platform for visualizing the 3D structure of the biological molecules. It is primarily designed to provide an engaging way to explore and understand the complex structure of the genome in 3D by integrating data from next generation sequencing (Hi-C) and modelling. For example, it allows the user to see a traditional Hi-C heat map overlaid with dynamically generated or precomputed 3D structures.
Script to generate the dicom files of CT-base pCT.
The tool performs by deep learning an automatic segmentation of the possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model architecture is Unet-based with residual operations, atrous dilation convolution and specific batch generator. It applies preprocessing steps as RAS conversion, resizing, z-score normalization, patching; and postprocessing operations. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
CT-ORG is a dataset for multiple organ segmentation in computed tomography. Morphological image segmentation scripts for CT scans. All scripts take an image, an optional vector of units, and possibly a mask of voxels to ignore. All scripts can be run with just the image, although the accuracy may be degraded.
CT Projection Simulator computes the parallel beam 2D projections of an object specified as a set of geometric shapes.
Set of functions performing ct reconstruction tasks
MATLAB mex function to filter ring artifacts from reconstructed CT images
This tool standardizes slice thickness in CT scans by resampling them to a common slice spacing. It is intended as a preprocessing step to harmonize CT data, improving consistency across scans acquired with varying slice thicknesses.
cTaG (classify TSG and OG) is a tool used to identify tumour suppressor genes (TSGs) and oncogenes (OGs) using somatic mutation data.
CTAT-LR-Fusion detects fusion transcripts from long-read RNA-seq data (PacBio Iso-seq or Oxford Nanopore) and can leverage Illumina RNA-seq data for additional exploration and quantification. It is a component of the Trinity Cancer Transcriptome Analysis Toolkit and is available via GitHub and Docker.
Tools for export and import classification trees and clusters to other programs.
A novel digital pathology approach to characterise circulating tumour cell biodiversity.
SHouT is a Python package used to analyze spatial cell graph data, as demonstrated in a recent publication on CTCL tissue organization compared to other skin conditions. The tool takes spatially resolved protein abundance maps and analyzes them to quantify heterogeneity.
ctcRbase is agene expression database of circulating tumor cells and microemboli Circulating tumor cells/microemboli (CTCs/CTM) are those cells that depart from cancerous lesions and shed into the bloodstream. Enumeration and analysis of CTCs/CTM may enable non-invasive monitoring of advanced cancers, as well as early detection of tumor metastases. ctcRbase (Gene expression database of circulating tumor cells/ microemboli) is a database to collect expression data of CTCs and CTM in all kinds of cancer types, including long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses. ctcRbase provides the expression level of primary tumors, CTCs/CTM and white blood cells (WBC). Moreover, the expression level of tumor metastasis was also provided. An easy-to-use interface was constructed to query and browse gene expression in CTCs/CTM.
Curated database about the interaction of environmental chemicals with gene products, and their effects on human health. New features include statistical analyses and analytical tools, including GeneComps and ChemComps, enriched Gene Ontology terms associated with chemicals, statistically ranked chemical-disease inferences, Venn diagram tools to discover overlapping and unique attributes of any set of chemicals, genes or disease, and enhanced gene pathway data content, among other features.
The Comparative Toxicogenomics Database (CTD)
An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models.
Tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health.
The ctDNAtools R package provides functionalities to analyze circulating tumor DNA (ctDNA)/ cell-free DNA (cfDNA) sequencing data. The tools cover analysis of ctDNA/cfDNA fragmentation and analysis of cancer minimal residual disease.
The R package CTDPathSim is a computational pipeline to compute similarity scores between patient samples and cell lines using a pathway activity-based approach. CTDPathSim integrates sample-specific expression and methylation profiles utilizing a deconvolution method. CTDPathSim has four main computational steps.
Comparative Toxicogenomics Database data extraction, visualization and enrichment of environmental and toxicological studies.
Dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.
Suite of tools to discover structural variations such as (larger) insertions and deletions in genomes from paired-end sequencing reads.
The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive UV cross-linking and immunoprecipitation (CLIP) data analysis.
Direct method for prediction of CTL epitopes crucial in subunit vaccine design.In direct methods the information or patterns of T cell epitopes instead of MHC binders were used for the development o f methods. The methods is based on elegant machine learning techniques like a Artificial Neural network and support vector machine .
A web application for scale-insensitive estimation of speed and distance traveled from animal tracking data.
Context-based Tandem Network for Semantic Segmentation.
The core Ontology of Clinical Trials (CTO) a structured resource integrating basic terms and concepts in the context of clinical trials.
A CrossTalk-based pathway enrichment analysis method for cancer research.
Combined transcriptome dataset of prostate cancer cell lines.
Cheminformatics Tool for Probabilistic Identification of Carbohydrates (CTPIC) is a tool that analyzes the covalent structure of a compound to yield a probabilistic measure for distinguishing saccharides and saccharide-derivatives from non-saccharides.
GUI based software for quality assurance of computed tomography (CT) scanners. Perform QA analyses on Catphan or water phantom images.
Cancer Treatment Response gene signature DataBase (CTR-DB). A database for basic and clinical researchers to access, integrate, and reuse clinical transcriptomes with cancer drug response.
A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs.
Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.
The Clinical Trials Sponsorship Network Dashboard (CTSND) uses force-directed network mapping algorithms to visualize clinical trials sponsorship data. ConflictMetrics is the public-facing portal for data on research funding and conflicts of interest in health and medicine. The site is devoted to providing public access to biomedical research sponsorship and funding data. The focus on data visualization is part of this project's broader aims of helping researchers, policymakers, providers, and patients rethink conflicts of interest. Research projects presented on ConflictMetrics have been supported by the National Endowment for the Humanities, the NSF’s Extreme Science and Engineering Discovery Environment (XSEDE), and the National Institutes of Health.
The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, pooling, normalization, and activation layers.
CuAS is an integrated database for Cucumber Alternative Splicing, includes genomic annotation, isoform-level functions, isoform-level features and tissue-specific AS events among multiple tissues.
CUBAP (Codon Usage Biases Across Populations) is an interactive web portal for analyzing codon usage biases across populations. Although synonymous codon usage does not change the protein primary structure, codon choice significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases.
Deep Learning for Ultrasound Image Formation. Ultrasound Beamforming with Deep Learning (CUBDL): Evaluation Framework and Open Datasets
A database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families, but based on all currently available vertebrate genomes.
Bayesian algorithm based on MCMC and show through well calibrated simulation study that it is possible to recover parameters of interest like tree height and length,
CUBIC-Cloud is a cloud-based framework for single-cell-resolution whole mouse brain analysis.
A workflow and software package for streamlining reproducible curation of large BIDS datasets.
CuBlock is a cross-platform gene expression microarrays normalization method. Microarrays from one platform can be normalized together. This method is useful when a study includes the analysis of microarrays originating from multiple platforms and standard normalization methods don't apply to reduce the inter-platform batch effect.
RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae.
A scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.
Motif discovery software based on MEME algorithm for a single GPU device using CUDA programming model. At present, it only supports the OOPS and ZOOPS models.
Python package providing CUDA GPU accelerated biochemical network simulation.
GPU-enhanced multiscale Monte Carlo chromatin 3d modelling.
CUDASW++ (compute unified device architecture) is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform fast sequence searches.
CpG impUtation Ensemble (CUE) is a method, which leverages multiple classical statistical and modern machine learning methods, to impute from the Illumina HumanMethylation450 (HM450) BeadChip to the Illumina HumanMethylationEPIC (HM850) BeadChip. DNA methylation at CpG dinucleotides is one of the most extensively studied epigenetic marks. With technological advancements, geneticists can profile DNA methylation with multiple reliable approaches. However, different profiling platforms can differ substantially in the CpGs they assess, consequently hindering integrated analysis across platforms.
Compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments.
Find significant changes in transcript expression, splicing, and promoter use.
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
Transcriptome assembly and differential expression analysis for RNA-Seq.
Cufflinks Support Package for the Bioinformatics Toolbox
A R pacakge cui2vec, which provides code for fitting embeddings to your own co-occurrence data.
CulebrONT is a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes.
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Non-parametric cumulative Mann-Kendall trend test
A functional scientific workflow language for large scale scientific data analysis. It enables integration of external tools written in any language and automatic parallelization of execution.
CuPCA is a web server for pan-cancer association analysis of large-scale cuproptosis-related genes, providing various prognostic analyses between cuproptosis and cancers at different levels.
Conserved Unique Peptide Patterns (CUPP) is a approach for sequence analysis employing conserved peptide patterns for determination of similarities between proteins. CUPP performs unsupervised clustering of proteins for formation of protein groups and can be used for fast annotation of enzyme protein family, subfamily and EC function of carbohydrate-active enzymes.
Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.
Curare and GenExVis provide a toolkit for analyzing and visualizing RNA-Seq data, streamlining workflows and facilitating differential gene expression experiments with a focus on reproducibility and user-friendliness. Curare builds RNA-Seq analysis workflows and GenExVis visualizes results.
Bioconductor package providing uniformly processed and manually annotated human microbiome profiles for thousands of people. Microbial taxonomy (from MetaPhlAn2) and metabolic functional potential (from HUMAnN2) can be analyzed with respect to numerous participant characteristics and health outcomes, simply and reproducibly on a normal laptop.
curatedAdipoArray is a curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing.
A GPU-accelerated reference-free compressor for high-throughput sequencing reads of FASTQ files.
An efficient curriculum learning-based strategy for molecular graph learning.
Scripts to curate metadata and sample genomes from GISAID for analysis and display in nextstrain and microreact.
Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints.
CurveAlign is a quantitative tool for interpreting collagen-tumor interaction in breast cancer tissue. It assesses up to ~thirty stromal fiber features and can incorporate data from CT-FIRE, another open-source tool.
Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.
Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding.
Create a codon usage table from nucleotide sequence(s).
Customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes.
Custommune is an Automated Tool for Designing Personalized and Population-Targeted Peptide Vaccines
Generate customized protein sequence database from RNA-Seq data for proteomics search.
CusVarDB is a tool for building customized sample-specific variant protein database from next-generation sequencing datasets. CusVarDB is a tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets.
Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis
Cutevariant is a cross-plateform application dedicated to maniupulate and filter variation from annotated VCF file.
Extract codon usage tables from CUTG database.
A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle.
Biophysics and Bioinformatics Laboratory, University of Athens
CuticleTrace is a toolkit for capturing cell outlines from leaf cuticles, streamlining and automating segmentation and measurement for paleoecological and paleoclimatological studies. It uses Fiji and R-based functions and offers improved measurement accuracy compared to existing methods.
Advances in a Runtime-Interpreted Analysis Description Language for HEP Data.
A flexible pipeline for CUT&RUN processing and footprint analysis | We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https: bitbucket.org qzhudfci cutruntools
A brain atlas for the camouflaging dwarf cuttlefish, Sepia bandensis.
Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s). Cuttlefish is a tool for constructing the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel modeling scheme of the de Bruijn graph vertices as finite-state automata, and constrains the state-space for the automata to enable tracking of their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that the algorithm scales much better than existing approaches, especially as the number and scale of the input references grow.
Script package for quantifying bacterial load within cells using images from a CV1000 microscope
Prediction model for cardiovascular events or all-cause mortality in incident dialysis patients | Some variables including age, comorbidity of diabetes, and so on at dialysis initiation are associated with patient prognosis. Cardiovascular (CV) events are a major cause of death, and adequate models that predict prognosis in dialysis patients are warranted. Therefore, we created models using some variables at dialysis initiation. We used a database of 1,520 consecutive dialysis patients (median age, 70 years; 492 women [32.4%]) from a multicenter prospective cohort study. We established the primary endpoint as a composite of the incidence of first CV events or all-cause death. A multivariable Cox proportional hazard regression model was used to construct a model. We considered a complex and a simple model
Molecular generative model based on conditional variational autoencoder for de novo molecular design.
CVCDAP (Cancer Virtual Cohort Discovery Analysis Platform) a web-based platform to deliver an interactive and customizable toolbox off the shelf for cohort-level analysis of TCGA and CPTAC public datasets, as well as user uploaded datasets. CVCDAP allows flexible selection of patients sharing common molecular and/or clinical characteristics across multiple studies as a virtual cohort, and provides dozens of built-in customizable tools for seamless genomic, transcriptomic, proteomic and clinical analysis of a single virtual cohort, as well as, to compare two virtual cohorts with relevance.
Incidence and risk of CVD in people with liver disease
Explainable artificial intelligence determination of the relationship of troponin to D-Dimer, mortality, and CK-MB in COVID-19 patients.
CVD Atlas is a comprehensive, multi-omics database of cardiovascular disease, compiling curated gene-disease associations, datasets, and prior knowledge from existing resources. It provides an interactive knowledge graph and analysis tools to facilitate CVD research.
Shiny app for interactive variant prioritisation in precision cancer medicine. Its input file is the output of the Oncotator Variant Annotation tool that summarises variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive prioritisation in this tool is based on known germline and cancer variants, DNA repair genes and functional prediction scores.
A Computational Pipeline for the Diagnosis of CVID Patients. Computational_Pipeline_CVID.
Conditional Variational Image Deraining (CVID) network for better deraining performance, leveraging the exclusive generative ability of Conditional Variational Auto-Encoder (CVAE) on providing diverse predictions for the rainy image. To perform spatially adaptive deraining, we propose a spatial density estimation (SDE) module to estimate a rain density map for each image. Since rain density varies across different color channels, we also propose a channel-wise (CW) deraining scheme.
CView is an alignment visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. The relationship that sequence regions that are currently on screen have to other regions of diversity within the alignment can be observed, thus increasing intuitive insight.
A tool for finding heterogeneously methylated genomic regions using ONT reads.
CVR-BBI is an open-source VR platform designed for multi-user collaborative brain-to-brain interfaces. It allows for EEG data collection, interactive stimulus management, and real-time analysis, enabling research into collaborative intelligence and brain function.
An online processing tool for CO2-inhalation and resting-state cerebrovascular reactivity (CVR) MRI data.
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
CVXB is a tool for image segmentation with artifacts and bias. Region-based image segmentation model with artifacts (outliers) detection and bias correction.
Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. Here we proposed two novel algorithms, the Direct Subsequence Dynamic Time Warping for nanopore raw signal search (DSDTWnano) and the continuous wavelet Subsequence DTW for nanopore raw signal search (cwSDTWnano), to enable the direct subsequence inquiry and exact mapping in the nanopore raw signal datasets.
CWAS-Plus is a software resource that estimates category-wide association of rare noncoding variation from whole-genome sequencing data by integrating user-provided functional data. It facilitates the identification of noncoding variant associations in genomic disorders and enables scalability for processing large-scale whole-genome sequencing data.
Unified framework for analyzing prion protein gene variability and spatial structure.
Automatically built VM used for a remote CWL training
CWLy-pred is a cell wall lytic enzymes identifier based on improved MRMD feature selection method.
CWLy-SVM is a Support Vector Machine-based tool for identifying the cell wall lytic enzymes.
Method used for identification of over-represented words in a set of ranked sequences. By default it is aimed at human miRNA analysis; you give a ranked list of differential expression values of genes across two conditions and it finds words in 3' UTRs of lengths 6 and 7 over-represented in the most regulated genes.
Program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.
Simple animations of Cytoscape networks.
CyAnno is a semi-automated approach for cell type annotation of mass cytometry datasets.
CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information.
CyanoCyc is a web portal providing a database and bioinformatics tools for cyanobacterial genomes and metabolic pathways. It offers a rich collection of annotated genomes, computational predictions, and data imported from external databases.
Manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.
CyanoMapDB is a database providing cyanobacterial protein-protein interactions (PPIs) with experimental evidence, consisting of 52,304 PPIs among 6,789 proteins from 23 cyanobacterial species.
An integrated omics database for functional genomic analysis of cyanobacteria.
CyanoPATH is a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms
Cyanorak is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from genomes covering most of the wide genetic diversity known so far within these groups, and which were split into clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites.
CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data
Cyber-T provides differential analysis tools for high-throughput data such as data from microarrays, next generation sequencing platforms and mass spectrometry. Various statistical analyses are computed using R-code.
For bugs and general help (Subject=CyberT)
For commercial licenses (Subject=CyberT)
CyberSco.py is a software written in Python for performing Conditional Microscopy. It was conceived to be available to none expert users with a simple intuitive GUI interface and easy syntax for predefined experiments.
CyBy2 is a library for writing chemical and biological data management systems. It is a strongly typed, purely functional framework for chemical data management. This library provides a set of utility functions and data types for writing purely functional client/server applications for handling and querying chemical and biological data. It is split into several modules and comes with an example implementation of a HTTP-server and web client for a fully functional chemical data management system.
A Python module for decomposing flow networks using simple cycles.
Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.
Online resource of cell-cycle-related experiments. It provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens.
CYCLeR is a software package for assembly of circRNA transcripts from RNA-seq data. Takes a set of BSJ prediction files and RNA-seq BAM files as an input and outputs circRNA trascnripts as FASTA, GTF and flat annotation files. The tools also outputs a padded FASTA to serve as an index for transcript EM abundance estimation.
CyclicPepedia is a database containing information on 8744 known cyclic peptides, offering a wealth of data on sources, structures, and applications. It includes calculation tools for cyclic peptide analysis and is described in a publication in Briefings in Bioinformatics.
CycloBranch is an open and platform-free software that provide the de novo generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles.
CYCLOPEp Builder is a web platform for designing, simulating, and visualizing cyclic peptides and nanotubes. It facilitates the creation of molecular topologies and allows for molecular dynamics simulations across various resolutions, providing a user-friendly resource for researchers.
CycloPsWeb generates structures for and displays properties of cyclised and linear peptides. Information includes solid-phase peptide synthesis feasibility, Octanol-water partition coefficient, and drug-like properties Structural representations are available in 1D SMILES, 2D .png image, and 3D .sdf formats Functionality for generating libraries of cyclised peptides, including commercially available non-natural amino acids is available in the standalone CycloPs client.
Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types.
Comprehensive database of membrane permeability of cyclic peptides. Includes supporting functions such as online data visualization, data analysis, and downloading.
CycPeptPPB is a predictor of Plasma Protein Binding rate for cyclic peptide with high performance focusing on residue-level features and circularity.
A tool for differential abundance analysis using mass cytometry data.
a plugin for importing and handling time series and other forms of repeated measurements data in Cytoscape
An interactive pathway-based resource for cystic fibrosis.
Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
Comprehensive yeast genome database (CYGD)
A cytoscape.js R Shiny Widget for network visualization and analysis.
CyLinter is a software tool for quality control in single-cell analysis of high-plex tissue profiles, designed to identify and remove noisy data points in multiplex images corrupted by artifacts. It allows users to work with both pixel-level and single-cell data.
CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.
Tool that is integrated as a Cytoscape APP to predict clinical outcome and identify network bio-markers by integrating gene expression data and PPI data.
CyPathia is a cytoscape app, that provides a user friendly and straightforward interface. The CyPathia app is based on Hipathia Bioconductor package, allowing the Cytoscape community the possibility of using mechanistic models.
CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data.
CYPRESS is an R/Bioconductor package for cell-type-specific power analysis in differential expression studies. It helps optimize experimental design and evaluate the impact of multiple influencing factors to reliably model and analyze bulk RNA-seq data.
CyProduct is a software tool for accurately predicting the byproducts of human Cytochrome P450 metabolism.
Turbocharging Cytoscape Access for External Tools via a RESTful API. It is a technology that powers Cytoscape Automation, which enables you to create reproducible workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc). This enables Cytoscape to scale to large collections of datasets and larger more complex workflows than is practical via keyboard and mouse.
Establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller. It can be used as a plug-in, e.g. to run R commands or to be used as a library to allow your plug-in to connect to R.
Human cysteine database based on experimental quantitative chemoproteomics.
A comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications.
Minimal/maximal spanning tree subnetwork discovery. Extracts a spanning tree from a given graph.
CystAnalyser is a software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders. It combines automatic image processing with a friendly graphical user interface (GUI) that allows researchers to supervise and easily correct the image processing before quantification. CystAnalyser is able to provide users the cystic index, the number of cysts and the cystic size profile.
Cyto is a docker-based application to run Anduril analysis pipelines on high dimensional cytometry data. Cyto aims to make available new computational cytometry tools to scientists with and without a bioinformatics background. Writing analysis pipelines using the workflow platform Anduril enables language-agnostic integration of new methods, Docker allows multi-OS compatibility, and Python libraries (flask and dash) allow user interaction.
Cyto-Feature Engineering is A Pipeline for Flow Cytometry Analysis to Uncover Immune Populations and Association with Disease
A Cytoscape app for qualitative consistency analysis, prediction and repair in biological networks.
CytoBrowser is a browser-based collaborative annotation platform for whole slide images. It can be used for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images, including, but not limited to, z-stacks (focus stacks) of cytology or histology whole slide images.
CytoCensus is an easily deployed implementation of supervised machine learning that extends convenient 2D ‘point-and-click’ user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection.
This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.
A robust and interpretable end-to-end deep learning model for cytometry data. An End-to-end Deep Learning Model for CyTOF data. This GitHub repository contains a tutorial for creating deep learning models tailored to CyTOF data. We will apply the model to diagnose latent cytomegalovirus (CMV) infection. We will also use a decision tree-based method to identify cell subsets that are associated with the CMV infection.
An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression.
CytoGLMM is an R package for Conditional Differential Analysis for Flow and Mass Cytometry Experiments.
Cytoscape CytoHubba is a plugin for Cytoscape that identifies hub genes within a network. It uses topological algorithms to predict and explore important nodes and subnetworks.
A cytokine communication map to analyse immune responses in inflammatory and infectious diseases.
Core data structure and API to represent and interact with the gated cytometry data.
CytoMAP is a Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues. CytoMAP is a histo-cytometric multidimensional analysis pipeline, which incorporates data clustering, positional correlation, dimensionality reduction, and 2D 3D region reconstruction to identify localized cellular networks and reveal features of tissue organization
cytomapper is an R/Bioconductor package for visualisation of highly multiplexed imaging data.
Multi-omics knowledge database for cytomegaloviruses.
This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.
cytoNet is a cloud-based image analysis software designed to quantify the structure of cell communities from microscope images using principles of graph theory.
An R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data.
A server to predict and classify cytokines.
CytoPy is a autonomous cytometry analysis framework for Python.
CytoSaddleSum provides Cytoscape users with access to the functionality of SaddleSum, a functional enrichment tool based on sum-of-weight scores.
Open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
An online implementation of Cytoscape Desktop that captures its interface and key visualization functionality while providing integration with web tools and databases.
Fiji Macro and GUI for CytoSeg to automatically extract and analyze the actin cytoskeleton from microscopy images. Please cite the following paper if you use the tool:.
Self-supervised models for encoding protein localization patterns from microscopy images.
CytoSet is a deep-learning based method used for predicting clinical outcome from cytometry data.
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.
CytoSpill is a R package for reducing spillover noise in the mass cytometry (CyTOF) data. The goal of CytoSpill is to compensate the spillover effects in CyTOF data which caused by technical effects without relying on control experiment.
CytoTree is an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. CytoTree is an R package to implement cellular subpopulations identification, trajectory inference, pseudotime estimation and visualization for flow and mass cytometry data.
R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data.
Library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.
CZ CELLxGENE Discover is a data platform providing curated and interoperable single-cell data, offering tools and features for exploration and meta-analyses.
The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) is a database of barcoded Chytridiomyceta and Blastocladiomycota cultures.
A functional human brain atlas termed D-BFA (DFC-based Brain Functional Atlas)
D-cellerate is a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file.
D-EE is a distributed dimensionality reduction and visualization tool. Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup.
D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.
D-miRT is a two-stream convolutional neural network for microRNA transcription start site feature integration and identification.
A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.
Web server to extract structural features of related but unaligned RNA sequences.
d-PBWT is a dynamic positional Burrows-Wheeler transform that can be used for haplotype matching.
D-Peptide Builder is a web Service to Enumerate, Analyze, and Visualize the Chemical Space of Combinatorial Peptide Libraries. Peptide-based drug discovery is re-gaining attention in drug discovery. Similarly, combinatorial chemistry continues to be a useful technique for the rapid exploration of chemical space. A current challenge, however, is the enumeration of combinatorial peptide libraries using freely accessible tools. To facilitate the swift enumeration of combinatorial peptide libraries, we introduce herein D-Peptide Builder. In the current version, the user can build up to pentapeptides, linear or cyclic, using the natural pool of 20 amino acids. The user can use non- and or N-methylated amino acids. The server also enables the rapid visualization of the chemical space of the newly enumerated peptides in comparison with other libraries relevant to drug discovery and preloaded in the server
D-SCRIPT is a deep learning method for predicting a physical interaction between two proteins given just their sequences. It generalizes well to new species and is robust to limitations in training data size. Its design reflects the intuition that for two proteins to physically interact, a subset of amino acids from each protein should be in con-tact with the other. The intermediate stages of D-SCRIPT directly implement this intuition, with the penultimate stage in D-SCRIPT being a rough estimate of the inter-protein contact map of the protein dimer. This structurally-motivated design enhances the interpretability of the results and, since structure is more conserved evolutionarily than sequence, improves generalizability across species.
d-SEAMS is a collection of analysis tools for molecular simulations. It has been implemented as a High Performance Cluster enabled engine in C++, with extensions via the Lua scripting interface. The code sheds light on the structures from simulation trajectories, in terms of their topology and it has been tailored for the analysis of nucleating systems. The framework is meant to be interfaced to a large variety of external tools and software, including R and other libraries. It is also the first and at-present only scientific analysis tool to use reproducible builds via nix.
d-StructMAn is a new improved implementation of our earlier tool StructMAn, shipped in a convenient and easily installable container form and extended to annotation of short in-frame indels and alterations arising as a consequence of alternative splicing events. d-StructMAn produces a wide range of structural features by combining information from experimentally resolved structures of many related proteins, which is a unique feature of the StructMAn family tools. Additionally to information from experimentally resolved protein structures, d-StructMAn can also harness all protein structure models stored in the AlphaFold Protein Structure Database.
Dual Disentanglement Network (D2-Net) for brain tumor segmentation with missing modalities, which consists of a modality disentanglement stage (MD-Stage) and a tumor-region disentanglement stage (TDStage).
D2Deep is a web server utilizing protein language models and evolutionary information to predict cancer driver mutations and provide interpretable visualizations of mutational landscapes.
A deep learning platform for predicting drug targets and for virtual screening against COVID-19.
A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2.
Platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening.
D3DistalMutation is a database to explore the effect of distal mutations on enzyme activity. In general, D3DistalMutation describes the effect of distal mutation (mutations more than 10 Å away from the active site) on enzyme activity and classified enzymes into four classes, viz., no activity change, decrease activity, loss of activity and increase activity. The D3DistalMutation provides information including mutation residues, active sites, the closest distances, activity change description and references.
An integrated suite of all databases of DSMZ Digital Diversity, including BacDive, BRENDA, SILVA, etc.
D3PM is a Comprehensive Database for Protein Motions Ranging from Residue to Domain
D3Similarity is A Ligand-Based Approach for Predicting Drug Targets and for Virtual Screening of Active Compounds Against COVID-19. D3Similarity was developed with two purposes based on the two-dimensional and three-dimensional similarity of molecular structure, one is for predicting target proteins for active compounds observed from experimental studies, and another is for virtual screening via 2D and 3D similarity evaluation. To this end, we developed a database composed of the bioactive molecules with known targets or/and well-explored mechanism related to the whole process of coronavirus infection, replication and release. “TargetPrediction” is for predicting target proteins, while “VirtualScreening” is for virtual screening against target proteins based on the 2D or 3D similarity evaluation.
D3Targets-2019-nCoV is a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.
D4 is a approch of Deep Drug-drug interaction Discovery and Demystification. D4 is a method for predicting drug-drug interactions along with their mechnsims of interaction. It uses 11 different mechanisms at pharmacokinetic, pharmacodynamic, multi-pathway, and pharmacogenetic levels. D4 utlizes a neuro-symbolic deep learning strategies to encode for background knowledge about basic biological processes and phenomena about drugs.
The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants | You need to sign in or sign up before continuing | Wellcome Centre for Integrative Neuroscience, University of Oxford's version control server
A tool for quantification of mRNA and punctate structures in time-lapse images of single cells. ABSTRACT Many biological processes are regulated by single molecules and molecular assemblies within cells that are visible by microscopy as punctate features, often diffraction limited. Here we present detecting-NEMO (dNEMO), a computational tool optimized for accurate and rapid measurement of fluorescent puncta in fixed-cell and time-lapse images. The spot detection algorithm uses the à trous wavelet transform, a computationally inexpensive method that is robust to imaging noise. By combining automated with manual spot curation in the user interface, fluorescent puncta can be carefully selected and measured against their local background to extract high quality single-cell data. Integrated into the workflow are segmentation and spot-inspection tools that enable almost real-time interaction with images without time consuming pre-processing steps.
A Bayesian model to integrate changes in splicing and RNA binding protein activity. MOTIVATION:Alternative splicing (AS) is an important mechanism in the generation of transcript diversity across mammals. AS patterns are dynamically regulated during development and in response to environmental changes. Defects or perturbations in its regulation may lead to cancer or neurological disorders, among other pathological conditions. The regulatory mechanisms controlling AS in a given biological context are typically inferred using a two step-framework: differential AS analysis followed by enrichment methods. These strategies require setting rather arbitrary thresholds and are prone to error propagation along the analysis
Method for identifying differential reactive regions from RNA structurome profiling data.
pyradiomics is a Python library for extracting radiomics features from medical images. The library is used to analyze intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) for determining the perineural invasion status of rectal cancer.
An open-source digital system for quantifying immunohistochemical staining with 3,3'-diaminobenzidine (DAB).
An end-to-end model DACPGTN for predicting ATC code for a given drug.
De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation
DACT is an R package for testing mediation effects in genome-wide epigenetic studies. DACT leverages the epigenome-wide data to estimate the relative proportions of the three null cases under the composite null hypothesis. The empirical null framework has been employed for large-scale inference.
Domestic Animal Diversity Information System is a communication and information tool for implementing strategies for the management of animal genetic resources. It provides the user with searchable databases of breed-related information and images, management tools, and a library of references, links and contacts of Regional and National Coordinators for the Management of Animal Genetic Resources. It provides countries with a secure means to control the entry, updating and accessing of their national data.
This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.
Command line wrapper to run DADA2 and obtain feature table and representative sequences from a set of FASTQ files.
Distance-based analysis of data-manifolds in Python.
DaDIA is a LC-MS feature extraction and annotation workflow in R.
Prediction of drugs against aspartate semialdehyde dehydrogenase of dad pathways
DAEi is a neural network architecture extended from Denoising AutoEncoder used for predicting Drug-Target Interactions.
Data Augmentation optimized for GAN (DAG).
Directed Acyclic Graphs using deep-learning VAriable SElection (DAG-deepVASE) is the first computational method that learns both linear and nonlinear causal relations and estimates the effect size using a deep-neural network approach coupled with the knockoff framework.
DAGBagM is a tool for Learning Directed Acyclic Graphs via Bootstrap Aggregation for Mixture of Continuous and Binary Variables.
DAGitty is a browser-based environment for creating, editing, and analyzing causal diagrams (also known as directed acyclic graphs or causal Bayesian networks).
Visualize significant conserved amino acid sequence pattern in groups based on probability theory.
A database for anti-cancer compounds with targets and side effect profiles.
The Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.
DALIA promotes the learning and teaching of Data Literacy through the curated supply of open teaching and learning content, empowering everyone to collect, analyze, critically evaluate, and use data in a FAIR way.
The Dalton Project is a Python platform for molecular- and electronic-structure simulations of complex systems. The Dalton Project provides a uniform platform access to the underlying Dalton and LSDalton software. The platform is designed as to host additional future software libraries and program modules.
This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.
A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution.
DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.
Comprehensive software package for genomic and phylogenetic data analysis.
Single script that automatically handles sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation.
The Damietta Toolkit is a web-based platform for protein design that integrates various tools and methods, providing a unified resource for researchers. It leverages a physics-based design engine and offers a range of functionalities including core design, symmetric design, and mutagenic scanning.
Tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes.
Manually curated database of known and putative antimicrobial peptides.
DAMpro is an in silico method, which is developed to predict Disease Associated Mutations.
Damsel is an R package for the end-to-end analysis of DamID sequencing data, providing quantification, testing, and visualization capabilities.
Calculate nucleic acid melting temperature.
Digital Anatomy Constructor is a program that can be used to reconstruct anatomical pictures. In general, it fills color into drawn shapes that collectively form a picture that represents the data. The main data source of this program is microarray data, but in situ hybridization-, Northern Blot-, Southern Blot- or any other data can be used. As a result, a picture is produced where the shapes are filled with color that corresponds to the gene expression level.
Efficient measurement of sequence growth and similarity.
Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.
Scoring system to detect difficult-to-assess regions with an easy-to-use track for looking at structural variant and repeat regions. This track, can be displayed alongside the existing Genome Reference Consortium assembly tracks to warn clinicians and biologists when variants of interest may be incorrectly called, of dubious quality, or on an insertion or copy number expansion.
This Data Coordination Center web page allows DANIO-CODE consortium members to submit and view their data sets annotated with standard metadata nomenclatures.
Browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals.
Designed for genome-wide comparative analysis of nucleosome maps. It detect single-nucleotide-resolution change in positions(location), enrichment (occupancy), and fuzziness (phasing, positioning) of each nucleosome unit.
danRerLib is a Python package designed for zebrafish transcriptomics researchers. It provides tools for gene ID mapping, orthology mapping, and functional enrichment analysis, leveraging human-annotated functional annotations to overcome limitations in zebrafish-specific data.
Protein quantitation, statistical analysis and visualization.
Domain based ANnotation of Transposable Elements (DANTE) uses database of Viridiplantae (Metazoa in progress) protein domains derived from transposable elements (Neumann at al 2019) Domains searching is accomplished engaging LASTAL alignment tool. Domains are subsequently annotated and classified using phylogenetic approach.
Tool for identifying complete LTR retrotransposons based on analysis of protein domains identified with the DANTE tool
This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.
Taking advantage of a decade of Daphnia '-omics' data for gene annotation | Welcome to the Daphnia Stressor database
Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites.
Database for drug action phenotype prediction. Here, you can search for predicted relationships of 1748 approved drugs to 454 ADRs or 178 ATCs, while also can predict the action phenotypes of approximately 110,000,000 compounds online (including about 168,000 natural products). In addition, you can explore potential mechanisms of ADRs or ATCs from phenotype-corresponding domains, or explore phenotype-corresponding substructures for structural optimization of drugs to eliminate serious adverse reactions.
A library enabling teams to distributed parameter sets between computational resources for faster parameter testing.
DAR is a database mapping disease-associated enzyme into Reactome pathways.
A database of aligned ribosomal complexes. Houses available cryo-EM maps and atomic coordinates of ribosomal particles from the Electron Microscopy Data Bank and Protein Data Bank aligned within a common system.
Data analysis for dark-field X-ray microscopy.
DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.
Mapping Darkness in the Protein Universe
A global database for bats in karsts and caves.
DarkQ is a messaging queue for microbial genomes. It tries to solve two problems: First, how to know about interesting genomes having been sequenced elsewhere, without having to download these genomes first. And second, how to retrieve the original genomes easily once we observe something interesting. Genomic surveillance is not only limited by the speed at which genomes can be shared, but by how fast they can reach the right person or algorithm to analyse them. If you are monitoring a regional outbreak of a multiresistant Klebsiella pneumoniae and I send you some viral genomes, this will not be too useful.
Darling is a web application, which utilizes Name Entity Recognition to identify human-related biomedical terms in PubMed articles, mentioned in OMIM, DisGeNET and Human Phenotype Ontology (HPO) disease records, and generates an interactive biomedical entity association network.
Darn is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM,snoRNA C/D-box and tRNA search.
Deep Automated Registration Qc (DARQ), a fully automatic quality control method based on deep learning that can replace the human rater and accurately perform quality control assessment for stereotaxic registration of T1w brain scans.
Denoising Algorithm based on Relevance network Topology is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.
Library-Search Algorithm for Mixture Analysis Using DART-MS.
RNA-seq mapper with a divide and conquer strategy.
The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.
An accessible genetic analysis platform for conservation, ecology, and agriculture.
DARTS, Domain-Associated RetroTransposon Search, is a pipeline developed for searching, mining and annotation of LTR retrotransposons.
DARUMA is a fast and user-friendly machine learning tool for predicting intrinsically disordered regions in proteins, utilizing physicochemical properties of amino acids and requiring minimal computational resources.
DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library.
Dashing Growth Curves is an open-source web application for rapid and interactive analysis of microbial growth curves. It enables researchers to visualize and analyze growth curves, extract features like growth rates, and generate downloadable summary plots.
R package for programmatic retrieval of information from DAS servers.
Server that allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.
The DASS App is an open-source web application that facilitates the application of three regulatory testing strategies for skin sensitization assessment, based on internationally harmonized guidelines. It supports data upload and analysis, and predictions are downloadable.
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
Visualization and integration of protein sequence feature annotations via DAS.
Converts Mascot results files back to MGF.
Visualisation and data mining of the public database of biomedical literature PubMed
A guide of data processing in NIR application for modeling
Data processing for modeling with the NIR data
User Interface Tool to ingest data to the UPV Reference Node through the QP-Insights API
Data Ingestion Tool (UPV Reference Node)
A tool that checks the clinical metadata quality (validity, completeness), the integrity between images and clinical metadata provided as well as their accuracy, the de-identification protocol applied, and existence of annotation together with the consistency between the images and the annotation files and informs the user on corrective actions prior to data upload.
Data Integration Quality Check Tool (DIQCT)
Data Virtualization for Flexible Data Architectures Built by data integration professionals for data integration professionals allowing you to meet ever-changing business needs Pipes automatically gets data from 200+ available sources in your data warehouse. With just a few clicks and without any coding. Pipes Professional enables you to build custom data pipelines with the best-in-class SQL editor
Converts MGF from Bruker DataAnalysis to TPP-friendly format for use with XPRESS and ASAPRatio.
Database for Bacterial Group 2 Introns: a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. General info on group 2 intron properties, structures and classification. Lists info for individual introns (insertion sites, DNA sequences, intron-encoded protein sequences, RNA secondary structure models). Tools fo ridentification and analysis of intron sequences.
Sequence database manager, including random database generation.
DatAC (Data Against COVID-19), a data fusion project with an interactive web frontend that integrates COVID-19 and environmental data in Spain. DatAC is provided with powerful data analysis and statistical capabilities that allow users to explore and analyze individual trends and associations among the provided data.
datacleanr is a flexible and efficient tool for interactive data cleaning, and is inherently interoperable, as it seamlessly integrates into reproducible data analyses pipelines in R.
Unveiling biological data relationships through distinctive color mapping.
Vendor-neutral visualization program for mass spectrometry imaging data (including imzML).
A tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.
DataJoint™ is a free, open-source framework for programming scientific databases and computational data pipelines. This resource ("Resource") provides an efficient approach for neuroscience labs to create and manage scientific data workflows: the complex multi-step methods for data collection, preparation, processing, analysis, and modeling that researchers must perform in the course of an experimental study. The work is derived from the developments in leading neuroscience projects and uses the DataJoint framework for defining, deploying, and sharing their data workflows.
DATAMAN is a global database of nitrous oxide and ammonia emission factors for excreta deposited by livestock and land-applied manure. The overall aim of DATAMAN is to provide access to the most up-to-date knowledge on managing manure GHG emissions.
Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.
DataPLAN is a FAIR and fast Data Management Plan (DMP) generator that focuses on plant science. The tool has a live-preview and is equipped with pre-written answers. DMPs can be generated in minutes by using DataPLAN.
DataRemix is a R package for universal data transformation for optimal inference from gene expression datasets.
Repository and search engine for bioinformatics datasets, tools and canned analyses.
Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD. DataSHIELD is an open source software and infrastructure that enables the privacy protected analysis of health and biomedical data. This space is for contributor and user support for DataSHIELD. A place for DataSHIELD contributors and users to have discussions. ||| CORRECT NAME OF TOOL COULD ALSO BE 'OBiBa'
Generates indices to split data to approximately equal parts.
Describe and share tabular data. It includes three components: (1) the Excel add-in; (2) the public web client; and (3) the private web service that mediates between the add-in and client and the ONEShare repository
smplot2 is an R package and associated guide designed to simplify data visualization, particularly for complex figures. The guide provides tutorials and examples for various plot types, including those commonly used in spatial vision research, and the package provides the routines.
Leveraging databases and analytical tools to reveal the dated Tree of Life. R package containing datelife's core functionality. Dashboard ⋅ phylotastic/datelife. Get a phylogenetic tree with branch lengths proportional to geologic time (aka a chronogram) of any two or more lineages of interest to you: use this R package or go to www.datelife.org to make a query of chronograms available for your lineages in the Open Tree of Life’s tree store. Welcome to the DateLife project. An R package, datelife for doing the calculations. Code coverage done right
DaTeR (short for "Dating Trees using Relative constraints") is a program for improved dating of microbial species phylogenies using relative time constraints (e.g., obtained from high-confidence horizontal gene transfer events).
The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.
A machine learning time series GUI toolbox for gap-filling and vegetation phenology trends detection.
DATMA (Distributed AuTomatic Metagenomic Assembly and annotation framework) is a distributed automatic pipeline for fast metagenomic analysis that includes: sequencing quality control, 16S-identification, reads binning, de novo assembly, ORF detection and taxonomic annotation.
‘datmat’ is a Python package aimed to easily gather data from a variety of sources and materialize it into a standardized format. It can download projects of imaging data from XNAT into the EUCAIM folder structure, and is designed to be extendible to support other inputs and outputs.
A Database of Biological Experimental Results.
A tool for clustering and visualising protein domain architectures.
The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
Bioinformatics resources which consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists.
An R package for retrieving data from DAVID, the Database for Annotation, Visualization and Integrated Discovery
Distributed automation for XNAT toolkit (DAX) provides large-scale image storage and analysis pipelines with an optimized job management tool for neuroimaging data
A database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DNA regulatory regions. Genome-wide association studies (GWAS) have shown many variants are found within putative enhancer elements. To provide insights into the regulatory role of enhancer-associated noncoding variants in cancer epigenome, and to facilitate the identification of functional noncoding mutations, we present dbInDel, a database where we have comprehensively analyzed enhancer-associated insertion and deletion variants for both human and murine samples using ChIP-Seq data. Moreover, we provide the identification and visualization of upstream TF binding motifs in InDel-containing enhancers. Downstream target genes are also predicted and analyzed in the context of cancer biology.
Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. An open-access database of DNA mismatch repair (MMR) gene variants in Chinese population. DNA mismatch repair (MMR) genes play an important role in maintaining genomic stability
Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is the manually-curated database. It has been developed to provide the information and analytical resources to the scientific community in order to develop antimicrobial compounds with the high therapeutic index.
DBAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method on genomic and proteomic data.
Database of anti-prokaryotic immune system genes. dbAPIS serves as a comprehensive data repository for experimentally validated viral anti-prokaryotic immune system (APIS) proteins and their associated protein families.
Database of missense single-nucleotide polymorphisms in human aquaporins.
Comprehensive repositories of new exon boundaries induced by pathogenic mutations in human disease genes. Aberrant 5’- and 3’-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions or elsewhere. Data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the algorithm-estimated splice-site strength.
A comprehensive bipolar disorder database for genetic research.
The database of bacterial quality scores.
dbCAN provides automated carbohydrate-active enzyme signature domain-based annotation for a set of proteins. Each carbohydrate-active enzyme has an assigned signature domain.
dbCAN-PUL is a data repository of prokaryotic CAZyme-containing gene clusters that have been experimentally validated to act on a carbohydrate substrate.
A online database dbCAN-seq to provide pre-computed carbohydrate-active enzyme (CAZymes) sequence and annotation data for 5,349 bacterial genomes.
Automated Carbohydrate-active enzyme ANnotation. Three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database.
Detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.
dbCNS is a database for conserved noncoding sequences.
DBCOVP is a database of coronavirus virulent glycoproteins. A Knowledge Based Resource for Exploring the Functional and Immunological Properties of Coronavirus Virulent Glycoproteins for Application in Vaccine Target Discovery.
Web server tool that provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.
Curated knowledgebase for regulation of radiation response in human cancer.
A database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org) is a database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and--when possible--detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event.
Predicted transcription factors in completely sequenced genomes.
Transcription factor prediction database (DBD)
Uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA. Queries can be specified by a PDB ID or the coordinates of a DNA-binding protein in PDB format.
A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications.
a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry.
The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates.
A dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.
A manually curated database of human and mouse essential lncRNA genes.
Division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
Database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim is to provide a comprehensive database for human pathogenic bacterial exotoxins.
DBFE is a Python library with feature extraction methods that facilitate classifier learning from distributions of genomic variants.
Access to entries from various up-to-date biological databases using entry identifiers or accession numbers.
The Database of Genotypes and Phenotypes (dbGAP) is a National Institutes of Health-sponsored repository charged to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in humans. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents.
An R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP) | Using dbgap2x, R package to explore, download and decrypt phenotypic and genomic data from dbGaP | On dbGaP, the phenotypic files are encrypted. We created a decryption function that uses a dockerized version on sratoolkit. To use that function, you need to have docker installed on your device (www.docker.com). If you are using the dockerized version of this software (available at hub.docker.com/r/gversmee/dbgap2x), docker is already pre-installed, but you'll need to upload your key on the jupyter working directory
Contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP).
dbGENVOC, a comprehensive, flexible database framework, developed with an aim to allow potential users to access, query, browse and download clinically relevant somatic and germline variation data from Indian oral cancer patients. This database will store variant calls from various studies that uses massively parallel sequencing to generate genome-scale data.
DBindR is a web server for prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Database for lipids and proteins in human lipid metabolism.
Database of autosomal monoallelic expression for investigating whether the gene/gene class of interest is inferred or measured to be monoallelic in mouse or human tissues.
A Database for Exploring the Mutation Markers of Anti-Cancer Drug Sensitivity
dBMHCC is a comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.
A manually curated database of conditional protein mis-localization events.
dbMTS is a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions. dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study.
An open source application suite to store biological studies. The central module (GSCF) stores the study design, which links out to modules that contain the measurements of specific measurement platforms.
Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study.
Pipeline for building a database of allele frequencies. The objective of this pipeline is to create and update a database of Allele Frequencies (AF) using vcf files. A metadata file in TSV must be provided with the sample id, family id and category (e.g. disease or phenotype) to calculate the AF. The AF is calculated for the whole cohort, subcohorts defined by each category and for a subset of samples acting as pseudocontrols defined by the whole cohort but the selected category (e.g. non-related diseases).
dbPepNeo is a manually curated database for human tumor neoantigen peptides.
Supervised learning model for computational recognition of DNA-binding proteins in model organisms.
DBPOM is a comprehensive database of pharmaco-omics for cancer precision medicine.
DataBase of Plant Research (DBHR) is an online data resource specifically designed for human research, which provides access to almost all latest human database on easy and friendly finding way, the classification based on data type is informative and straightforward, we assign one major category to each database, although one database may correspond to multiple categories. In what follows, we focus on databases categorized as DNA, RNA, protein, expression, pathway and disease. Dr. Shahid. DB-PR ( DataBase of Plants, Research ). Databases of plants have been an integral part of modern biology.
A web server for predicting DNA-binding residues in protein sequences
dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea).
An informative resource for protein post-translational modifications (PTMs).
An updated database for exploring regulatory networks and functional associations of protein post-translational modifications.
dbPUP is a database of polyphenol utilization proteins (PUPs) that have been experimentally characterized to metabolize polyphenol substrates.
DbRUSP is an interactive database for the analysis and interpretation of newborn screening (NBS) data and for studying the effects of covariates on blood metabolite levels.
DBSAV database reports GTS scores of human genes and DeepSAV scores of SAVs in the human proteome, including pathogenic SAVs, benign SAVs, gnomAD SAVs observed in exome sequencing, and all possible SAVs by single nucleotide variations. Each human protein has a designated web page that displays these SAVs along with various sequence, structural and functional properties. This database is a useful resource for mechanistic interpretation of human SAVs and their relationships with protein functions and human diseases.
DBSCAN-SWA is a tool for rapid prophage detection and annotation Bacteriophages are viruses that specifically infect bacteria and the infected bacteria are called bacterial hosts of the viruses. Passive replication of the bacteriophage genome relies on integrate into the host's chromosome and becoming a prophage. Prophages coexist and co-evolve with bacteria in the natural environment, having an impact on the entire ecological environment. Therefore, it is very essential to develop effective and accurate tools for identification of prophages. DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes, running faster than any previous tools and presenting great detection power based on the analysis using 184 manually curated prophages.
DBScope is an open-source toolbox for visualizing and analyzing sensing data from deep brain stimulation. It offers both a user interface and a programmable library for data import, processing, and biomarker search.
An Open-Source Software for Automated Accurate Analysis of Rodent Behavior in Forced Swim Test and Tail Suspension Test.
Deep Brain Stimulation Simulator (DBSim) is a free COMSOL Multiphysics-based stand-alone program developed by the Neuroengineering group for performing patient-specific FEM simulations of DBS based on the data generated by ELMA.
Database of single nucleotide polymorphism (dbSNP) contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
GUI for the retrieval of single nucleotide polymorphism data from dbSNP.
dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including humans. dbSNP-Q can be used to query human data from dbSNP for a variety tasks such as genomic mapping, SNP/gene functional properties, allele frequency data and information on the underlying experiments. It also includes documentation and download tools.
Stand-alone software tool for construction and analysis of mathematical models of biological systems.
DbStRiPs (Database of structural repeats in proteins) is a structural repeat database which classifies a protein structure into a structural repeat family based on graph based structural repeat identification algorithm, PRIGSA2.
A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.
A database of super-enhancers in mouse and human genome.
Display information about a public database.
Easy-to-use environment for customized fasta database manipulations.
Collection of programs to manipulate sequence databanks files.
Predicting MHC-peptide binding affinity by differential boundary tree.
A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.
DataBase of Transcription Start Sites is a database which contains precise positional information for transcription start sites of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequencing the 5-end of oligo-cap selected cDNAs in humans and mice. 31 different cell types or culture conditions are represented. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated.
NCBI's database of genomic structural variation – it contains insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex chromosomal rearrangements
Index the EDAM ontology using b+tree indices.
Index a fasta file database using b+tree indices.
Index a flat file database using b+tree indices.
Index a GCG formatted database using b+tree indices.
Index an obo ontology using b+tree indices.
Validate index and report internals for dbx databases.
Index a data resource catalogue using b+tree indices.
Index NCBI taxonomy using b+tree indices.
Exploration of MS detectable peptides via deep learning.
DCABM-TCM is a Database of Constituents Absorbed into Blood and Metabolites of Traditional Chinese Medicine.
Aligning biological sequences using co-evolution models and informed priors.
Differential composition analysis for flexible single-cell experimental designs.
Drug repositioning of single and drug combinations using Flux Balance Analysis
Identifying cancer pathway dysregulations using differential causal effects.
A deep neural network simulating basic eukaryotic cell structure and function.
Unveiling Differential Regulation from Differential Co-expression.
Deep learning approach for cancer subtype classification using high-dimensional gene expression data.
An R Package for Analysing Ontologies and Protein Domain Annotations.
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.
DCHap is a fast and accurate haplotype phasing tool for third-generation sequencing data. It works for both SMRT reads (PacBio) and Oxford Nanopore reads.
A tool for differential compartment analysis of Hi-C datasets
Implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al.
The Difference Causal Inference (DCI) algorithm directly learns the difference between two causal graphs given two datasets. DCI is implemented as a part of the causaldag package.
an IBD-based method to calculate genetic distance between polyclonal infections.
Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR
dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
Distance-based classification using mixture distributions on microbiome data.
DCMQI (DICOM for Quantitative Imaging) is a free, open source library that can help with the conversion between imaging research formats and the standard DICOM representation for image analysis results.
Disease Correlation Network (DCN) Analyser is a pipeline of disease correlation analysis with retrospective matched cohort study design using Cox Proportional Hazards (Cox-PH) regression in combination of interactive network display using graph theory.
Deconvolution network (DCNet), an "explainable" artificial neural network model was created to infer cell content from bulk RNA-Seq samples.
Predictor of Disulfide Connectivity in Proteins.
DConStruct is a tool for hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins.
DCP (Diffusion Connectome Pipeline) is a pipeline toolbox for diffusion connectome. The diffusion connectome pipeline is used for for building DTI networks.Firstly, it provides a friendly graphical user interface, and the users only need to use the mouse to set the parameters which are used in the whole process and click the button with label ‘RUN’. The DCP will process every participant’s data automatically, and generate DTI network of every participant. And the default parameters we provide are currently recognized as classic processing parameters. When the program is running, the user can accurately get which step the program is running through the monitor window. After the program is finished, a folder of quality control is generated, and the registration results of each subject are saved for quality checking.
Scripts for deep consistency-preserving hash auto-encoders for neuroimage cross-modal retrieval.
Digital Cell Sorter (DCS) is a single cell RNA-seq analysis toolkit for clustering, cell type identification, and anomaly detection.
A deeper and more compact split-attention U-Net for medical image segmentation.
A method utilizing deep cycle transfer learning (DCTL) in order to detect apicomplexan parasites, by utilizing deep learning-based microscopic image analysis. DCTL is based on observations of parasitologists that Toxoplasma is banana-shaped, Plasmodium is generally ring-shaped, and Babesia is typically pear-shaped. Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL).
DCTPep is an open data repository of cancer therapy peptides, comprising a peptide library and a drug library. It aims to facilitate the design and screening of future cancer therapy peptides.
A Graphical User Interface for Deep Learning-Accelerated Virtual Screening of Large Chemical Libraries (Deep Docking).
Tool for processing Bio-Rad ddSEQ single cell RNA-seq data.
DDAPRED is a computational method for predicting drug repositioning using regularized logistic matrix factorization
Nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the patent sequence, released a new submission tool of the Sequence Read Archive (DRA) and the Read Annotation Pipeline.
Software for detection of conserved secondary structures in multiple alignments.
Prediction of Protein Solubility Based on Sequence Feature Fusion and DDcCNN.
ddcMD is a fully GPU-accelerated molecular dynamics program for the Martini force field. ddcMDconverter should be used to convert GROMACS inputs to ddcMD inputs
Approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results if the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using this method.
DDecon is an ImageJ plug-in that provides a GUI for super-resolution measurement of thin filament lengths by applying distributed deconvolution analysis to periodic line scans collected from fluorescence images.
DDeep3M is a dockerized deep-learning model for image segmentation of MOST, based on CDeep3M. The model was verified for brain tumors segmentation in BraTS too.
Predicting the impact of mutations on protein stability from sequence using protein language models
Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.
DDGun is an untrained method for predicting the stability change upon mutation
DDI-CPI, is a web server that predicts Drug-Drug Interactions through implementing the Chemical-Protein Interactome.
DDIEM is a Drug Database for inborn errors of metabolism. DDIEM database is a database on therapeutic strategies for inborn errors of metabolism. These strategies are classified by mechanism and outcome in DDIEM Ontology. DDIEM uses this ontology to categprise the experimental treatments that have been proposed or applied. It includes descriptions of the phenotypes addressed by the treatment and drugs participating in treatment and procedures.
DDIMDL is a multimodal deep learning framework for predicting drug-drug interaction events. DDIMDL builds multimodal deep learning framework with multiple features of drugs to predict drug-drug-interaction (DDI) events.
An online drug-drug interaction database towards improving clinical decision-making and patient safety.
Drug-drug interaction prediction with fingerprint (DDIPF): A web-server for predicting the probability that two drugs can interact.
A network-based strategy identifies disease signals by linking high-throughput omics datasets to disease knowledge.
A deep learning model that efficiently and accurately predicts the changes in PPI binding free energy upon single and multiple point mutations.
This tool visualizes a disease-disease network augmented with genetic correlations derived from clinical biomarkers, allowing users to explore connections between diseases and associated biomarkers. The network is based on UK Biobank data and aims to improve understanding of genetic associations in cardiometabolic disorders.
DDN 3.0 is a tool for determining significant rewiring of biological network structures with differential dependency networks. It improves upon previous methods with new algorithms for unbiased model estimation, accelerated learning, and data-driven hyperparameter determination.
DDNA is a software for interaction energy between protein and DNA
Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and transcription regulation. It enables biologist to circumvent the large amount of energy and time spent in analyzing pertinent biological problems involving PC.
ddpcr is a R package for droplet digital polymerase chain reaction visualization and analysis.
Automated quantification of non-orthogonal, multiplexed ddPCR data.
DDRP is a platform for real-time phenology and climatic suitability modeling of invasive insects. A final production version of the DDRP platform that includes cohorts, parallel processing, and improving mapping routines. The objective of the Degree-Day, establishment Risk, and Pest event mapping system (DDRP) is to predict phenology and climate suitability of invasive, biocontrol, and IPM species for the conterminous United States. DDRP is ….
DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, pandas, SciPy, and SQLAlchemy to build and simulate complex computational models. Similar to Simula, DE-Sim models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time.
DE-STRESS (DEsigned STRucture Evaluation ServiceS) is a web application that provides a suite of tools for evaluating protein designs.
Fast read alignment with incorporation of known genomic variants. deBGA-VARA is a novel variation-aware high-throughput sequencing read aligner. VARA is a variation-aware read global alignment algorithm. We developed deBGA-VARA by integrating VARA into deBGA. It is suitable for aligning various kinds of high-throughput sequencing reads to multiple similar reference genomes.
de Bruijn Graph Constructor in Scalable Memory.
deML is a maximum likelihood demultiplexing algorithm that allows probabilistic sample assignments. We compute the likelihood of assignment to various samples and assign to the most likely sample. We then compute the assignment quality to avoid ambiguous assignments. This is similar to how mapping quality solves the problem of ambiguous assignments.
fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
Fast and accurate classification of metagenomics long reads with sparse approximate matches | DeSAMBA(de Bruijn graph-based Sparse Approximate Match Block Analyzer) is a tailored long read classification approach using a novel sparse approximate match-based pseudo alignment algorithm. Benchmarks on real datasets demonstrate that deSAMBA enables to simultaneously achieve fast speed and good classification yields, which outperforms state-of-the-art tools and has many potentials to cutting-edge metagenomics studies
DEAP, Differential Expression Analysis for Pathways, which capitalizes on information about biological pathways to identify important regulatory patterns from differential expression data. DEAP makes significant improvements over existing approaches by including information about pathway structure and discovering the most differentially expressed portion of the pathway. On simulated data, DEAP significantly outperformed traditional methods: with high differential expression, DEAP increased power by two orders of magnitude; with very low differential expression, DEAP doubled the power. DEAP performance was illustrated on two different gene and protein expression studies. DEAP discovered fourteen important pathways related to chronic obstructive pulmonary disease and interferon treatment that existing approaches omitted. On the interferon study, DEAP guided focus towards a four protein path within the 26 protein Notch signalling pathway.
Deep autoencoder enables deconvolution of data-independent acquisition proteomics.
A Python Package Index for predicting the number of daily COVID-19 deaths.
A manually curated database of protein-protein interactions for Death Domain Superfamily. The DD superfamily is one of the largest classes of protein interaction modules, and plays a pivotal role in apoptosis, inflammation, necrosis and immune cell signalling pathways.
debar is an R package designed for denoising sequence data for the animal DNA barcode marker: cytochrome c oxidase I (COI-5P, or the five prime portion of COI). The package is designed to detect and correct insertion and deletion errors within barcode sequences. This is accomplished through comparison of input sequences against a profile hidden Markov (PHMM) model using the Viterbi algorithm and adjustment of the sequence based on the reported Viterbi path (debar depends on functions from the R package aphid for the PHMM structure and for running the Viterbi algorithm).
DEBay is a computational tool for deconvolution of quantitative PCR data for estimation of cell type-specifc gene expression in a mixed population. DEBay estimates cell type-specific gene expression by deconvolution of quantitative PCR data of a mixed population. It will be useful in experiments where the segregation of different cell types in a sample is arduous, but the proportion of different cell types in the sample can be measured. DEBay uses the population distribution data and the qPCR data to calculate the relative expression of the target gene in different cell types in the sample.
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.
debCAM is an R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.
DEBIAS-M is a framework for correcting processing bias in microbiome data by learning bias-correction factors that minimize batch effects and maximize cross-study associations with phenotypes. It improves the generalizability and interpretability of microbiome-based prediction models.
DEBKS is a convenient and user-friendly program to streamline the discovery of differentially expressed circRNA (DEC) between two RNA-seq sample groups with replicates. DEBKS includes four modules: (1) "merge" collects circRNA junction information from output file of circRNA detection software. (2) "anno" annotates circRNA based on the circRNA position. (3) "count" calcuates linear junction based on the circRNA position. (4) "dec" identifies DEC with rMATS statistical model.
deboost is A Python Library for Weighted Distance Ensembling in Machine Learning.
Deciphering the exact breakpoints of structural variations using long sequencing reads.
Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, MA plots and heatmaps.
Species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.
Comprehensive, Automatic Post-processing Program for HDX-MS Data.
Deuterium Exchange Correction and Analysis (DECA)
DECA is a distributed re-implementation of the XHMM exome CNV caller using ADAM and Apache Spark.
DeCAF (DEconvoluted cell type Allele specific Function): Identify cell-type specific QTL effects in tumors by leveraging both allelic and total expression information
DeCban is a tool for the prediction of circRNA-RBP interaction sites by using double embeddings and cross-branch attention networks.
decenttree is a cross-platform C++ library, and stand-alone command-line application, for generating phylogenetic trees (in newick format) from distance matrices (supplied in phylip distance matrix formats), or alignments (supplied in fasta format), using well-known algorithms.
Parallel and distributed error correction algorithm for high-throughput short reads.
DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF), a statistic that quantifies the proportion of cells which acquired the SNV or whose ancestors acquired the SNV. DCF is related to the commonly used cancer cell fraction (CCF) but further accounts for SNVs which are lost due to deleterious somatic copy-number aberrations (CNAs), identifying clusters of SNVs which occur in the same phylogenetic branch of tumour evolution.
DECIMER (Deep lEarning for Chemical ImagE Recognition), a deep learning method based on existing show-and-tell deep neural networks which makes very few assumptions about the structure of the underlying problem.
A toolset for deciphering and managing biological sequences.
A decision-tree approach for the differential diagnosis of chronic lymphoid leukemias and peripheral B-cell lymphomas | BACKGROUND AND OBJECTIVE:Here we propose a decision-tree approach for the differential diagnosis of distinct WHO categories B-cell chronic lymphoproliferative disorders using flow cytometry data. Flow cytometry is the preferred method for the immunophenotypic characterization of leukemia and lymphoma, being able to process and register multiparametric data about tens of thousands of cells per second. METHODS:The proposed decision-tree is composed by logistic function nodes that branch throughout the tree into sets of (possible) distinct leukemia lymphoma diagnoses. To avoid overfitting, regularization via the Lasso algorithm was used
This code implements a classification tree and plots the ROC curves for each target class
Decision Trees and Predictive Models with cross-validation and ROC analysis plot
DECO is a framework for jointly analyzing de novo and rare case/control variants, and biological pathways.
Determining correlations among diseases using protein interaction networks.
Change the letters of your name to the closest DNA bases, search every one of 168,297 protein sequences from 8826 animals, plants and microorganisms and return to you, the protein that contains the closest match to the letters of your name.
Degenerate codon design for complete protein-coding DNA libraries. To run DeCoDe, you will need a local installation of Gurobi with an appropriate lisence (academic licenses are provided for free direct from Gurobi). You will also need to install gurobipy and make sure that you are able to import it from within your local environment.
A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays.
DECODE is a python package that allows the user to generate explanations for a TCR binding model.
Optimization of degenerate codon libraries for machine learning-assisted protein engineering.
Fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.
DECOMICS is an R-Shiny web application for unsupervised cell type deconvolution and biological interpretation of bulk omic data, offering various algorithms, enrichment analysis, and visualization tools. It can be launched locally or within a cloud environment.
R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.
It is designed to find the differential expressed genes (DEGs) for complex disease, which is characterized by the heterogeneous genomic expression profiles. Different from the established DEG analysis tools, it does not assume the patients of complex diseases to share the common DEGs. By applying a bi-clustering algorithm, DECD finds the DEGs shared by as many patients.
DecompPipeline provides a comprehensive list of preprocessing functions for performing reference-free deconvolution of complex DNA methylation data.
DeCompress is a semi-reference-free method to deconvolve targeted panels of mRNA expression into tissue compartment. A tissue compartment is a group of cells of similar type or biological function (i.e. immune or stroma or tumor compartments).
Decon2 is a statistical framework for estimating cell counts using molecular profiling such as expression or methylation data from heterogeneous samples (Decon-cell) and consecutive deconvolution of expression quantitative trait loci (Decon-eQTL) into each cell subpopulation.
DECONbench is a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification.
DeconBenchmark is an R package and GitHub repository providing a benchmark of cellular deconvolution methods. It aims to facilitate the selection of appropriate deconvolution methods for researchers by providing a comprehensive review and benchmark, addressing challenges related to the numerous methods and lack of performance assessment.
Tool for accurate precursor ion monoisotopic mass determination for tandem mass spectra.
DeconPeaker is a deconvolution method to estimate cell type proportions in chromatin accessibility data (ATAC-Seq), as well as gene expression data (RNA-Seq & Microarray).
R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.
DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based versions.
deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.
Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.
DECoNT (Deep Exome Copy Number Tuner) is a deep learning based software that corrects CNV predictions on exome sequencing data using read depth sequences.
Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples.
Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.
Advanced peak picking of MS and LC-MS(/MS) data using THRASH and other algorithms.
Increasing axial resolution of ultrasonic imaging with a joint sparse representation model
Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells. Estimate the fractions of immune cells from expression profiles of tissues. This method is created as described in the manuscript - "Deconvolution of bulk gene expression profiles from complex tissues to quantify subsets of immune cells". The tool is designed to estimate the fractions of immune cells from the expression profiles of tissues, such as tumor masses, PBMCs, etc.
deconvolution estimate immune cell subsets
DeconvTest is a Python-based simulation framework that allows the user to quantify and compare the performance of different deconvolution methods. The framework integrates all components needed for such quantitative comparison and consists of three main modules: (1) in silico microscopy, (2) deconvolution, and (3) performance quantification.
Deconwolf is an open-source software for high-performance deconvolution of widefield fluorescence microscopy images, enabling accurate quantification and improved chromosome tracing. It runs efficiently on laptop computers and requires minimal parameter setting, facilitating the use of deconvolution in various bioimaging applications.
DecoPath is a web application for decoding pathway enrichment analysis and visualizing and exploring the results of pathway enrichment analysis.
decorate is a R package for differential epigenetic correlation test.
Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.
Decosus, an R package that integrates seven methods and signatures for deconvoluting cell types from gene expression profiles (GEP)
Ensemble of computational methods to infer biological activities from omics data.
Redundancy reduction in a set of aligned or unaligned sequences
DEep learning for identifying Cis-Regulatory ElementS is an extension of the Deep Learning Tutorials developped by LISA lab (www.deeplearning.net/tutorial/). Although it is developped for the identification of CREs, it can also be used for other applications.
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products. decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER). Alexander M. Kloosterman, Peter Cimermancic, Somayah S. Elsayed, Chao Du, Michalis Hadjithomas, Mohamed S. Donia, Michael A. Fischbach, Gilles P. van Wezel, and Marnix H. Medema. decRiPPter is a genome mining tool for detection of novel biosynthetic gene clusters (BGCs) of ribosomally synthesized and post-translationally modified peptides (RiPPs). Number of operons with antismash overlap. Nr of operons with known RiPP domains.
Tandem mass spectrometry data analysis of human proteome for presence of point alterations. Subsequently, deduces DNA/mRNA alterations whenever possible.
A tool for systematic cell type annotations of single-cell RNA sequencing data among human tissues.
DecXpert is a computer-aided detection (CAD) software developed to assist in the radiological diagnosis of tuberculosis from chest X-rays, particularly useful in resource-constrained settings. A recent study validated its performance with promising results, demonstrating potential to improve early detection and management of TB.
Cytoscape 3.0 app for producing an morphing data-driven and structure-driven network layouts.
DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells.
This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F and B statistics. It also implements a new methodology called Differential Expression via Distance Summary, which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.
DEEMD: a computational pipeline using deep neural network models within a multiple instance learning framework, to identify putative treatments effective against SARS-CoV-2 based on morphological analysis of the publicly available RxRx19a dataset.
Tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).
A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli.
Deep-ABPpred is a tool for identifying antibacterial peptides in protein sequences.
Identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM
A separable temporal convolutional networks based deep learning technique for discovering antiviral medicines. The model behind this app is based on Temporal Convolutional Network (TCN). It uses the amino acid sequences of a given peptide as input and predicts whether the peptide is antifungal or not. The model consists of a word embedding layer, a spatial dropout layer, two TCN blocks, a global average pooling layer, a dense layer, and a dropout layer.
A deep learning–based multi-model framework model, called Deep-B3, to predict the BBB permeability of candidate compounds.
Deep-COVID is a tool for predicting COVID-19 from chest X-ray images using deep transfer learning.
Deep-DRM is a computational Method for Identifying Dis-ease-related Metabolites based on Graph Deep Learning Approaches
A Distributed, Scalable, and Edge-Oriented Framework for Real-Time Analysis of Video Streams.
An R-Shiny applet for network-based classification and prediction of Host-Pathogen protein-protein interactions.
Deep-Kcr is a tool for detection of lysine crotonylation sites using deep learning method.
Deep-loop is a sequence-based deep learning approach to predict CTCF-mediated chromatin loop.
Deep-PK is a deep learning platform for predicting the pharmacokinetic and toxicity properties of small molecules. It utilizes graph neural networks and graph-based signatures to optimize and understand drug candidates.
Deep-PLA is a web server developed for understanding the reversible enzyme-specific lysine acetylation regulation for histone acetyltransferases
3-Class Retinal Classification via Deep Network Features and SVM Classifier
Automatically segments 2D retinal vessels using N4 fields, CNN, and probabilistic vessel tracking
Deep4mC is a web server for computational prediction of 4mC sites in the DNA sequences.
Deep4mcPred is a webserver for predicting 4mC sites.
A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species.
Network-based deep learning approach to in silico drug repositioning.
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities | End-to-end deep learning toolkit for predicting protein binding sites and motifs | deepRAM is an end-to-end deep learning toolkit for predicting protein binding sites and motifs. It helps users run experiments using many state-of-the-art deep learning methods and addresses the challenge of selecting model parameters in deep learning models using a fully automatic model selection strategy. This helps avoid hand-tuning and thus removes any bias in running experiments, making it user friendly without losing its flexibility. While it was designed with ChIP-seq and CLIP-seq data in mind, it can be used for any DNA/RNA sequence binary classification problem
Extracts deep features from MR images using pretrained neural networks. These features can be used for classification, clustering, or survival prediction tasks in medical imaging.
Deep features extraction (EUCAIM-SW-059_T-02-01-007)
Self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data.
A dual EEG pipeline for developmental hyperscanning studies.
A novel deep learning method for the identification of lysine succinylation sites.
A fully convolutional (with no pooling layers) model was trained on a set of noisy images with the ground truth being the original image without the (synthetic) noise. Different levels of noise and types were incorporated into the training set. The experiments showed reduction in noise levels, but it can impact image quality when T2ws without noise is provided to the model.
We develop a novel deep learning approach for multi-stage malaria parasites recognition in blood smear images using Deep Transfer Graph Convolutional Network (DTGCN). And this work is the first application of GCN on multi-stage malaria parasites recognition in blood smear images. The proposed DTGCN model is based on unsupervised learning by transferring knowledge learnt from source images that contain the discriminative morphology character-istics of multi-stage malaria parasites. These transferred information guarantees the effectiveness on the target parasites recognition.
Deep Transfer Graph Convolutional Network
Deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features.
DeePaC-Live is a deep learning framework for real-time detection of novel pathogens during sequencing.
A convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA.
Automatic segmentation of anatomical cross-sectional area in ultrasound images of human lower limb muscles using deep learning.
MATLAB toolbox for automated classification of animal behavior in video.
A deep learning application for predicting amyloid standardized uptake value ratio through PET for Alzheimer's prognosis.
DeepAE is deep learning framework to identify the key dimensions from high-dimensional gene expression profiles. DeepAE is composed of an input layer, seven hidden layers, and output layer to form the encoder and decoder phases that are corresponded to the compression and decompression.
Deep learning-based strategy to predict cancer driver mutations.
Predicting antibody paratope by bidirectional long-short-term memory neural networks and transformer encoder with concatenated CDR sequences
The python package 'DeepAnnotation' can be used to perform genomic selection (GS), which is a promising breeding strategy for agricultural breeding. DeepAnnotation predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework.
deepAntigen is a method for neoantigen prioritization via 3D genome and deep sparse learning.
DeepAPS is a tool for automatic Phenotyping Segmentation. DeepAPS is a composite method that combines two readily available algorithms in order to create a precise mask for an animal image. DeepAPS allows for the rapid and accurate quantification of multiple phenotypic measurements while minimizing study cost.
An integrated deep learning framework that uses sequence, domain and Gene Ontology information to predict PPIs of Arabidopsis thaliana. DeepAraPPI currently consists of three basic models: (i) a Siamese recurrent convolutional neural network (RCNN) model based on word2vec encoding, (ii) a multiple layer perceptron model based on Domain2vec encoding, and (iii) an multiple layer perceptron model based on GO2vec encoding. Finally, DeepAraPPI combines the results of three individual predictors using a logistic regression model.
A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes.
DeepArk is a set of models of the worm, fish, fly, and mouse regulatory codes. For each of these organism, we constructed a deep convolutional neural network that predict regulatory activities (i.e. histone modifications, transcription factor binding, and chromatin state) directly from genomic sequences. Besidese accurately predicting a sequence's regulatory activity, DeepArk can predict the effects of variants on regulatory function and profile sequences regulatory potential with in silico saturated mutagenesis.
Artificial intelligence driven discovery of peptide drugs for viral infections.
Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates.
Evaluation of deep learning models for identification of immunogenic B-cell epitopes.
A Novel Behavior Tracking Method for Laboratory Animals Based on Deep Learning.
DeepBindBC is a deep learning based binary classifier for identifying native-like protein-ligand complexes.
DeepBindPoc is a deep learning based method for identifying highly potential pocket for given ligand from a fpocket generated pocket decoys set of the given protein .
DeepBIO is an automated and interpretable deep-learning platform for biological sequence prediction, functional annotation, and visualization analysis.
DeepBiome is a deep Learning package using the phylogenetic tree information for microbiome abandunce data analysis.
DeepBL is a deep learning-based approach for beta-lactamase classification using protein or genome sequence data. DeepBL is a high-throughput and deep learning-based multi-class classifier, to accurately identify beta-lactamase classes by incorporating sequence-derived features. DeepBL was implemented based on the Small VGGNet architecture and using the TensorFlow deep learning library. We evaluated DeepBL on carefully prepared benchmark and independent test datasets and the results of the 10-fold cross-validation and independent test demonstrate DeepBL’s robustness and generalization.
deepBlink is a tool for threshold-independent detection and localization of diffraction-limited spots. DeepBlink relies on neural networks to automatically find spots without the need for human intervention.
EU grant No. HEALTH-F5-2011-282510 (BLUEPRINT project)
German Science Ministry Grant No.01KU1216A (DEEP project)
Provides a central data access hub for large collections of epigenomic data. It organizes the data from different sources using controlled vocabularies and ontologies. The data is stored in our server, where the users can access the data programmatically or by our web interface. It contains a set of commands designed to perform operations on the epigenomic data. Users can execute all operations in a pipeline fashion in the server and transfer only meaningful data.
Accessing the DeepBlue Epigenetics Data Server through R.
Accurate identification of transcript boundaries via deep convolutional neural fields.
An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery.
DeepBrainNet is a convolutional Neural Network trained for age prediction using a large set of MRI scans from a highly diversified cohort spanning different studies, scanners, ages, ethnicities and geographic locations around the world.
DeepBSA is a bulked segregant analysis (BSA) software for the dissection of complex traits. Two algorithms are developed in DeepBSA named deep learning (DL) and k-value (K), which can be applied on different number (at least 2) of bulked pools.
DeepBSRPred, a binding site residue prediction method using protein sequence and predicted structures from AlphaFold2.
DeepC is a neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
Incorporating transcription factors in genome-wide prediction of chromatin accessibility.
Versatile deep learning platform for target- and cell-based anticancer drug discovery.
Accurate identification and investigation of protein lysine crotonylation sites based on capsule network.
Deep Learning-Powered Carcinogenicity Prediction Using Model-Level Representation.
A tool for modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches.
A general causal inference framework named DeepCausality to empirically estimate the causal factors for suspected endpoints embedded in the free text.
A deep learning framework for identifying cell-cell interactions from single-cell rna sequencing data.
DeepCDA is a tool for Deep Cross-Domain Compound-Protein Affinity Prediction through LSTM and Convolutional Neural Network.
DeepCDR is a hybrid graph convolutional network for cancer drug response prediction. It takes both multi-omics data of cancer cell lines and drug structure as inputs and predicts the drug sensitivity (binary or contineous IC50 value). DeepCDR is a hybrid graph convolutional network for cancer drug response prediction. It takes both multi-omics data of cancer cell lines and drug structure as inputs and predicts the drug sensitivity (binary or contineous IC50 value). This work has been accepted to ECCB2020 and was also published in the journal Bioinformatics.
DeepCEL0 for 2D Single Molecule Localization in Fluorescence Microscopy.
Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning. Home — DeepCell 1.0.0 documentation. Free document hosting provided by Read the Docs
DeepCellEss, a sequence-based interpretable deep learning framework for cell line-specific essential protein predictions.
A deep learning-based framework for the classification of cervical cells using hybrid deep feature fusion techniques.
A multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs.
DeepciRGO is a computational method for microRNA Gene Ontology function prediction. It constructed a global heterogeneous network through circRNA co-expression, circRNA-protein association, and protein-protein interaction data. The potential network feature vector of the global network is extracted by Hin2vec and are further used for the construction of deep neural network classifier to predict circRNA Gene Ontology function.
DeepCLA uses a deep learning apprach to predict clathrin, which is implemented by deep learning library Tensorflow backend.
A deep learning framework for computing solution statistics of the chemical master equation.
Graph-based model for accurate prediction of circRNA-miRNA interactions with multiple information.
DeepCNV is a deep learning approach for authenticating copy number variants.
DeepCob is a tool for precise and high-throughput analysis of maize cob geometry using deep learning with an application in genebank phenomics.
A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling.
DeepCoy (Generating Property-Matched Decoy Molecules Using Deep Learning) is a tool that generates decoys to a user’s preferred specification in order to remove biases or construct sets with a defined bias.
DeepCPI is a deep learning based framework for large-scale in silico drug screening.
DeepCSO is an online prediction tool for the recognition of Cysteine S-sulphenylation (CSO) sites. DeepCSO contains three LSTM models: two species-specific models and one general model.
A deep learning platform for enhanced cytochrome P450 activity prediction.
DeepCys is structure-based multiple cysteine function prediction method trained on deep neural network.
A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence.
DeepDDS (Deep Learning for Drug–Drug Synergy prediction) A deep graph neural network with attention mechanism to predict synergistic drug combinations.
software tool for the annotation and discovery of novel immune systems in prokaryotes
DeepDigest is a deep learning-based tool to predict the proteotypic cleavage sites for eight commonly used proteases (trypsin, ArgC, chymotrypsin, GluC, LysC, AspN, LysN, and LysargiNase).
DeepDILI is a tool for Deep Learning-Powered Drug-Induced Liver Injury Prediction Using Model-Level Representation
Accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.
DeepDist is a tool for real-value inter-residue distance prediction with deep residual convolutional network.
Predicting regulation types of small molecule inhibitors on modulating lncRNA expression by deep learning.
DeepDRK (Deep learning of Drug Response using kernel-based data integration) a deep learning framework for drug repurposing through kernel-based multi-omics integration.
DeepDRPBind is developed to predict DNA, RNA and protein binding residues in intrinsically disordered protein sequence.
DeepDrug is a general graph-based deep learning framework for drug-drug/protein interaction prediction.
DeepDTAF is a deep learning architecture, which integrates local and global features to predict the binding affinity between ligands and proteins.
DeepECA is an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. It can be used for predicting protein contact residues and secondary structures from its amino acid sequence by using Deep Neural Network.
2D convolutional neural network model for identifying families of efflux proteins in transporters.
Deep-learning based particle recognition program.
DeepEthogram is a Python package for automatically classifying each frame of a video into a set of pre-defined behaviors. Designed for neuroscience research, it could be used in any scenario where you need to detect actions from each frame of a video.
DeepEventMine is a tool for end-to-end neural nested event extraction from biomedical texts.
DeepFeature converts non-image samples into image-form and performs element selection via convolutional neural network (CNN).
Deep learning for peptide identification from metaproteomics datasets.
A deep learning approach for forecasting symptomatic influenza A infection based on pre-exposure gene expression.
Deep learning-based algorithm for fast automatic analysis of DNA double-strand break ionizing radiation-induced foci.
Enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.
DeepForest is a Python package for RGB deep learning tree crown delineation.
Deep Fingerprint Learn (DFPL) is an aI for predicting chemical-effect associations at the universe level. Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets.
DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such that the resulting extension is also highly complementary to the receptor.
DeepFrag-K is a set of deep learning methods to directly classify any protein into one of the well-known folds.
DeepFRI is a structure-based protein function prediction (and functional residue identification) method using Graph Convolutional Networks with Language Model features.
DeepFun is a deep learning based approach to predict the functional impacts of sequence alterations at single nucleotide resolution.
DeepG4 is a deep learning model developed to predict the probability of DNA sequences to form active G-Guadruplexes (found both in vitro and in vivo). DeepG4 is built in keras+tensorflow and is wrapped in an R package.
A general deep learning-based predictor for multiple genomic signals and regions.
DeepGMAP is a Deep learning-based Genotype MAPping platform to predict them. It can train different architectures of neural networks with epigenomic data, and "map" potential gene regulatory regions on a genome.
DeepGOA is a deep Graph Convolutional Network based model to predict GO annotations of proteins. DeepGOA firstly quantifies the correlations (or edges) between GO terms and updates the edge weights of the direct acyclic graph (DAG) by leveraging GO annotations and hierarchy, then learns the semantic representation and latent inter-relations of GO terms in the way by applying GCN on the updated DAG.
DeepGOWeb is a webserver for protein function prediction from amino acid sequence. DeepGOWeb uses the DeepGOPlus function prediction model.
Improving protein function prediction from sequence and zero-shot learning based on ontology axioms.
Graph neural network for large-scale, multispecies protein function prediction.
DeepGraphh is an open-source web service that features a conglomerate of powerful graph-based neural networks methods, with highly configurable parameters support via the graphical user interface (GUI).
DeepGRN is a tool for predicting transcription factor binding site across cell-types using attention-based deep neural networks.
DeepGRP is a python package used to predict genomic repetitive elements with a deep learning model consisting of bidirectional gated recurrent units with attention.
DeepH3 is a deep residual network architecture to predict probability distributions of inter-residue distances and angles for CDR H3 loops in antibodies. This work is protected by https://creativecommons.org/licenses/by-nc/3.0/.
DeePhage is a tool for identifying temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning. DeePhage is designed to identify metavirome sequences as temperate phage-derived and virulent phage-derived sequences.
DeephageTP is an alignment-free deep learning framework for identifying phage-specific proteins from metagenomic datasets. DeephageTP predicts phage-specific proteins using deep learning methods. The method has good prediction precision for phage-specific proteins (TerL,Portal and TerS), and it also can be used to predict sequences from the viromic data. CNN can automatically learn protein sequence patterns and simultaneously build a predictive model based on the learned amino acid sequence patterns.Compared to the alignment methods, the CNN is a natural generalization of amino acid based model, can find the similarities of viral proteins at high latitudes. The more flexible CNN model indeed outperforms the alignment methods on viral protein sequence prediction problem.
DeePhase predicts the propensity of proteins to undergo homotypic liquid-liquid phase separation (LLPS).
DeepHE is a deep learning framework for essential gene prediction based on sequence data and PPI network.
DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. Ab initio training could be performed according to our published code. We provided trained models for various depth of low-coverage sequencing Hi-C data. The depth of input data is estimated by its distribution comparing with those of the downsampled Hi-C data we used in training.
DeepHisCoM (Deep-learning pathway analysis using Hierarchical structured CoMponent models) which uses deep learning analysis to find complex relationships between biological factors and pathways.
A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning.
DeepHIT is a deep learning framework for prediction of hERG-induced cardiotoxicity.
Deep learning-based method for non-classical HLA binder prediction.
DeepHomo is a tool for accurate prediction of inter-protein residue-residue contacts for homo-oligomeric or homo-dimeric protein complexes.
Predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation.
DeepHost is a phage host prediction with convolutional neural network.
Adeep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions.
DeepHPV was designed for detection of HPV virus in DNA integration. The data provided here is for the model of DeepHPV with HPV integration sequences + TCGA Pan Cancer and the model of DeepHPV with integration sequences + RepeatMasker.
A machine learning-assisted platform for electrophysiological phenotyping of human neuronal networks.
Inter-domain distance prediction based on deep learning for domain assembly.
Tool for protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network.
DeepImageTranslator is a free, user-friendly graphical interface for image translation using deep-learning and its applications in 3D CT image analysis.
DeepImmuno is a tool for deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity.
Deep Neural Network Intellectual Property Protection with Passports.
Comprehensive assessment and computational identification of phosphorylation sites of SARS-CoV-2 infection using a deep learning-based approach.
An End-to-End Deep Learning-Based Workflow for Biomedical Knowledge Graph Extraction, Optimization and Applications.
DeepKhib is a web server that could predict lysine 2-Hydroxyisobutyrylation sites. it takes protein sequence data as input and uses one-hot encoding scheme and One-Dimensional Convolution Neural Network.
DeepKinZero is a zero-shot learning approach to predict the kinase acting on a phosphosite for kinases with no known phosphosite information.
DeepKme is the predictor for lysine methylation sites in human proteome.
DeepLabCut™️ is a toolbox for state-of-the-art markerless pose estimation of animals performing various behaviors.
A Bi-LSTM and multi-scale CNN-based deep learning method for predicting linear B-cell epitopes.
Retention time prediction for (modified) peptides using Deep Learning.
A deep learning framework, DeepLensNet, for the detailed assessment of age-related cataract
A biomedical knowledge graph-based method for drug-drug interactions prediction through combining local and global features with deep neural networks.
DeepLIIF is a tool for deep-learning inferred multiplex immunofluoresence for IHC quantification.
DeepLION is a deep multi-instance learning (MIL) method for identifying cancer-associated T cell receptors (TCRs) and detecting cancer samples using TCR-sequencing data.
DeepLncLoc is a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding.
An interpretable convolutional neural network model for identifying long non-coding RNA promoters.
Prediction of eukaryotic protein subcellular localization using deep learning.
DeepLPI is a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms.
Deep-LUCIA (Deep Learning-based Universal Chromatin Interaction Annotator) is a deep learning based model to predict chromatin loops from genomic and epigenomic profile without CTCF signal.
DeeplyEssential is a Deep neural network for the identification of Essential genes in bacteria species. The dataset used for the learning of the nework contains 30 bacterial species collected from DEG.
DeeplyTough is a tool for Learning Structural Comparison of Protein Binding Sites
A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy.
A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues.
DeepMalaria is a tool for Artificial Intelligence Driven Discovery of Potent Antiplasmodials. Code available upon request.
deepManReg is a deep manifold-regularized learning model for improving phenotype prediction from multi-modal data.
DeepMEL is a tool that identifies orthologous enhancers across distantly related species, where sequence alignment fails, and the model highlights specific nucleotide substitutions that underlie enhancer turnover. DeepMEL can be used from the Kipoi database to predict and optimize candidate enhancers and to prioritize enhancer mutations.
Transformer network incorporating multilayer graph information for Drug-Target interaction prediction.
DeepMIB is user-friendly and open-source software for training of deep learning network for biological image segmentation.
DeepMicrobes is a tool for taxonomic classification for metagenomics with deep learning.
DeepMitoDB is a database of experimental and predicted subcellular localization of mitochondrial proteins with exteded functional annotation.
DeepMM is a too for automatic de novo atomic-accuracy structure determination for cryo-EM maps using deep learning.
DeepMol is an AutoML framework for computational chemistry, automating data preprocessing, algorithm selection, and model configuration to predict molecular properties. It leverages machine learning techniques and is open-source with detailed documentation and examples.
DeepMotifSyn is a deep-learning-based model to synthesize heterodimeric motifs from monomeric motif pairs.
Deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Deep learning framework for predicting drug-target interactions based on multi-modal representation with meta-path semantic analysis.
DeepMPTB is a deep neural network tool utilizing vaginal microbiome data to predict preterm birth risk with an accuracy of 84.10%. The tool is open-source and accessible via a Streamlit application, Docker, and GitHub.
Investigating the causal knowledge of genomic deep learning models.
DeepMRM is a targeted proteomics data interpretation package using deep-learning. It takes MRM, PRM, or Data-Independent Acquisition (DIA) data and target list as input and outputs peaks of targeted peptides, along with their abundances and quality scores. The targeted endogenous (light) peptides are detected and quantified using their stable isotope labeled (heavy) peptides.
DeepMSA2 is a pipeline that generates high-quality multiple sequence alignments (MSAs) for protein monomers and complexes by leveraging large-scale genomic and metagenomic datasets, significantly improving the accuracy of protein tertiary and quaternary structure predictions.
DeEPn is a deep neural network based tool for enzyme functional annotation.
DeepNano-blitz is a base caller for MinION Nanopore Sequencers.
DeepNC (Deep Generative Network Completion) a method to recover the missing part of a network. The method for inferring the missing parts of a network based on a deep generative model of graphs. Specifically, the method first learns a likelihood over edges via an autoregressive generative model, and then identifies the graph that maximizes the learned likelihood conditioned on the observable graph topology.
A framework for drug-target interaction prediction with graph neural networks.
DeepnCCA is a tool for deep learning corpus callosum segmentation as a neurodegenerative marker in multiple sclerosis. The tool extracts the intracranial and corpus callosum area as a biomarker, normalized corpus callosum, for neurodegeneration in multiple sclerosis.
A multimodal deep learning model, DeepNCI, is proposed for improving noncovalent interactions (NCIs) calculated via density functional theory (DFT).
DeepND is a cross-disorder gene discovery algorithm (Deep Neurodevelopmenal Disorders algorithm) It analyzes comorbid neurodevelopmental disorders simultaneously and explicitly learns the shared and disorder-specific genetic features using multitask learning. Thus, the predictions for the disorders depend on each other's genetic architecture. The proposed DeepND architecture uses graph convolution to extract associations between genes from gene coexpression networks that model neurodevelopment. This information is processed by a mixture-of-experts model that can self-learn critical neurodevelopmental time windows and brain regions for each disorder etiology which makes the model interpretable. We provide a genomewide risk ranking for each disorder.
A novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning.
Webserver for predicting immunogenic neoantigens.
DeepNetBim is a deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information.
DeepNeuro is an open-source toolset of deep learning applications for neuroimaging. A deep learning python package for neuroimaging data.
DeepNOG is a tool for protein orthologous groups assignment. Assign proteins to orthologous groups (eggNOG 5) on CPUs or GPUs with deep networks. DeepNOG is much faster than alignment-based methods, providing accuracy similar to HMMER.
DeepO-GlcNAc is a web server for predicting protein O-GlcNAcylation sites using deep learning, offering a user-friendly platform for researchers. The tool leverages LSTM, CNN, and attention mechanisms and is available for investigation and usage by the scientific community.
DeepOlf is a deep neural network-based prediction model, developed on a large dataset of odorants, non-odorants and olfactory receptors (ORs), using a potential set of physiochemical properties and molecular fingerprints. It allows accurate inference of an odorant over a set of olfactory receptors.
DeepOMe is a web server for the prediction of 2'-O-Me sites based on the hybrid CNN and BLSTM architecture.
A multimodal deep learning framework for functional interpretation of genetic variants in personal genome.
A deep learning framework for predicting protein functions with co-occurrence of GO terms.
An R package for phenotype generation and association analysis for phenome-wide association studies.
DeepPhospho is a tool to accelerate DIA phosphoproteome profiling by Deep Learning. It is used for the prediction of fragment ion intensity and retention time for phosphopeptides. DeepPhospho is a hybrid deep neural network combining LSTM and transformer modules and it is specifically developed for accurate prediction of fragment ion intensity and indexed retention time (iRT) for any given phosphopeptide.
Approach for pure ion chromatogram construction from liquid chromatography-mass spectrometry data using deep learning. Extract PICs from raw data files directly and automatically. The DeepPIC method has already been integrated into the KPIC2 framework. The combination can provide the entire pipeline from raw data to discriminant models for metabolomic datasets.
DeepPocket is a 3D convolutional Neural Network framework for ligand binding site detection and segmentation from protein structures.
DeepPod is a convolutional neural network based quantification of fruit number in Arabidopsis.
An ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
Structure-aware protein binding site prediction using ESMFold and pretrained language model.
DeepPROTACs is a deep learning-based targeted degradation predictor for proteolysis targeting chimera (PROTACs).
A deep learning-based method, DeepPSE, to predict polypharmacy side effects in an end-to-end way.
Deep Learning-based Pseudo-Mass Spectrometry Imaging Analysis for Precision Medicine.
A Deep Learning Library for Compound and Protein Modeling, DTI, Drug Property, PPI, DDI, Protein Function Prediction
A deep representation on heterogeneous drug network, termed DeepR2cov, to discover potential agents for treating the excessive inflammatory response in COVID-19 patients.
DeepRC is a tool that that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification.
DeepReac+: An universal framework for quantitative modeling of chemical reaction based on deep active learning.
A Deep Learning Powered Multi-scale Modeling Framework for Predicting Out-of-distribution Ligand-induced GPCR Activity.
Deepred-Mt is a novel method to predict C-to-U editing sites in angiosperm mitochondrial RNA. Given an RNA sequence consisting of a central cytidine flanked by 20 nucleotides on each side, Deepred-Mt scores if the central cytidine is edited.
DeepRefiner is a tool for high-accuracy protein structure refinement by deep network calibration.
DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq
DeepReI is a deep learning-based gas chromatographic retention index predictor.
DeepRepeat is a computational method to detect STRs from nanopore sequencing data through direct analysis of electric signals rather than basecalled reads
DeepRescore is an immunopeptidomics data analysis tool that leverages deep learning-derived peptide features to rescore peptide-spectrum matches (PSMs). DeepRescore takes as input MS/MS data in MGF format and identification results from a search engine. The current version supports four search engines, MS-GF+, Comet, X!Tandem, and MaxQuant.
A web server for characterising protein-solvent interaction starting from sequence.
DEEPrior is an inherently flexible deep learning tool that predicts the probability of a gene fusion being a driver of an oncogenic process, by directly exploiting the amino acid sequence of the fused protein and it is able to prioritize gene fusions from different tumors. Unlike state of the art tools, it also support easy retraining and re-adaptation of the model.
DeepRKE is a deep neural network model, which combines primary RNA sequence and secondary structure information to effectively predict RNA binding protein binding sites.
DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.
DeeProPre, based on convolutional neural network and bidirectional long short-term memory model connecting attention mechanism. It is used for the computational recognition of promoters of with TATA-box, without TATA-box and mixed data types.
DeepS is a web server for image optical sectioning and super resolution microscopy based on a deep learning framework.
Deep neural network for protein solvent accessibility and contact number prediction.
DEEPsc is a system-adaptive, deep learning-based method to impute spatial information onto a scRNA-seq dataset from a given spatial reference atlas.
An efficient convolutional neural network surrogate model for the screening of therapeutic antibody viscosity.
DEEPScreen is a tool for virtual screening with deep convolutional neural networks using compound Images for high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations.
Detecting super-enhancers among typical enhancers using only sequence feature embeddings.
Deep learning framework for secreted protein discovery in human body fluids.
DeepSeg: is deep neural network framework for automatic brain tumor segmentation using magnetic resonance FLAIR Images.
Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing.
DeepSELEX is a tool for inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs.
An deep learning framework to separate neural signal and artifacts in the embedding space and reconstruct the denoised signal
Prediction of secretory signal peptides in protein sequences
SeepSimDEF offers single- and multi-channel deep learning models for functional analysis of genes using Gene Ontology annotations of gene products (RNAs, proteins, etc).
DeepSimulator is a deep learning based simulator to mimic the entire pipeline of Nanopore sequencing. Starting from a given reference genome or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally.
DeepSinse is a tool for deep learning based detection of single molecules.
Precise prediction of regulatory effects on miRNA expression mediated by small molecular compounds using competing deep learning frameworks.
Fusing Deep Learning and SMOTE for Imbalanced Data.
DEEPSMP is a deep learning model for predicting the ectodomain shedding events of membrane proteins.
This package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages are integrated to provide a wide range of tools for gene expression analysis.
DeepSpectrumLite is a Python toolkit to design and train light-weight Deep Neural Networks (DNNs) for classification tasks from raw audio data.
Identifying spatial domains in spatial transcriptomics by deep learning.
An AI based web tool to predict the melting temperature (Tm) of proteins based on their amino acid sequence and various growth conditions.
DeepSTORM3D is a tool for dense 3D localization microscopy and PSF design by deep learning. DeepSTORM3D enables the study of biological processes in whole cells at timescales that are rarely explored in localization microscopy.
DeepSuccin is a tool for the prediction of protein succinylation sites with deep learning model.
DeepSurf is a surface-based deep learning approach for the prediction of ligand binding sites on proteins.
DeepSVFilter is a deep learning based tool designed to filter false positive structural variants (SVs) obtained by any computational approaches from short read whole genome sequencing data. It can be used as either a stand-alone tool to filter SVs or coupled with commonly used SV detection tool to improve specificity.
DeepSVP is a computational method to prioritize structural variants involved in genetic diseases by combining genomic information with information about gene functions. It incorporates phenotypes linked to genes, functions of gene products, gene expression in individual celltypes, and anatomical sites of expression, and systematically relate them to their phenotypic consequences through ontologies and machine learning.
Using deep learning to identify recent positive selection in malaria parasite sequence data. Deepsweep is a supervised machine learning approach for estimating positive selection in whole-genome sequenced data.
Predicting anti-cancer drug synergy with Deep Learning.
Inferring diagnoses from veterinary clinical notes. This contains the source code for the DeepTag Project.
DeepTE is aimed to classify transposons with unknown classification via Convolutional Neural Network. A computational method for de novo classification of transposons with convolutional neural network.
DeepTESR can be used to predict the degree of TESR for gene expression control and to decipher the mechanism of translational control with ribosome profiling.
DeepTFactor is a deep learning-based tool that predicts whether a protein in question is a transcription factor. DeepTFactor uses a convolutional neural network to extract features of a protein. It showed high performance in predicting TFs of both eukaryotic and prokaryotic origins,
DeepTL-Ubi is a novel deep transfer learning method for effectively predicting ubiquitination sites of multiple species.
DeepTMInter is a tool for improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning.
Ttopology prediction of alpha-helical transmembrane proteins
An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome.
User-friendly tools for the normalization and visualization of deep-sequencing data.
A Deep Learning Model for Thermophilic Protein Prediction.
DeepTracer is a tool for Cryo-EM Protein Structure Modeling and Special Studies on CoV-related Complexes.
A ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks.
DeepTSS, a novel computational method for processing CAGE samples, that combines genomic signal processing (GSP), structural DNA features, evolutionary conservation evidence and raw DNA sequence with Deep Learning (DL) to provide single-nucleotide TSS predictions with unprecedented levels of performance.
Ultrafast Shape Recognition-based Protein Model Quality Assessment using Deep Learning.
DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
DeepVF is a deep learning-based hybrid framework for recognizing virulence factors using the stacking strategy.
DeepViral is a tool for the prediction of novel virus–host interactions from protein sequences and infectiousdisease phenotypes.
DeepVISP is a deep learning tool for virus site integration prediction and motif discovery.
Identification and classification of phage virion proteins using deep learning
DeepWAS is a tool for directly integrating regulatory information into GWAS using machine learning. Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
DeepYY1 is a deep learning approach to identify YY1-mediated chromatin loops.
DeepZF, a deep-learning-based pipeline for predicting binding ZFs and their DNA-binding preferences given only the amino acid sequence of a C2H2-ZF protein
DEER-PREdict is a package for double electron-electron resonance (DEER) and paramagnetic relaxation enhancement (PRE) predictions from molecular dynamics ensembles.
DeeReCT-APA is a tool for prediction of alternative polyadenylation site usage through deep learning.
A novel meta-learning-based method annotates TSS in multiple cell types based on DNA sequences and RNA-seq data.
An interactive atlas of human differential gene expression.
DeeZ (a.k.a. DeeNA-Zip) is a tool for compressing SAM/BAM files, or more formally, a tool which does reference-based compression by local assembly
SVM-based supervised learning foot-printer for the detection of footprints containing motifs.
Deriving and Using Descriptors of Elementary Functions in Rational Protein Design.
Deform-nu is a DNA deformation energy-based predictor for nucleosome positioning.
Covert between different data formats used by differential gene expression analysis tools.
Defpred is a web server that predicts the presence of Defensins in given query protein sequqnces.
Assemble Sanger sequencing reads, identify ORFs and blast these as well as annotating them with InterPro.
A software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.
This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature you choose.
Remove non-alphabetic (e.g. gap) characters from sequences.
A tool for annotation of mitochondrial genomes
DeGenPrime is a console-based PCR primer design tool that utilizes thermodynamic properties, filtration metrics, and conserved region finding, expanding the target range for a single primer set. It is written in C++ and distributed under a BSD-3-Clause license.
R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data.
The DEGnext is a CNN model proposed to predict UR and DR genes from RNA-seq cancer datasets.
deGPS is a tool for detecting differential expression in RNA-Seq data.
Implements recent hypothesis testing methods to assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches. These recent methods consider the topology of the network to yield more powerful detection procedures. It provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.
Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.
A deep learning model to predict E3 binding sites (degrons) on protein substrates.
DegronMD: protein-targeted degradation, mutation and drug response to degrons.
Web server for proteome-wide inspection of degrons. Search for degrons, their modifications, conservation, emergence after proteolysis, predict stability of protein N-/C-terminus and many more.
R package to identify differentially expressed genes from RNA-Seq data.
DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data analysis workflows that offers ease of development and access to efficient algorithmic implementations.
DeLA-Drug is an artificial intelligence-based platform able to generate drug-like analogues starting from a single user-defined query compound.
Wrapping an array-like object in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects, Matrix objects, and ordinary arrays and data frames.
A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.
DELEAT (deletion design by essentiality analysis tool). Gene essentiality prediction and deletion design for bacterial genome reduction.
DelFTa, an open-source toolbox for the prediction of electronic properties of drug-like molecules at the density functional (DFT) level of theory, using Δ-machine-learning
DELIA is a tool for deep learning model for protein-ligand binding site prediction based on amino acid distance matrix.
Delila-PY is a custom pipeline to make it quick and easy to run the Delila software packages required to construct a binding site logo while providing the high level of flexibilty and control present in the Deilia software.
Process-based species delimitation leads to identification of more biologically relevant species. Most approaches to species delimitation to date have considered divergence-only models. Although these models are appropriate for allopatric speciation, their failure to incorporate many of the population-level processes that drive speciation, such as gene flow (e.g., in sympatric speciation), places an unnecessary limit on our collective understanding of the processes that produce biodiversity. To consider these processes while inferring species boundaries, we introduce the R-package delimitR and apply it to identify species boundaries in the reticulate taildropper slug (Prophysaon andersoni). Results suggest that secondary contact is an important mechanism driving speciation in this system.
DELiVR is a deep-learning pipeline for detecting cells in three-dimensional datasets, trained using virtual reality annotation. It is available as a Docker container and Fiji plugin, and facilitates data visualization and customization.
Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.
DELPHI (DEep Learning Prediction of Highly probable protein Interaction sites) is a deep learning program for protein-protein interaction site prediction.
Calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.
DelPhi-based script, allowing to calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.
An R package for a rapid detection of differential gene presence between related bacterial genomes. An R package for a rapid differential gene presence analysis between similar genomes. deltaRpkm is an R package whose main purpose is to quickly identify genes potentially involved in a given trait by performing a differential analysis of genes coverage between two sets of closely related bacterial genomes. An R package for a rapid differential gene presence analysis between large datasets of similar bacterial genomes
The ABRF database of protein post-translational modifications.
Prediction of apparent free energy difference for a potential transmembrane helix.
Identifying distinct subpopulations through multiscale time series analysis.
Automated detection and visualization of mass shifts in proteomic open search results.
DeltaNet is a network analysis tool for predicting genetic perturbations from gene expression data.
DeltaProt is a software toolbox for comparative genomics.
A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development. Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ΔSCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination).
Feature selection for preserving biological trajectories in single-cell data.
DEMA (Distance-bounded Energy-field Minimization Algorithm) an algorithm to model and layout biomolecular networks with quantitative properties.
This software predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.
DeMaSk is a web server and library for deep mutational scanning substitution matrix and its use for variant impact prediction.
EMBF is a database of enzymes of microalgal biofuel feedstock.
A standard format for demographic models with different tools for describing and manipulating demographic models.
deMeta is a tool for removing sub-studies from meta-analysis of genome wide association studies.
DEMO (Domain Enhanced MOdeling, version 2) is an significantly improved version for automated assembly of full-length structural models of multi-domain proteins by integrating analogous template alignments with deep-learning predicted inter-domain spatial restraints.
DeMoS (Dense Module based Gene Signature Detection through Quasi-Clique) is an application for performing cervical cancer prognosis.
Pharmacokinetic and toxicodynamic concepts in idiosyncratic, drug-induced liver injury. DemoTox-PK documentation. DemoTox-PK allows the user to visualize how such alterations might lead to a toxic reaction. The illustrations presented provide a framework for conceptualizing idiosyncratic reactions and could serve as a stimulus for future discussion, education, and research into modes of action of IDILI.
R/Bioconductor package for demultiplexing scRNAseq data
Deconvolution of sample identity and identification of multiplets when multiple samples are pooled by barcoded single cell sequencing.
DENA (Deeplearning Explore Nanopore m6A). Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
A web resource for dendrimer pharmacokinetics investigation and prediction. Abstract: The development of nanomedicines currently suffers from a lack of efficient tools to predict pharmacokinetic behaviour without relying upon testing in large numbers of animals, impacting success rates and development costs. The aim of this work was therefore to present dendPoint, the first in silico model to predict the intravenous pharmacokinetic profiles of a commonly explored drug vector, based on dendrimer physicochemical properties
Dendrimer Pharmacokinetics Prediction (dendPoint)
DENDRAL is (or was) an expert system for interpreting mass spectra of organic compounds, and one of the first applications of "artificial intelligence" in science.
De novo Driver Exclusivity is an algorithm to discover mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples.
DENDRO (Dna based EvolutioNary tree preDiction by scRna-seq technOlogy) is an R package, which takes scRNA-seq data for a tumor (or related somatic tissues) and accurately reconstructs its phylogeny, assigning each single cell from the single cell RNA sequencing (scRNA-seq) data to a subclone.
DendroNet is an approach to train neural networks in the context of evolutionary data. DendroNet explicitly accounts for the relatedness of the training/testing data, while allowing the model to evolve along the branches of the phylogenetic tree, hence accommodating potential changes in the rules that relate genotypes to phenotypes.
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats.
DendroScan is an open source tool to conduct comparative statistical tests and dendrogrammatic analyses on particle morphometry.
program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees.
An interpretable framework for clustering single-cell RNA-Seq datasets.
For every organization data and its related infrastructure is constantly evolving. As a result, enterprise data will always remain distributed. The Denodo Platform gives IT organizations the flexibility to evolve their data strategies, migrating to the cloud, or logically unifying data warehouses and data lakes, without affecting business. The Denodo Platform also accelerates data provisioning through reduced data replication, it enables consistent security and governance across multiple systems, and it gives your business users the flexibility to choose their preferred applications. The only way you can accomplish this is through a logical data fabric powered by data virtualization. The Denodo Platform is the only solution that can meet this need. Read about the benefits of the Denodo Platform in this Forrester TEI Repo
An interactive ImageJ plugin for semi-automated image denoising in electron microscopy. DenoisEM offers several state-of-the-art denoising and deconvolution algorithms such as non-local means, BLS-GSM, Tikhonov deconvolution, etc. Fast and advanced image denoising of large-scale 3D electron microscopy data. DenoisEM is developed by the TELIN department at Ghent University and the Bio Informatics Core at VIB . The GPU backbone is driven by Quasar , an in-house programming language of the TELIN department. Apache/2.4.7 (Ubuntu) Server at bioimagingcore.be Port 443.
The tool is designed to perform a customisable image pre-processing to reduce noise and inhomogeneity field effect, thus improving image quality and reproducibility of radiomics features. This tool consists of two independent steps: one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means (NLM)), and another for the ANTs N4 and another for the ANT's N4 bias correction filter. The parameter configuration of this tool has been optimised for TW1, T2W, DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but it can also be configured with some of their parameters using a JSON parameter configuration file.
Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.
DeNovoCNN is a deep learning approach to call de novo mutations (DNMs) on whole-exome (WES) and whole-genome sequencing (WGS) data. DeNovoCNN uses trio recalibrated BAM/CRAM + VCF (or tab-separated list of variants) files to generate image-like genomic sequence representations and detect DNMs with high accuracy.
DeNovoGear is a tool to detect denovo mutations using sequencing data of related individuals. DeNovoGear calls denovo SNP's and INDEL's in trios. DeNovoGear can also be used to phase denovo mutations using genotype information at neighboring SNP sites. In addition, DeNovoGear can also be used to analyze a pair of samples and call SNP's and INDEL's present in one sample but not the other.
Graphical user interface for de novo sequencing of tandem mass spectra.
DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.
DenovoProfiling is a webserver for de novo generated molecule library profiling.
Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) performs annotation based transcript level quantification on nascent RNA sequencing data. Although it was developed on PRO-seq data it should be generally applicable to any nascent sequencing dataset which has been processed such that each read is represented as a single count representing the 3' end of the transcript being synthesized. For a pipeline to process PRO-seq data in this manner see the Danko Lab's PRO-seq 2.0 pipeline here. DENR quantifies nascent transcript abundance based on reference. Package can be installed with the following line of code:.
DENSE (DE Novo emerged gene SEarch) is a Nextflow pipeline for identifying de novo emerged genes in eukaryotes. It combines phylostratigraphy and genome comparisons and is accessible via a command-line tool and a web server for the filtering step.
The DenseCPD server predicts the probabilities of 20 natural amino acids for each residue in a protein structure.
A web service for streaming slices of 3D volumetric data, most notably the electron density data available in the Electron Density Server (EDS) and electron microscopy imaging data from the Electron Microscopy Data Bank (EMDB).
DENTIST uses long reads to close assembly gaps at high accuracy.
Serostatus testing and dengue vaccine cost-benefit thresholds | R package for manuscript "Serostatus Testing & Dengue Vaccine Cost Benefit Thresholds"
DenvInD is a database containing dengue virus inhibitors for clinical and molecular research.
Scalable and high-throughput virtual screening using graph neural networks with atomic and surface protein pocket features.
This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant.
DEP2 provides an comprehensive analysis workflow for mass spectrometry based proteomics data, developed from the previous package DEP.
A tool to detect and visualize co-evolution of protein domains
A program using Multiple Interdependency to detect functional interactions between amino acids in proteins.
Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences
Depicter is a tool for computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.
Deep representation clustering for histology annotation.
Web-based primer design tool for protein interaction experiments.
R Shiny app to systematically link genetic and pharmacologic dependencies of cancer.
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data .
depmap is an R data package that disseminates cancer dependency omics datasets from the Broad Institute website depmap. As the DepMap screening efforts continue, the depmap package will updated on a quarterly basis, in line with the Broad Institute depmap cancer dependency mapping initiative.
Machine learning tool for the targeted identification of phage depolymerases.
DeProj is a MATLAB app made to yield accurate morphological measurements on cells in epithelia or tissues.
DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.
DepthSizer: Read-depth based genome size prediction. Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C.
DEqMS is a statistical package for testing differential protein expression in quantitative proteomic analysis. It is a method for accurate variance estimation in differential protein expression analysis.
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.
DeRegNet is a tool for de novo identification of maximally deregulated subnetworks based on multi-omics data.
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
Helper package for speeding up the derfinder package when using multiple cores.
This package provides plotting functions for results from the derfinder package.
Deriver is a single framework which facilitates the integration of a number of tunable generative methods, permits discrimination of molecules based on arbitraryor shifting objectives, and combines these two processes in a separable manner
Integrated peak and differential caller, specifically designed for broad epigenomic signals.
DescFold is a web server for protein fold recognition,which can predict a protein’s fold type from its amino acid sequence.
DescribePROT (DatabasE of StruCtuRe and functIon residue-Based prEdictions of PROTeins) is a database of amino acid-level protein structure and function predictions.
Describing engagement in the HIV care cascade.
Alter the name or description of a sequence.
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Interpretable prediction of drug-drug interactions using drug-induced gene expressions.
DeSignate is a tool for detecting diagnostic character positions for taxon diagnoses. The analysis is based on a novel representation of the gene sequence data, which enables a ranking of all positions according to their diagnostic relevance and a classification of the characters. DeSignate is also able to detect diagnostic combinations of characters. The tool guides the user step-by-step through the analysis and presents the results without need to post-process the output data.
The Australian Cancer Atlas is an online platform visualizing cancer incidence and survival data across Australia, aimed at identifying and addressing geographical health disparities. It focuses on communicating data uncertainty for multiple audiences, as described in a peer-reviewed publication.
It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes.
The main aim of this server is to make more efficient siRNA against a target site using nucleotide mismatch approach.
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.
A flexible framework for systematic error simulation in DNA storage and can be adapted to a wide range of experiment pipelines.
DESpace is a Bioconductor package that identifies spatially variable genes and differential spatial patterns using edgeR. It summarizes spatial information via spatial clusters and enables joint modeling of multiple samples for increased statistical power.
A web database for sequence and shape motif analyses and identification.
Integrative and cross-modality analysis of single-cell chromatin accessibility data.
DestVI is a tool for multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation.
A network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features.
A density estimation tool for enzyme classification and its application to Plasmodium falciparum. The tool, a probabilistic method for enzyme prediction that accounts for the sequence diversity across enzyme families. By comparing the global alignment scores of an unknown protein to those of all known enzymes, an integrated likelihood score can be readily calculated, ranking the reaction classes relevant for that protein.
detectEVE is an open-source tool for the accurate identification of non-retroviral endogenous viral elements (nrEVEs) in genomic assemblies. It utilizes a scaling system for protein sequence similarity searches and is implemented as a snakemake workflow.
DetectImports is a R package aimed at distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease.
This work Implements the Segmentation Procedures like (i) Watershed and (ii) Level Set procedure .
Detection of Brain Tumor using 2D MRI Slices
A tool for detecting perfect and imperfect inverted repeats in genomes.
DetectIS is a pipeline specifically designed to detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data. The workflow manager nextflow is used with a configuration file and a Singularity image.
Detective-QSAR is a web applications to evaluate the known/unknown spectra aquired by MS
Diagnostic tool which return the propensity of a given mRNA to be translated into peptide.
DetEdit is a tool to visualize and annotate events from large acoustic datasets. It is highly configurable and can be used for multipurpose ranging from annotation and classification of individual or batches of signals and evaluation of signal properties to removing false detections and obtaining false positive rates.
A Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets.
DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
DetR DB is a database of ionizing radiation resistance determinants contains a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced ionizing radiation tolerance. The database provides search tools including taxonomy, common gene name, and BLAST. DetR DB will be a useful tool for research community by facilitating the extraction of the necessary information to help further analysis of radiation-resistant mechanisms.
Quantifying peptide isotope precision and kinetic proteomics.
Web based software platform for determining backbone amide H/D ratios.
Longitudinal resource for population neuroscience of school-age children and adolescents in China.
Interactive shiny application for differential expression analysis, data visualization, and enrichment analysis of transcriptomics data.
devfOLD: A toolbox for designing age-specific fNIRS channel placement.
DEVILS (Display Enhancement For Visual Inspection of Large Stacks) is a ImageJ-plugin for the visualization of large datasets with a high dynamic range.
Integrated multi-omics database of human and mouse early embryo.
Deleterious variants on uncovered regions in whole-exome sequencing.
Performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.
DEXOM is a Matlab library for the reconstruction and enumeration of diverse optimal context-specific metabolic networks.
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
An interactive graphical software package which can be used to quantitate isotopologues for a wide variety of metabolites detected by gas chromatography-mass spectrometry. It performs targeted automated metabolite identification, isotopologue mass and abundance determination and natural isotope abundance correction. As it is designed to detect metabolites irrespective of the extent of isotopic labelling, this software may also be used to perform targeted analysis on unlabelled data sets.
DExTER is a tool dedicated to the identification of LREs and apply it to the analysis of the genomes of different eukaryotes including P. falciparum.
Extracts three categories of textual information for a protein: titles, abstracts from literature, and function description in UniProt.
This tool identifies differentially expressed genes in RNA-seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions, but also for known conditions, for example for RNA-Seq data with two or multiple conditions. It works as an statistical model that is selected in a Bayesian framework by an EM algorithm.
The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations.
Flexible prokaryotic genome annotation pipeline for faster genome publication.
A database of food-derived bioactive peptides (DFBP), containing a total of 6276 peptide entries in 31 types from different sources.
DFCNN is a deep learning based model for fast identify protein-ligand interaction, and suitable for larget scale drug virtual screening.
Discriminative Feature-oriented Dictionary Learning
A end-to-end graph embedding-based method named DFinder to identify DFIs. DFinder combines node attribute features and topological structure features to learn the representations of drugs and food constituents.
DFLpred webserver is designed for the prediction of disordered flexible linker (DFL). The server generates numeric score for each residue in the input protein sequence that quantifies putative propensity to form a DFL.
This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.
DFTB+ is a software package for efficient approximate density functional theory based atomistic simulations. It is an implementation of the Density Functional based Tight Binding method.
A software package for the analysis of any type of reentry and focal activation of simulated, experimental or clinical data of cardiac arrhythmia.
DGAT-onco is a tool designed to detect oncogenes by comparing the functional impacts profile between cancer population and natural population.
Performs differential correlation analysis on input matrices, with multiple conditions specified by a design matrix. Contains functions to filter, process, save, visualize, and interpret differential correlations of identifier-pairs across the entire identifier space, or with respect to a particular set of identifiers (e.g., one).
Deep learning with Graphical clustering for CyTOF (DGCyTOF), is a tool used to identify cell populations. The method novelty is to distinguish the calibration cell population and the new cell population by a sequential four steps with an iteration calibration system.
Provides a list of groups of co-located and duplicated genes.
Dynamic graph attention network for predicting drug-target binding affinity.
Dissecting the Genetic Heterogeneity of complex diseases using Gene Ontology (GO), an interactive and user friendly web application.
DGIdb (The Drug Gene Interaction Database) is a research resource that can be used to search candidate genes or drugs against the known and potentially druggable genome.
DGINN is an automated and highly-flexible pipeline for the Detection of Genetic INNovations on protein-coding genes. It automatizes all the necessary preliminary steps for evolutionary analyses, including retrieval of homologs, assignment to orthology groups, codon alignment and reconstruction of gene phylogeny. Following the obtention of the alignements and corresponding phylogenies, three major genetic innovations are detected: duplication events, recombination events, and signatures of positive selection.
Python package for graph neural networks in chemistry and biology
Knowledge-graph prediction of disease-gene associations. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/adpenetrance (ROSALIND.KCL.AC.UK)
A method to identify cancer driver genes by jointing directed graph convolutional network (DGCN) and multilayer perceptron (MLP).
A knowledge database of dense granule proteins of the Apicomplexa.
dGPredictor is an automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
DGraph is a simple utility to visualize a Distance Graph in two dimensions. Targeted for Biotech use, but is entirely general.
DGRPool is a web tool providing harmonized phenotyping data from the Drosophila Genetic Reference Panel (DGRP). It enables users to study complex traits and run GWAS and PheWAS association studies.
Differential Gene Set Enrichment Analysis (DGSEA) is a R package that provides statistical approach to quantify the relative enrichment of two gene sets.
DGT is a operator splitting method for the Euler Elastica model for image smoothing.
The Database of Genomic Variants archive ((DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species.
DGW is an open source software package for simultaneous alignment and clustering of multiple epigenomic marks.
Provides analysis of the hierarchy of protein domain structures. It detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.
An interpretable model for hypertension and hyperlipidemia prediction based on EMR data.
Identification of hub genes in a gene co-expression network from gene expression data. The differential network analysis for two contrasting conditions leads to the identification of various types of hubs like Housekeeping, Unique to stress (Disease) and Unique to control (Normal) hub genes.
Improving Dental-Based Human Identification Using Generative Adversarial Networks
DHRLS is one novel computational method, which utilizes Multiple kernels learning and Hypergraph Regularized Least Squares to predict the association between diseases and genes.
Program that fine-maps qualitative traits by linkage disequilibrium.
Accurate prediction of dihydrouridine sites using position and composition variant features on diverse classifiers.
DI2 (Distribution Discretizer) a prior-free and multi-item discretization of biological data and its applications.
Library-free framework for comprehensive peptide identification from data-independent acquisition data.
DIADpredictor: in silico prediction for drug-induced autoimmune diseases (DIAD) with machine learning.
A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment.
A proteomics hub for pinpointing discriminative spectral clusters.
DiagnoTop is a computational pipeline for discriminating bacterial pathogens without database search.
Shiny application and R package to process the output from DIA-NN. It returns the quantification of either the precursors, the peptides, the proteins, or the genes thanks to the MaxLFQ algorithm. In addition, the latest version provides the Top3 and iBAQ quantification and the number of peptides used for the quantification. In the end, DIAgui produces ready-to-interpret files from the results of DIA mass spectrometry analysis and provides visualization and statistical tools that can be used in a user-friendly way.
A web server that provides structural alignment of RNA without the help of a reference genome. It takes into account nucleotide sequence similarity, dihedral angle similarity and nucleotide base-pairing similarity.
DIALib is an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides. DIALib will help enable DIA glycoproteomics as a complementary analytical approach to DDA glycoproteomics.
Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.
DIALIGN-TX is an update to DIALIGN. It combines the greedy heuristic method of DIALIGN with a traditional progressive method.
Diffraction Integration for Advanced Light Source.
DIAMIN is a high-level software library to facilitate the development of distributed applications for the efficient analysis of large-scale molecular interaction networks.
Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.
Efficient algorithm for variant detection that compares DNA sequences directly to one another, without aligning them to the reference genome. When used to analyze exome sequences from family trios, or to compare normal and diseased samples from the same individual, this method produces a dramatically smaller list of candidate mutations than previous methods, without losing sensitivity to detect the true cause of a genetic disease.
DIANA is a DICOM imaging informatics platform that can be attached to the clinical systems with a very small footprint, and then tuned to support a range of tasks from high-resolution image archival to cohort discovery to radiation dose monitoring. It provides DICOM services, image data indexing, REST endpoints for scripting, and user access control through an amalgamation of free and free and open source (FOSS) systems.
Incorporates an extensive collection of miRNA:lncRNA interactions. The database includes more than 70,000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm.
DIANA-mAP is an automated microRNA analysis pipeline with an emphasis on pre-processing.
Dedicated to miRNA target prediction and functional analysis and is widely used since 2009 from the scientific community. It predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser. Updates include sophisticated workflows.
Performs a combined Differential expression analysis(DEA) of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.
Provides accurate cell-line-specific miRNA gene transcription start sites, coupled with genome-wide maps of transcription factor binding sites in order to unveil the mechanisms of miRNA transcription regulation. The database schema and web interface facilitates user interaction, provides advanced queries and innate connection with other DIANA resources for miRNA target identification and pathway analysis.
Dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. It support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data.
Standardization of drug names in the FDA adverse event reporting system.
Web-based computational tool that identifies potentially altered molecular pathways by the expression of a single or multiple microRNAs.
DIANE (Dashboard for theInference and Analysis of Networks from Expression data) is a web application for inferring and analyzing gene regulatory networks from multi-factorial expression data.
DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.
diaPASEF is an appproch for parallel accumulation-serial fragmentation combined with data-independent acquisition.
DIAproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independent (DIA) proteomics data.
Database driven web application that is designed to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes.
diArk - a resource for eukaryotic genome research
DiaThor is a R package for computing diatom metrics and biotic indices. DiaThor calculates several diatom-based indices commonly used for water quality assesment, directly from your species' data.
Diatoms.org represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology.
Diatools is a software package for analyzing mass-spectrometer data acquired using data independent acquisition (DIA) mode.
Infer complex population histories from whole genome sequencing data.
DICE is a Monte Carlo molecular simulation software. It is a Monte Carlo code for molecular simulation including the configurational bias Monte Carlo method.
Deep learning-based cell segmentation for imaging mass cytometry. Dice-XMBD1 is marker agnostic and can perform cell segmentation for multiplexed images of different channel configurations without modification. This project contains code, a generic model, and example test datasets for single cell segmentaion of multiplexed imaging data.
Performs cluster analysis using an ensemble clustering framework. Results from a diverse set of algorithms are pooled together using methods such as majority voting, K-Modes, LinkCluE, and CSPA.
Diiffuse Cluster Estimation and Regression (DiCER) is a tool for Identifying and removing widespread signal deflections from fMRI data.
DichroMatch webserver identifies proteins with similar spectral characteristics as a way to detect possible structurally and functionally related proteins and homologues. Users input a query spectrum which is searched against the protein circular dichromism data bank or a user provided data set.
A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.
DICODerma is a tool and a preliminary standard to reconcile the best of both worlds - the simplicity of consumer image tools and the DICOM and PACS-based enterprise imaging infrastructure.
DiCoExpress is a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models.
Apply 3D UNet (Semantic Segmentation) into medical CT image without wasting time for labeling.
Use DICOM RT for 3D Semantic Segmentation of Medical images
This module provides a command line tool to validate DICOM SEG files against predefined requirements specified in an Excel file. It contains components for finding relevant DICOM files, loading and parsing validation requests and applying validation rules. The main validation process checks each DICOM file for compliance with the Type 1, 1C, 2, 2C and 3 attributes specified in the requirements file. A detailed report is generated highlighting issues such as missing, invalid or conditionally required attributes, including file paths and affected DICOM tags. The tool is designed to ensure data integrity and compliance with DICOM standards.
MATLAB toolbox for reading one or more DICOM files from a directory.
This tool can be used to remove facial features ("defacing") from DICOM images. It may be used 1) only for facial removing, or 2) for a complete import and anonymization using DICOM transfer. Defaced images needs to be manually quality checked, and this is done through a web interface to a local server supplied with the Docker containers
The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files. Status: Deployed
DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
Detects duplicate or visually similar DICOM series using a tiered approach that combines metadata analysis, hash-based comparison, and pixel-level similarity metrics. Ideal for: 1. High-level series comparison and classification, and 2. Detecting duplicates even after post-processing (e.g., denoising, filtering). For scenarios requiring strict, image-level deduplication based on pixel content, fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]
Scans the DICOM files of a defined directory at the series level, and produces as output either 1/one single csv file containing all preselected DICOM tags for each detected series; 2/ one single csv file only containing the patientID and the corresponding StudyUIDs.
A Python Implementation for Converting Whole-Slide Images to Digital Imaging and Communications in Medicine Compliant Files.
DicomAnnotator is a configurable software program for efficient DICOM image annotation.
This repository provides tools for segmentation files conversion in DicomSEG, with a primary focus on: DICOM RTSTRUCT to DICOM SEG: A Python script (rtstruct/rtstruct2dcmseg.py) converts DICOM Radiotherapy Structure Set (RTSTRUCT) files, along with their referenced DICOM image series, into DICOM Segmentation (SEG) objects. It can also optionally convert the individual Regions of Interest (ROIs) defined in the RTSTRUCT into separate NIfTI (.nii.gz) files. Nifti Conversions via dcmqi and Custom Scripts: The Docker image built from this repository also includes command-line tools from dcmqi (DICOM Quantitative Imaging Toolkit) and custom Python scripts for various conversions, such as: ITK image formats (NIfTI, NRRD) to/from DICOM SEG. DICOM series to NIfTI. DICOM SEG to NIfTI (custom alternative).
Library for extracting and converting DICOM file metadata for persistence and indexing in a SQL database
Database for the biology and genomics of the social amoeba Dictyostelium discoideum.
Center for Genetic Medicine, Northwestern University
Database for the biology and genomics of the social amoeba Dictyostelium discoideum. It provides well integrated, high quality data and tools for Dictyostelium discoideum and related species. It houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a reference genome in the Amoebozoa clade.
An interactive, web-based exploratory data analytics application providing access to over 1,000 Dictyostelium gene expression experiments from Baylor College of Medicine.
Neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Defocus Image Deblurring Network With Defocus Map Estimation as Auxiliary Task.
Digenic Diseases Database (DiDA) provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.
dietaryindex is an R package for standardizing dietary pattern analysis in epidemiological and clinical studies. It calculates multiple dietary indexes and provides 1-step functions for common datasets and tools.
An Optimization Method for Convolutional Neural Networks. Abstract Stochastic Gradient Decent (SGD) is one of the core techniques behind the success of deep neural networks
Open-source toolbox for calculating and visualizing differential networks.
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions.
diffBUM-HMM is a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data.
A differential peak analysis method for high throughput sequencing data with biological replicates based on limma.
Identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs).
An R package to analyze and visualize differential correlations in biological networks. This package can explore differential correlations between 2 conditions in the context of post-genomics data types, namely transcriptomics and metabolomics. DiffCorr is simple to use in calculating differential correlations and is suitable for the first step towards inferring causal relationships and detecting biomarker candidates.
Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on (i) high-resolution clustering and (ii) empirical Bayes moderated tests adapted from transcriptomics.
DiffeoRaptor, a diffeomorphic inter-modal/contrast image registration algorithm based on RaPTOR and geodesic shooting in bandlimited space.
End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images.
Extraction of differential features on 3D Images.
RNA-seq pipeline for differential gene expression analysis (paired-end, pooled samples, animals). Illumina RNA Sequencing differential expression analysis pipeline between two collections of eukaryote samples. The collections represents the two conditions being compared, and the datasets in each collection is defined by the user.
The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk
DifferentialRegulation is a Bayesian hierarchical method for detecting differentially regulated genes between experimental groups, leveraging spliced and unspliced mRNA abundances obtained from single-cell RNA-sequencing data. It is distributed as an R package within the Bioconductor project.
DiffGR is a statistical method for detecting differential genomic regions at TAD level between two Hi-C contact maps. Briefly, DiffGR utilizes the stratum-adjusted correlation coefficient (SCC), which can effectively eliminate the genomic-distance effect in Hi-C data, to measure the similarity of local genomic regions between two contact matrices, and then applies a nonparametric permutation test on those SCC values to detect genomic regions.
Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
Easy-to-use tool to visualize motif differences.
A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.
A collection of functions to detect gene probes with different means or variances between two groups in (epi)-genomic data analysis, including classical F test and Levene's test for equal variance, likelihood ratio test for equal mean and equal variance.
This software is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. It takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.
An RNA-Seq data driven method for differential expression analysis using changepoint detection.
Compare and report features of two similar sequences.
Find differences between nearly identical sequences.
Graph centrality method to detect essential proteins of a protein-protein interaction network.
A Cytoscape application for network propagation for finding new genes that are most relevant to a disease state.
Extracts diffusion-related maps (e.g., ADC, IVIM, Kurtosis) from DWI sequences to evaluate microstructural properties of tissues, commonly used in oncology and neurology.
Diffusion maps extraction (EUCAIM-SW-057_T-02-01-005)
DiffusionLab is software designed to extract valuable information about the motion from single-molecule or particle trajectories obtained with e.g. super-resolution localization microscopy.
Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation and benchmarking.
The diffUTR R package streamlines differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3' UTR usage analysis.
Distance field representation to resolve motion artifacts in computed tomography
Simple but flexible in silico digester of protein sequences in the FASTA format. It allows for almost any enzyme to be simulated, including "MS/MS" enzymes to generate CID or ECD/ETD fragments.
Versatile and interactive visualization of sequence alignment for comparative genomics.
A web tool for in vitro identification of potential nuclease (e.g. CRISPR-Cas method) off-target sites from whole-genome sequencing data.
DiGePred is a tool for identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible.
DIGEST is a (“validation of disease and gene sets, clusterings or subnetworks”), is a Python-based validation tool available as a webinterface, as a standalone package, or over a REST API.
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Domain Interaction Graph Guided ExploreR (DIGGER) integrates protein-protein interactions and domain-domain interactions into a joint graph and maps interacting residues to exons. DIGGER allows the users to query exons or isoforms individually or as a set to visually explore their interactions.
Prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria.
Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm.
Analysis, visualisation and data mining of POCT experiments. Simultaneous detection and quantification of DNA and protein biomarkers in spectrum of cardiovascular diseases in a microfluidic microbead chip. digilogger is available as the latest development version of the code by using the devtools R package.
digIS is a pipeline command-line tool for detecting distant and putative novel insertion sequences in prokaryotic genomes. As an input, digIS accepts contigs in FASTA format. Optionally, the user can provide a GenBank annotation file for a given input sequence(s). This annotation is later used to improve the classification of identified IS elements.
A database of immunoglobulin variable domain sequences and related search and modelling tools.
How DNA can be used as a digital storage device in theory
Digital encoding and decoding in DNA sequences
MATLAB script for enhancement of digital mammography images.
DIGS is a database-integrated genome screening approach used to explore the dark genome and map vertebrate virus fossil records. It identifies endogenous viral elements (EVEs) within vertebrate genomes using a similarity search-based pipeline and relational database management system.
DIGS (Database-Integrated Genome Screening)
Web server for understanding the association between diseases and genes. This cancer version searches Medline abstracts for evidence sentences describing the genes involved in the development of cancer through biological events.
Diinamic is a method for clustering analysis in single-molecule localization microscopy (SMLM) that combines different density-based analyses and optional thresholding. It facilitates the detection of clusters and nanodomains in SMLM data.
Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.
Matthew Betts (problems with the server)
Rob Russell (questions, comments or bug reports)
DILS is a tool made to infer demographic histories with linked selection from fasta sequencing datasets. DILS is a DNA sequence analysis workflow to study the demographic history of sampled populations or species by using Approximate Bayesian Computations.
Functional and physical interactions among conserved protein-domains, including experimental data and computational predictions.
Data-Driven Selection of an Imputation Algorithm.
DIMEDR (Disparate Metabolomics Data Reassembler) is a algorithm for agglomerating incongruent LC-MS metabolomics datasets. (DIMEDR) attempts to bridge the inconsistencies between incongruent LC-MS metabolomics datasets of the same biological sample type. A single “primary” dataset is postprocessed via traditional means of peak identification, alignment, and grouping. DIMEDR utilizes this primary dataset as a progenitor template by which data from subsequent disparate datasets are reassembled and integrated into a unified framework that maximizes spectral feature similarity across all samples. This is accomplished by a novel procedure for universal retention time correction and comparison via identification of ubiquitous features in the initial primary dataset, which are subsequently utilized as endogenous internal standards during integration.
A long-read, single-molecule method for mapping protein-DNA interactions genome wide.
Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.
Dimont is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.
A bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.
Deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology.
DiMSum is an error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies.
DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.
The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences.
Differential Network Analysis in R. Reveals hidden patterns of plant signaling dynamics. DiNAR presents three main functions: dynamic visualisation of complex multi-conditional experiments, identification of strong differential interactions, and recall of latent effects that are present in multi-conditional experiments. Furthermore, it can manage other background knowledge networks in combination with experimental dataset of interest such as transcriptomics, proteomics, metabolomics.
DINAX is a comprehensive database of inherited ataxias.
A new AutoDock-based protocol for docking large ligands.
A webserver for ensemble docking with flexible SARS-CoV-2 proteins.
Calls small indels from short-read sequence data.
Tool based on Supervised analysis enables the prediction of potential interactions between drug molecules and target proteins, based on drug data and omics-scale protein data. The users can use any data as the input, as long as they are represented as the tab-delimited matrices or profiles.
De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters.
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. Dino is an R package for the normalization of single-cell RNA-seq data using a flexible mixture of negative binomials model of expression.
DINTD is a tool for the detection and inference of tandem duplications from short sequencing reads.
Functional annotation of genomic and proteomic data.
This tool allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.
DiPCell is a webserver for the predicting inhibitory activity of unknown molecules and designing their analogs against pancreatic cancer cell lines.
DipCheck is a validation tool for the evaluation of protein backbone geometry, developed by Joana Pereira and Victor Lamzin at the EMBL Hamburg. The tool uses a Euclidian 3D space (DipSpace) of the orthogonal descriptors of the geometry of a 5-atom dipeptide unit: CAi-1-Oi-1-CAi-Oi-CAi+1. The DipSpace database contains 1,024,000 data points derived from well-refined structures deposited in the PDB.
An Open-Source Pipeline to Generate Ensembles of Disordered Segments Using Neighbor-Dependent Backbone Preferences.
R package for implementing the Depth Importance in Precision Medicine (DIPM) tree and forest based method
The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
DIPPER is a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics.
Database which is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.
Dinucleotide property database (DiProDB)
DiProGB is a genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and –, as well as for the double strand.
Direction-projection-permutation (DiProPerm) is an R Package for two-sample hypothesis test for comparing two high-dimensional distributions.
Python package for searching di-PWM motifs.
Discriminative, Restorative, and Adversarial Learning for Self-supervised Medical Image Analysis.
A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.
directLFQ is an open-source Python package for quantifying protein intensities based on peptide intensities or fragment-ion intensities measured with from Mass Spectrometry-based proteomics.
R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view.
A database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data.
Disambiguating two species in next generation sequencing data from grafted samples. Operates on DNA or RNA-seq alignments to the two species and separates the components at very high sensitivity and specificity.
DisBalance is a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data.
DISC is a tool for highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.
Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins.
DIscBIO is a user-friendly pipeline for biomarker discovery in single-cell transcriptomics. An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them.
DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.
Disco Cross Docking Benchmark server for automated pose and ranking prediction of ligand binding.
Sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data.
DISCO+QR, a new approach to rooting species trees that first uses DISCO to address GDL and then uses QR to perform rooting in the presence of incomplete lineage sorting.
Framework for using the physical constraints imposed by microfluidic traps, the shape based morphological constraints of budding yeast and temporal information about cell growth and motion to allow tracking and segmentation of cells in microfluidic devices.
Disorder Consensus-based Predictor (disCoP) is a web tool implementing the consensus-based method designed for in-silico prediction of per-residue protein disorder propensities.
Determine differential correlation of molecular feature pairs from -omics data using mixture models.
This software is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
Prediction of discontinuous B cell epitopes from protein three dimensional structures.
DiscoTope-3.0 is a B-cell epitope prediction tool that utilizes inverse folding latent representations and a positive-unlabelled learning strategy to predict epitopes from solved and predicted protein structures. The tool is accessible via a web server and downloadable package and facilitates large-scale prediction across millions of proteins.
DISCount Pytorch implementation for seed and radicle detection using the You-Only-Look-Once object detector.
Discount is a Spark-based tool for k-mer counting, and for analysis of minimizer orderings. It is able to analyse large metagenomic-scale datasets while having a small memory footprint.
Variant caller designed for state-of-the-art data. It can call variants on a region by region basis, potentially tiling an entire large genome. Its variant calling is under active development and transitioning to VCF.
Genome assembler designed for state-of-the-art data. It can generate de novo assemblies for both large and small genomes. It currently does not call variants.
DISCOVER is a discriminative, conditional random field (CRF) based model used for supervised motif discovery on metazoan genomes.
DisCovER is a tool for distance- and orientation-based covariational threading for weakly homologous proteins.
Cerebrovascular system is a complex network of vessels that supply vital nutrients and oxygen to the brain. Like any other body part it is vulnerable to bleeding, infection, blood clot and other forms of damage. These damages in brain functioning require brain surgery. The main problem with such surgeries on brain blood vessels is that in most cases, place of operation cannot be accessed directly. Therefore alternative entry points and paths have to be discovered. The proposed system is designed to help doctors/surgeons find the shortest distance between two points in brain blood vessel system, using image processing and path finding techniques over MRA images.
Discovering Shortest Path between Points in Cerebrovascular System
Numerous methods for expression and promoter analysis.
DiscoverySpace is a tool for gene expression analyses and biological discovery.
Coarse-Grained Molecular Dynamics simulation package.
Institute for Research in Biomedicine Barcelona
To discrete continuous data, CACC is a promising discretization scheme proposed in 2008
Discretization algorithms: Class-Attribute Contingency Coefficient
Discriminative HMMs (Hidden Markov models) predicts localizations using motifs that are present in a compartment but absent in other, nearby, compartments by utilizing an hierarchical structure that mimics the protein sorting mechanism.
Discovery of Markers. Identify conserved regions and design primers based on multiple sequence alignments of putative orthologous sequences from whole‐genome or whole‐transcriptome data.
Discover discriminative sequence motifs.
A complete GUI for disease detection in animals using color channel extraction.
Classification, content and workflow expansion. Each import consists of two files: a *_terms.txt file and a *_import.owl file. The .txt file is used to generate the .owl import module using ROBOT extract. This browser does not support visualization of term relationships on the Disease Ontology website. Please use Chrome, Safari or Firefox when using the Disease Ontology website to unlock visualization capabaility. Open the corresponding .txt file and do a text search to ensure the ID has not yet been added. Save the file, and then in terminal, run the desired make command (see below). Name Synonym Definition Subset DOID Alternate ID Xrefs DO_AGR_slim DO_cancer_slim DO_FlyBase_slim DO_GXD_slim DO_IEDB_slim DO_MGI_slim DO_rare_slim NCIthesaurus TopNodes_DOcancerslim.
The Disease Ontology (DO) has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.
Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scattered along multiple databases.
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.
Zhou Lab, University of Southern California
The Human Disease Methylation Database Version 3.0 is a web-based resource that focuses on the abnormal methylome of human diseases.
DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.
A computational tool for prediction of disordered/unstructured regions within a protein sequence.
Computational tool for prediction of disordered/unstructured regions within a protein sequence.
DisEnrich—the database of human proteome IDRs that are significantly enriched in particular amino acids.
A visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers.
DISGENET is a comprehensive knowledge database integrating and standardizing information on disease-associated genes and variants. It covers the full spectrum of human diseases as well as normal and abnormal traits, including adverse events of drugs. Due to the adherence to FAIR data principles, DISGENET is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D. DISGENET simplifies the process of accessing genetic evidence for diseases and therefore can streamline the incorporation of this type of evidence in research, drug R&D and precision medicine applications. DISGENET is available for free for academic users. License fees are applicable for the commercial use of DISGENET. Learn more here https://www.disgenet.com/plans DISGENET is the new evolution of the community-recognized DisGeNET platform, cited by over 6000 publications and one of the ELIXIR Recommended Interoperability Resources.
Atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics.
Fast and robust method to identify ligand-receptor interactions at subunit level from single-cell RNA-sequencing data.
Prediction of cysteine connectivity patterns in a protein chain.
DiSMed is a de-identification methodology for Spanish medical texts based on Named Entity Recognition (NER). It is based on spaCy and partially based on the networks designed by Gillaume Genthial implemented on Tensorflow 1. DiSMed includes both the Python code and the curated dataset, available under request under a research use agreement.
DISMISS is a new software package that detects strand-associated DNA methylation from existing MeDIP-Seq analyses
The DiSNEP package implemented the Disease-Specific Network Enhancement Prioritization (DiSNEP) framework. The DiSNEP framework first enhances a comprehensive gene network specifically for a disease through a diffusion process on a gene-gene similarity matrix derived from a disease omics data. The enhanced disease-specific gene network thus better reflects true gene interactions for the disease and may improve prioritizing disease-associated genes subsequently.
DISNET is a framework for extracting phenotypic disease information from public sources.
Prediction of protein intrinsic disorder and its functions using graph-based interaction protein language model.
DisoFun is a tool for differentiating isoform functions with collaborative matrix factorization. Description :This page includes the codes of DisoFun which are implemented and tested on Matlab2014a version by Mr. Wang (Keyao Wang, Email: l: keyaowang@email.swu.edu.cn) an) and free for academic usage. You can run it at your own disk. For other purposes, please contact Dr. Yu (Guoxian Yu, Email: l: gxyu@swu.edu.cn). I). If you have any problem on using these codes, just contact us via Email.
Accurate prediction of disordered lipid binding residues in protein sequences with deep recurrent networks and transfer learning.
DisoMine is a tool that predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding.
DISOPRED3 represents the latest release of our successful machine-learning based approach to the detection of intrinsically disordered regions.
DisoRDPbind is a web predictor of disorder-mediated RNA, DNA and protein binding regions. DisoRDPbind predicts the RNA-, DNA-, and protein-binding residues located in the intrinsically disordered regions.
Disp R-CNN is a tool for shape prior guided instance disparity estimation for 3D object detection.
An integrative database of diseases related variations in liquid-liquid phase separation proteins.
DispHred is server to predict pH-dependent order-disorder transitions in intrinsically disordered proteins. DispHred uses a sliding window to calculate hydrophobicity and net charge.
DispHScan is a multi-sequence web tool for predicting protein disorder as a function of pH and spot folding transitions in large datasets.
DisplayFam browses protein families via the “Rich Family Description” format.
DisPredict is a predictor of disorder residues in protein. It takes protein sequence (standard FASTA format) as input and outputs per residue binary annotation (disorder or order) along with two real values corresponding to probability of that residue being disorder and order.
Dispredict3.0 allows the prediction of intrinsically disordered proteins with protein language model.
Database of protein disorder. It is a community resource annotating protein sequences for intrinsically disordered regions from the literature.
DISQOVER is a data integration platform for public, licensed and internal data. The Data Ingestion Engine enables transforming data into Linked Data which can be searched, navigated and analysed via the user interface and the API. The publicly accessible DISQOVER platform contains 140+ public data sources in life sciences and related domains.
DISSCO is a JAVA application for direct imputation of summary statistics allowing for covariates.
Dissect (DIScovery of Structural Alteration Event Containing Transcripts) is a transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.
Accurate estimation of microbial sequence diversity with Distanced | Distanced is a bioinformatics tool that estimates diversity of microbes. Specifically, it estimates the diversity of ribosomal DNA sequences within microbial communities. Estimating diversity of microbes is a challenge because errors in sequence create false sequences and inflate diversity. Distanced overcomes this problem by correcting values of mean pairwise distance, a measure of within-sample diversity, for the expected increase after sequencing | Distanced requires a set a DNA sequence reads in fastq format. A set of reference sequences in fasta format is optional. If reference sequences are provided, Distanced will report the actual diversity of the DNA sequences, providing a check on accuracy
Prediction of distance constraints between amino acids in proteins from the amino acid sequence.
distAngsd is a software to simulate and infer phylogenetic relationships between two individuals, in which two novel methods (i.e., geno and nuc) are proposed.
Prediction of the quality of single protein model using deep learning and residue-residue distance maps
DISTEVAL is a web server for evaluating predicted protein distances.
Diseases and traits in linkage disequilibrium (LD) blocks. Data from HapMap Project is used to partition chromosomal regions which are associated with a disease into LD blocks. This allows researchers to answer the question of which SNPs associated with diseases are in LD with a gene of interest?
Data integration system to identify links in expression regulation.
A distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts.
distinct is a general method for differential analysis of full distributions that is well suited to applications on single-cell data, such as single-cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. distinct is based on a hierarchical non-parametric permutation approach and, by comparing empirical cumulative distribution functions (ECDFs), identifies both differential patterns involving changes in the mean as well as more subtle variations that do not involve the mean.
A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster.
Create a distance matrix from a multiple sequence alignment.
R package for interactive checking of dimension-reduction visualizations.
DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.
European FP7 e-Infrastructure grant, WeNMR, grant no. 261572
European H2020 e-Infrastructure grant, EGI-Engage, grant no. 654142
European H2020 e-Infrastructure grant, INDICO-DataCloud, grant no. 653549
European H2020 e-Infrastructure grant, West-Life VRE, grant no. 675858
Netherlands Organization for Scientific Research (NWO) , TOP-PUNT grant no. 718.015.001
Netherlands Organization for Scientific Research (NWO), ECHO grant no.711.011.009
Netherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442
Visualize and quantify the information content of distance restraints between macromolecular complexes. A full and systematic 6 dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. It outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space.
DiTA is a free database indexing studies of diagnostic test accuracy related to physiotherapy practice, designed for clinicians, researchers, and patients. It provides citation details, abstracts, and links to full-text resources.
DiTA (Diagnostic Test Accuracy database)
Differential Taxa Abundance including Similarity Correction.
An algorithm for Defining IntraTumor Heterogeneity based on EntRopy.
DiTing is designed to determine the relative abundance of metabolic and biogeochemical functional pathways in a set of given metagenomic/metatranscriptomic data.
dittoSeq is universal, user friendly, single-cell and bulk RNA sequencing visualization R package that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
A platform dedicated to the visualization and analysis of diurnal plant co-expression and co-function networks.
diurnal.plant.tools is a database containing diurnal gene expression profiles from 17 members of the Archaeplastida lineage, expanded to include four agriculturally significant crop species and Marchantia. It facilitates cross-species comparisons to better understand the plant circadian clock.
DIVA is a tool for natural navigation inside 3D images using virtual reality.
DivBiclust is an effective biclustering-based framework for identifying cell subpopulations from scRNA-seq data.
DivBrowse is a web application for interactive visualization and exploratory analysis of genomic diversity data stored in Variant Call Format (VCF) files of any size. By seamlessly combining BLAST as an entry point together with interactive data analysis features such as principal component analysis in one graphical user interface, DivBrowse provides a novel and unique set of exploratory data analysis capabilities for genomic biodiversity datasets. The capability to integrate DivBrowse into existing web applications supports interoperability between different web applications. Built-in interactive computation of principal component analysis allows users to perform ad-hoc analysis of the population structure based on specific genetic elements such as genes and exons. Data interoperability is supported by the ability to export genomic diversity data in VCF and General Feature Format (GFF3) files.
A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons.
The progressive web application DiversityNaviKey (DNK) is a generic tool primarily designed for any kind of diagnosis and interactive identification of organisms or other items as well as item groups which are part of or related to biodiversity, geodiversity or environmental research, by means of a set of pre-defined characteristics. It allows for sophisticated selection based on highly structured data sources (datasets) with descriptive data (trait data with descriptors, descriptor categorical states, descriptor values). The browser-based tool is optimized to build and run determination keys based on the consecutive selection of descriptors, descriptor states and values during the identification process. Selection criteria might be predefined by individual user or changed during the identification process.
A scalable stepwise algorithm with local data-driven feature space adaptation for segmenting high-dimensional datasets.
DiVil is a javascript based tool that produces interactive graphs
Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. DIVIS, an easy-to-use, extensible, and customisable cancer genome sequencing analysis platform which including the functions of variant Detection, Interpretation, Visualisation, and one can use DIVIS as an infrastructure of genome analysis.
DIYABC is an inference software implementing Approximate Bayesian Computation (ABC) combined with supervised machine learning based on Random Forests (RF), for model choice and parameter inference in the context of population genetics analysis.
DiZyme open access resource for quantitative prediction of nanozyme catalytic activity
An open-source modeling platform for computational chemistry and materials science with a Python interpreter.
This package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.
Disease Knowledge Transfer (DKT) is a technique for transferring biomarker information between related neurodegenerative diseases. DKT infers robust multimodal biomarker trajectories in rare neurodegenerative diseases even when only limited, unimodal data is available, by transferring information from larger multimodal datasets from common neurodegenerative diseases.
DL-m6A: Identification of N6-methyladenosine Sites in Mammals using deep learning based on different encoding schemes
A hybrid DL-ML approach that uses a deep neural network for extracting features and a non-DL classifier for classification tasks.
DL4papers is a deep learning approach for the automatic interpretation of scientific articles. DL4papers is a method based on deep learning that is capable of analyzing and interpreting papers in order to automatically extract relevant relations from the published literature, and between specific keywords. DL4papers receives as input a set of desired keywords, and it returns a ranked list of papers that contain meaningful associations between them.
Deep Local Analysis evaluates protein docking conformations with Locally oriented Cubes.
DLAB-Deep learning methods for structure-based virtual screening of antibodies.
Deep Learning Application Engine (DLAE). DLAE is a software framework and application that enables users to design, train, validate, and coherently encapsulate and deploy deep learning (DL) models in medical imaging, while hiding programmatic implementation details.
dLagM is a R package for distributed lag models and autoregressive distributed lag (ARDL) bounds testing to explore the short and long-run relationships between dependent and independent time series. Distributed lag models constitute a large class of time series regression models including the ARDL models used for cointegration analysis.
DLBEpitope is a deep learning-based model for linear B-cell epitope prediction.
A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring. DLEAMSE (based on Siamese Network) is trained and tested with a larger dataset from PRIDE Cluster. The repository stores the encoder and embedder scripts of DLEAMSE to encode and embed spectra.
A web application for building deep learning models in biological research.
A multi-module deep learning framework for prediction of S-sulfinylation sites in proteins.
Deep Learning and Feature Fuse-based ACP prediction (DLFF-ACP). Pprediction of ACPs based on deep learning and multi-view features fusion.
DLocalMotif is a discriminitive motif discovery web service specifically designed to discover local motifs in protein sequences that are aligned relative to a defined sequence landmark. It uses three discriminitive scoring features, motif spatial confinement (MSC), motif over-representation (MOR) and motif relative entropy (MRE). These features establish if a motif is positioned in a constrained sequence interval in positive data set and absent in negative data set.
A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.
DLPAlign is a a deep learning-based progressive alignment for multiple protein sequences.
DLpTCR a computational framework that integrated three deep-learning models for predicting the likelihood of the interaction between TCR and peptide presented by MHC molecules. DLpTCR obtained excellent performance on independent testing dataset, thereby allowing robust identification of immunogenic T cell epitopes.
Dynamic Learning Rate for Test-time Adaptation on Cross-domain Medical Images.
Imports Gatan .DM3 format files with tags (images, spectra, & spectral images) into a MATLAB struct.
DM3Loc is a web tool for multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism. DM3Loc is a novel Deep-learning framework with multi-head self-attention for multi-label mRNA subcellular localization prediction and analyses, which provide prediciton for six subcellular compartments, including nucleus, exosome, cytoplasm, ribosome, membrane, and endoplasmic reticulum.
Dmatch is a method that leverages an external expression atlas of human primary cells and kernel density matching to align multiple scRNA-seq experiments for downstream biological analysis. Dmatch facilitates alignment of scRNA-seq datasets with cell-types that may overlap only partially, and thus allows integration of multiple distinct scRNA-seq experiments to extract biological insights.
It is a novel profiling tool for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data.
dmdScheme is an R package for creating a template domain specific scheme. It contains the basic functionality needed for all metadata schemes based on the dmdScheme.
Tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD.
Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing.
DMEAS is a user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.
DMF (Dragon Motif Finder) is a simple ab-initio motif finding tool that allows the processing of relatively large sequence sets in a relatively short amount of time on the web.
DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular force field models.
Predicting protein disorder molecular functions based on protein cubic language model.
Deep Multimodal Graph-Based Network for Survival Prediction from Highly Multiplexed Images and Patient Variables.
Predicting isoform function using deep multi-instance learning.
DMINDA: An integrated web server for DNA motif identification and analyses.
A Deep Learning Method for MiRNA/IsomiR Target Detection.
DMKPred is a SVM based webserver for the prediction of binding of chemical molecules with specific kinases. Here user can paste or upload the molecular descriptors off chemical molecules and our prediction method calculate the binding of these chemical with protein kinases.
DMLDA-LocLIFT is a tool for identification of multi-label protein subcellular localization using direct multi-label linear discriminant analysis dimensionality reduction and Label-specIfic FeaTures classifier.
A dual-stream marker-guided network (DMNet) for segmentation of touching cells in microscopy videos of many cell types.
Densely Connected Multi-scale Pyramid Network (DMPNet) for count estimation and the generation of high-quality density maps.
DMPortal is offered by BioData.pt, the Portuguese biological data infrastructure and national node of ELIXIR. The portal aims to support the national life sciences research community by enabling FAIR research practices. DMPortal is open to all life sciences fields, but has traditionally been more focused in supporting research in COVID-19, human health, and plant sciences.
DMPortal - BioData.pt Data Management Portal
Dmppred: Prediction of T1DM associated peptides
Automated mathematical model construction of large-scale metabolic systems.
Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.
De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.
DMRdb is a disease-centric Mendelian randomization database that systematically assesses causal relationships between diseases and genes, proteins, CpG sites, metabolites, and other diseases. The database aggregates high-quality disease GWAS data and results from MR analyses, providing a valuable resource for advancing understanding of disease mechanisms and identifying potential therapeutic targets.
Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data.
This tool compares n>=2 unique samples regarding their methylation profile in either single CpG locus or region based analysis, defining regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional classes and differential methylation is evaluated by comparing the methylation values within each region between individual samples.
This software fuses diffusion MRI and microscopy data to reconstruct 3D brain connectivity, overcoming limitations of each technique individually. The method generates microscopy-informed tractography for whole-brain coverage and improved accuracy.
DMRichR is an R package designed for analyzing differentially methylated regions (DMRs) in epigenetic research, particularly useful for non-model organisms. It leverages existing algorithms (dmrseq, bsseq) and provides tools for data processing, annotation, and visualization.
A scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features.
It detects differentially methylated regions, using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund solution, ii) an important sampling as suggested by Zhang, and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.
Scan the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available.
dms-view is an interactive visualization tool for deep mutational scanning.
dms_tools2 is a software package for analyzing deep mutational scanning data. It is tailored to analyze libraries created using comprehensive codon mutagenesis of protein-coding genes
A Package for Analysing Multivariate Mixed Models.
Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework.
DN3 (Deep Neural Networks for Neuro-physiology) is an open-source Python library for large-scale raw neurophysiology data assimilation for more flexible and standardized deep learning.
a framework to compute a consolidated metric for benchmarking quality of de novo assemblies | de novo Assembly Quality Evaluation Tool (dnAQET) | The de novo Assembly Quality Evaluation Tool is a framework designed to evaulate the contigs of a de novo assembly against a trusted reference genome. It generates a quality score for each contig based on the misassemblies observed in the alignments and the total alignment percentage of that contig | The de novo Assembly Quality Evaluation Tool (dnAQET) is a framework designed to evaluate a de novo assembly along with its scaffolds/contigs against a trusted reference genome. It first generates a quality score for each scaffold of an assembly based on its length, the misassemblies observed in the alignments and the total alignment percentage of a scaffold. Based on the quality scores assigned to the contigs/scaffolds, it computes an overall quality score for the whole assembly | An official website of the United States government | U S
DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.
New method to construct phylo tree using Chaos Game Representation, discrete Fourier transform
Numerical encoding of DNA sequences by Chaos Game Representation
DNA Features Viewer is a Python library to visualize DNA features. Dna Features Viewer automatically produce simple and clear plots even for sequences with many overlapping features and long labels. The libray plays well with Matplotlib and Biopython, and the plots can be output to many different formats (PNG, JPEG, SVG, PDF), e.g. for report generation, article figures, or LIMS interfaces.
Case study used in Biomedical and Image Processing seminars (highlights algorithm development).
DNA MicroArray Image Processing Case Study
A generalized DNA modifications predictor for multiple species based on powerful sequence encoding method.
Error correction scheme for storing information on DNA using Reed Solomon codes. For the inner code we decide on a symbol size mi of 6 bit, for the outer code the symbol size mo is 14 bit. These values reflect considerations on accessible DNA sequence lengths and optimal code length.
DNA error correction information storage
DNA Scanner is a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors.
DNA4mC-LIP is a linear integration method to identify N4-methylcytosine site in multiple species.
DNA6mA-MINT is a web DNA-6mA Modification Identification Neural Tool
Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.
Windows Explorer clone dedicated to DNA sequence analysis and manipulation.
DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects. It is particularly suited to working with chromatogram files from ABI machines, and is one of the few programs able to edit as well as view these files. The program has powerful DNA translation and restriction enzyme analysis facilities, and works with external programs to produce multiple alignments and contigs with ease.
Software for analysis of Next-Generation Sequencing data.
A new algorithm for de novo DNA assembly, which uses the relative frequency of reads to properly restore tandem repeats. The main advantage of the algorithm is that long tandem repeats, which are much longer than maximum reads length and the insert size of paired-end tags can be properly restored.
An algorithm for a DNA assembly which uses the relative frequency of reads to properly reconstruct repetitive sequences.
The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.
DNABERT is pre-trained bidirectional encoder representation to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts.
DNAbinder is a webserver developed for predicting DNA-binding proteins from their amino acid sequence using various compositional features of proteins. The SVM models have been developed on following datasets using following protein features.
Designed to predict DNA-binding residues, based on the fluctuations of residues in high-frequency modes by the Gaussian network model.
DNACLUST is a tool for clustering millions of short DNA sequences. The clusters are created in such a way that the “radius” of each clusters is no more than the specified threshold.
Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.
A deep learning tool for DNA cyclizability prediction.
A deep learning framework for population genetics inference.
A machine-learning approach to predict DNA binding affinities of transcription factors
DNAforge is a web tool that provides a user-friendly interface for designing DNA and RNA wireframe nanostructures, supporting multiple design methods and allowing for sequence generation and visualization.
R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies.
DNAgenie (DNA-type specific predictor of DNA-binding residues in protein sequences).
dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available, list of other melting temperature calculation servers also provided.
Source code for paper "Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI" by A. Kalyakulina, I. Yusipov, M.G. Bacalini, C. Franceschi, M. Vedunova, M. Ivanchenko.
DNAModAnnot is a R toolbox for DNA modification filtering and annotation. It can be used for DNA modification filtering and annotation using long-read sequencing data. DNAModAnnot is a R package providing a comprehensive toolkit for the genome-wide analysis and annotation of DNA modifications (Mod) (e.g. 6-methyladenine (6mA) or 5-methylcytosine (5mC)). Its modular architecture allows the analysis of Mod detection performed using Pacific Biosciences (PacBio) kineticsTools or Oxford Nanopore Technologies via DeepSignal software. DNAModAnnot also provides customized visualization functions to describe DNA modification patterns.
DNAmoreDB is a database of DNAzymes. Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates.
DNAnamer is a framework and toolkit for supervised classification of DNA sequences based on N-gram frequency patterns. It utilizes N-grams to identify species, functional gene elements, and other characteristics of DNA sequences.
Tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (&lt,30Kb size limit).
DNAPlotter is a collaborative project between Jemboss and Artemis. It makes use of the existing circular plot in Jemboss and the Artemis sequence libraries.
DNAr is a R package developed to design and simulate formal Chemical Reaction Networks (CRN) and DNA-based reaction networks using Strand Displacement reactions. The theoretical field of Chemical Kinetics has developed brightly the last years, being capable of design many circuits and algorithms (such as the Message Passing Inference and a Least mean Squares Estimator) using CRNs as a building block.
A web service providing assignment of nucleic acid conformers used in bioinformatic analysis of nucleic acids and protein/DNA interfaces.
DNAscent is a software for detecting contiguous regions of base analogues incorporated in Oxford Nanopore reads. It is able to detect replication forks in Nanopore sequencing data with deep learning.
DNase I footprinting analysis of DNase-seq data in R
Web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data.
Tool to train and apply gradient boosting classifiers to predict TFBSs within ChIP-seq data sets by combining sequence and DNA shape information. Sequence information is encoded using either classical PWMs, TFFMs, or 4-bits. DNA shape features are obtained from the GBshape browser.
R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.
This web-server allow to compute the length of DNA or protein fragments from its electropheric mobility using a graphical method. It is based on computer program DNASIZE
Multiple attribute ranking tool for DNA data storage systems.
DNASU is a central repository for plasmid clones and collections. DNASU currently stores and distributes over 130,000 plasmids including over 45,000 human and mouse plasmids, full genome collections from numerous organisms, and the protein expression plasmids from the Protein Structure Initiative (PSI).
Institute of Biotechnology AS CR, Prague, Czech Republic
Includes predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.
Database dedicated to comprehensive and rich annotations of genome dynamics during cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study.
This function translates DNA nucleotides into Amino Acids
Convert a DNA sequence in an amino acids sequence
A series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment.
DNA Zoo data includes genome assemblies, genome annotations, DNA-Seq data, and Hi-C maps.
DNAzymeBuilder is a web application enabling the in situ choice and assembly of DNA- and RNA-cleaving DNAzymes.
DNEA is an R package for fast and versatile data-driven network analysis of metabolomics data, enabling identification of differentially enriched metabolic modules. It builds upon the Filigree tool and provides a more flexible and powerful implementation for analyzing large metabolomics datasets.
Statistical software package for calculating gene set enrichment for de novo mutations (typically detected by exome sequencing) of a disease cohort.
Improvement of causal MiRNA-disease association prediction based on deep network imputation.
Deformable non-negative matrix factorization (dNMF) framework that jointly optimizes registration with signal demixing.
DNMFilter_Indel is a machine learning based tool designed to filter out false positive de novo indels obtained by any computational approaches from whole genome or exome sequencing data. It can be used as either a stand-alone tool to detect de novo indels or coupled with other commonly used de novo indel detection tool to improve specificity.
DNMSO is an ontology for representing de novo sequencing results from Tandem-MS data. For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and as such drives proteomics.
DNNBrain is a unifying toolbox for mapping deep neural networks and brains.
Deep Neural Networks For Predicting Restricted Mean Survival Times. A deep neural network model to predict restricted mean survival time.
A manually curated database of experimentally determined dNTP pools and pool changes in biological samples.
DO-Conv is a depthwise over-parameterized convolutional layer, which can be used as a replacement of conventional convolutional layer in CNNs in the training phase to achieve higher accuracies.
Tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
The Domain Change Presenter (DoChaP) is a project designed for advancing the study of the effect of alternative splicing on protein domains.
Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data. The dockNmine portal aims at gathering public and private data into a unique service. Automated queries on protein targets and ligand definitions are performed to Uniprot, PubChem and ChemBL to enhance the results of pre-computed docking experiments. When available, public data are automatically added to the docking results to produce state-of-the-art protein-ligand binding analysis such as ROC curves or enrichment analysis. Users can also upload their own private data to analyze them automatically
DockCoV2 is a drug database against SARS-CoV-2. It can be used for coronavirus (SARS-CoV-2) drug screening.
Open consensus docking and ranking pipeline for virtual screening of small molecules.
docker4seq provides a general schema and an infrastructure to distribute robust and reproducible workflows. It guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture. docker4seq R package contains all the R functions required to handle all the steps of RNAseq and miRNA-seq workflow.
An integrated graphic user interface tool for molecular docking and virtual screening.
DOCKGROUND resource for protein recognition studies.
DockingPie is a plugin of the popular molecular graphics system PyMOL that offers a versatile and user-friendly graphical user interface for assisting molecular and consensus docking analyses.
An efficient Siamese graph-based neural network method which predicts contact residues between two interacting proteins.
A Python code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces. Automatization for adsorbing molecules on surfaces and screening the different adsorption modes and molecular configurations.
DockQ is a software tool for assessing the quality of modeled biomolecules, including proteins, nucleic acids, and small molecules. The tool has been reimplemented in pure Python, featuring improved portability, speed, and novel functionalities like automatic chain mapping and calculations for multiple interfaces.
A webserver for ranking protein-protein docked poses.
Brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within.
A docking wrapper to enhance de novo molecular design.
DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market.
DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorporates different ontologies with an accompagnying R package that allows easy access, exploration, and definition of disease concepts of interest. It can work as the intermediate player to facilitate access and exhaustive extraction of information from other life science databases without the need to harmonize these up front.
Dodona is a free online exercise platform for learning to code. It wants to teach students how to program in the most meaningful and effective way possible, by using different techniques to apply the advantages of personalized coaching in contexts where students usually only have access to traditional coaching (e.g. lectures or exercise sessions) or even no coaching at all (e.g. independent learning or homework).
The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.
DOE Joint Genome Institute Genome Portal
Doelan is an tool designed to monitor the quality of DNA microarray production.
A python package for optimizing processing pipelines using statistical design of experiments (DoE). A systematic approach to optimizing multi-level and multi-step data processing workflows. Optimize your data processing pipelines with doepipeline. The optimization strategy implemented in doepipeline is based on methods from statistical Design of Experiments (DoE). Use it to optimize quantitative and/or qualitative factors of simple (single tool) or complex (multiple tool) pipelines
Rare variant association test based on position density estimation.
DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.
University of Hamburg, ZBH - Center for Bioinformatics
Automated pocket detection and analysis tool enabling the identification of potential binding pockets and subpockets in protein structures. Additionally, global properties, describing size, shape and chemical features of the predicted (sub)pockets, are calculated. Per default, a simple druggability score is provided for each (sub)pocket, based on a linear combination of the three descriptors describing volume, hydrophobicity and enclosure.
University of Hamburg - Center for Bioinformatics
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Database of local biomolecular conformers, stores DNA structural data including the information about DNA local spatial arrangement.
Improve the classification of human missense variants using protein domains information.
DolphinNext is a web server for distributed data processing of high throughput genomics.
dom2vec is tool for unsupervised protein domain embeddings capture domains structure and function providing data-driven insights into collocations in domain architectures.
Accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.
Mutual annotation-based prediction of protein domain functions.
Method to identify domains in a protein sequence from similarity searches using PSI-BLAST. The identified domains are used in individual PSI-BLAST searches to improve detection of distant homologous sequences. The tool iterates until no new domains are found.
Domain adaptation toolbox for medical data analysis.
DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are
Accurate domain structure annotation including those with non-contiguous topologies.
DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact.
Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.
DomainViz allows users to identify and visualize protein domains on one or more protein sequences using multiple domain prediction platforms (Pfam and Prosite) to understand the consensus positionality and abundance of different domains within protein groups and families.
DomArchive is a data package compiling dominance interaction data published over a century of research. The goal of the package is to facilitate comparative research on the structure and function of dominance hierarchies.
DomFun is a system to assign functions to unknown proteins using a systemic approach without considering their sequence but their domains associated with functional systems. It uses associations calculated between protein domains and functional annotations as training dataset and performs predictions over proteins (using UniProt identifiers) by finding their domains and if they have been associated with functional annotations (in GO molecular functions, biological processes, KEGG and Reactome pathway terms).
Collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated version includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. New features include a new classification scheme to assign confidence levels to predicted DDIs.
Bioinformatics tool for informative marker development from both NGS data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution.
The DOMINO web-server for active module identification analysis.
The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.
Database of Macromolecular interactions. Includes interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.
The Database of Pollinator Interactions (DoPI) documents British pollinator-plant associations.
Its main function takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data, phenotype/clinical data, and "smoking guns" - supposedly unique identifiers found in pData(eset).
Quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, it can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
A database of RNA interactions in post-transcriptional regulation.
Max Delbrück Centre for Molecular Medicine
DoRothEA is a tool for exploring and analyzing transcriptional regulatory networks, particularly focusing on nucleus pulposus (NP) cells and their role in intervertebral disc degeneration (IVDD). It facilitates the identification of transcription factors and their target genes, aiding in understanding the underlying molecular mechanisms of IVDD.
It focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.
This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
Function to fit a dose-response data to a 4 parameter dose-response curve.
DosePredict is a Shiny-based graphical user interface software that can be used for the conduct of dose predictions.
Plots dose/response curve and calculates EC50 and Hill Coefficient.
An application for personalized vancomycin dose adjustment for neonates.
A webtool for investigating the prognostic power of a single or combined cancer biomarker.
An automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues
Dot plot tool with very helpful learn by example interpretations of sample outputs.
Draw a threshold dotplot of two sequences.
Displays a thresholded dotplot of two sequences.
Draw a non-overlapping wordmatch dotplot of two sequences.
Dots-on-Plots is a web application that calculates mechanical properties from stress-strain curves of soft tissue.
A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis.
Display a wordmatch dotplot of two sequences.
Displays a wordmatch dotplot of two sequences.
DOUBLER is a tool for Unified Representation Learning of Biological Entities and Documents for Predicting Protein–Disease Relationships.
DoubleRecViz is a tool for visualizing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. It displays reconciled gene trees embedded in species trees and reconciled transcript trees embedded in gene trees, with annotations on the nodes of the trees corresponding to the underlying co-evolutionary events.
Detecting doublets in single-cell DNA sequencing data.
doubletrouble is an R/Bioconductor package for identifying, classifying, and analyzing gene and genome duplications. It detects duplication modes, calculates substitution rates, and provides visualization tools, with a user-friendly web interface for exploring duplicated gene repertoires across eukaryotic genomes.
Tool for facilitating protein domain detection among remotely related protein sequences.
Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks. A Deep-learning based dOcking decoy eValuation mEthod. Dove evaluates computational protein-protein docking models by 8 deep learning networks and provides the probability that the decoy is correct.
Downloads an image and updates an openDS object with the filesystem location
Dowser is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). Dowser provides a set of tools for performing phylogenetic analysis on B cell receptor repertoires. It supports building and visualizing trees using multiple methods, and implements statistical tests for discrete trait analysis of B cell migration, differentiation, and isotype switching.
A novel SVM-based antioxidant proteins identifier.
Dissimilarity propagation-guided graph-Laplacian principal component analysis (DP-GLPCA) is a model for constrained clustering. By fully utilizing a limited number of weakly supervisory information in the form of pairwise constraints, the proposed DP-GLPCA is capable of capturing both the local and global structures of input samples to exploit their characteristics for excellent clustering.
Software for segmentation of 3D structures contained in 3D microscopy.
Python workflow for DP5 and DP4 analysis of organic molecules
The DP5 probability, quantification and visualisation of structural uncertainty in single molecules.
DPCfam is a method for unsupervised protein family classification.
Explore UHGP-50 clustering results generated by the DPCfam algorithm! DPCfam automatically classifies homologous protein regions into putative protein families, called Metaclusters or MCs. Each MC is a collection of protein sequence regions, called seed sequence regions; these regions are then used as seeds to subsequently build profile-HMMs.
Density Peak Clustering of UHGP50 (DPCfam-UHGP50)
DPCfam automatically classifies homologous protein regions into putative protein families, called Metaclusters or MCs. Each MC is a collection of protein sequence regions, called seed sequence regions; these regions are then used as seeds to subsequently build profile-HMMs.
Density Peak Clustering of UniRef50 (DPCfam-UR50)
dpCNV is a density peak-based method to detect copy number variations from next-generation sequencing data.
Universal R-package and shiny app for the automated analysis of multiplex digital PCR data.
DPCT is a dynamic method for detecting protein complexes from TAP-aware weighted PPI network.
Detail Preserving Coarse-to-Fine Matching for Stereo Matching and Optical Flow.
DPDDI is a deep predictor for drug-drug interactions.
Privacy-Preserving Tensor Factorization for Collaborative Health Data Analysis. Tensor factorization has been demonstrated as an efficient approach for computational phenotyping, where massive electronic health records (EHRs) are converted to concise and meaningful clinical concepts. While distributing the tensor factorization tasks to local sites can avoid direct data sharing, it still requires the exchange of intermediary results which could reveal sensitive patient information. Therefore, the challenge is how to jointly decompose the tensor under rigorous and principled privacy constraints, while still support the model's interpretability. We propose DPFact, a privacy-preserving collaborative tensor factorization method for computational phenotyping using EHR. It embeds advanced privacy-preserving mechanisms with collaborative learning
Drug perturbation gene set enrichment analysis (dpGSEA) can detect phenotypically relevant drug targets through a unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets.
The deep propensity network using a sparse autoencoder (DPN-SA) is a deep learning architecture for propensity score matching and counterfactual prediction to tackle the problems of high dimensionality, nonlinear/nonparallel treatment assignment, and residual confounding when estimating treatment effects.
DPProm: A two-layer model combined DPProm-1L and DPProm-2L, named DPProm, for predicting promoters and their types on the whole genomes of phages.
DPROT is a PSSM based predictor for the prediction of disordered proteins. A simple two state prediction id done over the query protein.
DPSleep is a tool for longitudinal sleep analysis from accelerometer data.
Web tool for QSAR modeling and high-throughput virtual screening.
Information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on related animal viruses.
A graphical user interface for the MIRACUM data quality assessment tool.
The R package 'DQAstats' provides core functionalities to perform data quality assessment (DQA) of electronic health record data (EHR).
Bulked segregant analysis methods are used to identify various types of quantitative trait loci for complex traits via extreme phenotype individuals in bi-parental segregation populations (F2, backcross, doubled haploid and recombinant inbred line).
Dr AFC is a tool for drug repositioning through anti-fibrosis characteristic.
Combining Transfer Learning with Retinal Lesions Features for Accurate Detection of Diabetic Retinopathy.
Distribution Regularization for Text-to-Image Generation.
DR2S (Dual redundant reference sequencing) is an algorithm and R package for DR2S - dual redundant reference sequencing
DR4DNA is a software toolkit for DNA storage data recovery utilizing fountain codes and file type-specific knowledge. It automatically reconstructs corrupted or missing data and is demonstrated through in-silico and in-vitro experiments.
Detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data
A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data.
DRAGoM (Detection of RNA using Assembly Graph from Metagenomics data) is a tool for metagenomic noncoding RNA profiling and biomarker discovery. DRAGoM is a tool designed to predict and assemble ncRNA from next generation sequencing data.
DRAGON (Determining Regulatory Associations using Graphical models on multi-Omic Networks), calibrates its parameters to achieve an optimal trade-off between the network’s complexity and estimation accuracy, while explicitly accounting for the characteristics of each of the assessed omics ‘layers.’
Dragonfly is a software package that can assemble macromolecular structures from large data sets obtained through single-particle imaging.
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.
Aligning human concepts with machine learning latent dimensions for the visual exploration of small multiples.
The DRaW is a convolutional neural network to predict new virus-antiviral interactions VAIs from approved antivirals.
DrawAlignR is an R package for the visualization of aligned ms2 chromatograms. DrawAlignR expects extracted ion chromatogram data and feature (peak-group) scoring data, which is generated/extracted from upstream workflows using OpenMS, OpenSWATH and Pyprophet.
Plots a filled bacteria cell with a given length, width, position, angle, and color specified.
Chromosome analysis and idiogram construction.
Visualisation of protein schematics based on the data obtained from the Uniprot Protein Database.
A machine learning-based predictor of cancer-causing SNPs.
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers.
R package for fitting growth curves and performing dose-response data analysis.
Dense Residual Dual-shuffle Attention Net (DRDA-Net) : an efficient framework for breast cancer detection. Overall workflow of the proposed framework is shown below-.
Android app for skin disease prediction using deep learning
Explainable drug response prediction from differential analysis of multi-omics networks.
DRDOCK is a drug repurposing platform integrating automated docking, simulations and a log-odds-based drug ranking scheme. DRDOCK performs online automatic virtual drug screening of 2016 FDA-approved drugs on a user-submitted target protein. Its goal is to facilitate the drug repurposing to extend the possible treatments toward life-threaten and epidemic diseases. This is achieved by combining the molecular docking and molecular dynamic (MD) simulations to prioritize drugs of strong binders from non-binder. The only things the user required to provide are a well-patched protein structure made of a single peptide chain in PDB format and the target residues IDs to which the drugs expected to bind.
DREAM is a toolbox to decode rhythms of the brain system. DREAM is a toolbox with a graphical user interface for achieving local and remote decoding rhythms of the brain system.
A database of experimentally supported protein-coding RNAs and drug associations in human cancer.
Software for data-independent acquisition (DIA) data analysis with deep representation features.
DreamDIA-XMBD is a tool for for data-independent acquisition (DIA) proteomic data processing with deep representation features.
A web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.
Deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection.
DREAMTools is a Python package for evaluating DREAM challenge scoring metrics. DREAMTools provides a command line interface that enables researchers to test new methods on past challenges, as well as a framework for scoring new challenges.
DREBIOP is a software resource designed to identify patterns in drug repurposing scenarios based on biological pathways. It aims to uncover the importance of these pathways by analyzing successful repurposing cases and identifying diminished significance of drug's gene target.
DRED is a manually-curated database containing information on genes related to repeat expansion diseases, including known genes and predicted candidates. The database provides detailed repeat information, links to external resources, and user-friendly interfaces.
DrEdGE (Differential Expression Gene Explorer) is a Web-based tool to visualize RNAseq data.
Regular expression search of nucleotide sequence(s).
A web application and R package for the detection of regulatory DNA sequences using GRO-seq data.
DREIMT is a bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.
Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.
The first comprehensive landscape of drug resistance information.
Tool to explore dose–response relationships and drug–drug interactions.
Software designed to map di-base reads (SOLiD color space reads) to reference genome assemblies; in a fast and memory-efficient manner.
A package for preforming dynamic recursive feature elimination with sklearn.
DrGA is a novel R package that has been developed based on the idea of our recent driver gene analysis scheme.
A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies.
A multi-agent system framework for concept drift detection.
DRIM is a web-based system for investigating drug response at the molecular level by condition-specific multi-omics data integration.
DRIMC is a drug repositioning approach using Bayesian inductive matrix completion.
R codes for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events ('PCAreduce', 'SC3', 'PCA', 't-SNE', 'Monocle', 'TSCAN', etc). It can improve the performance of such software by imputing dropout events.
The package provides two frameworks. One for the differential splicing analysis between different conditions and one for the sQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts, exons or exonic bins) with Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
DRIMUST is a software implementation of a new statistical and algorithmic approach that we developed to enable efficient motif searches, covering a broader range of motif spaces comparing with state of the art motif searching tools. In particular, DRIMUST can efficiently search for variable gapped motifs, long motifs and motifs over large alphabets. The motif structure that DRIMUST searches comprises two half sites separated by a gap, that can be of a variable length.
R package for the Analysis of Ribosomal RNA Fragments, generally generated by Ribosome Profiling (Ribo-Seq) experiments.
DrivAER is a method for identification of Driving transcriptional programs based on AutoEncoder derived Relevance scores. DrivAER infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.
driveR is an R Package for Prioritizing Cancer Driver Genes Using Genomics Data. It is a method for prioritizing cancer driver genes using somatic genomics data.
Identifying driver genes and driver pathways in cancer based on MutSigCV and statistical methods.
DriverGroup is a tool to detect driver gene groups by using gene expression and gene interaction data.
Package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph. A greedy algorithm is used to find the possible driver genes, which may be mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.
DriverPower is a tool used to discover potential coding and non-coding cancer driver elements from tumour whole-genome or whole-exome somatic mutations.
DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph
DriveWays is a method for identifying possibly overlapping driver pathways in cancer.
DrivR-Base is a toolkit for feature extraction related to single nucleotide variants, designed to aid in variant effect prediction model construction. It utilizes a Docker container for reproducibility and integrates data from various databases and tools.
DRjCC is a cript for joint learning dimension reduction and clustering of single-cell RNA-sequencing data.
Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis.
Quality control routines for multiplex immunoassay data, including several approaches for: treating the background noise of the assay, fitting the dose-response curves and estimating the limits of quantification.
Comprehensive reference map of drug resistance mechanisms in human cancer.
Double Recalibration Network for Few-Shot Semantic Segmentation.
DrNote is an open tagging tool for text annotation and entity linking based on OpenTapioca and WIkiData/Wikipedia. It provides an entity linking service with pre-trained data for medical annotations in multilingual settings. The processing of raw text as well as PDF by a tesseract backend is supported.
Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. It contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores.
DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a “comparative computational microscope” for observing the biophysical effects of mutations and other chemical changes in proteins.
Clustering tool for single-cell RNA sequencing data that uses Locality Sensitive Hashing algorithm.
dropkick is a Python package for automated quality control and cell identification of droplet-based single-cell data. dropkick works primarily with scanpy's AnnData objects, and accepts input files in .h5ad or flat (.csv, .tsv) format. It also writes outputs to .h5ad files when called from the terminal.
DropletQC R package which utilises a novel QC metric, the nuclear fraction, to identify droplets containing ambient RNA or damaged cells.
Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.
DroPNet is a webserver for generating and analyzing Drosophila protein-protein interaction networks. Input data is a list of genes from an experiment such as RNAi screen.
DrosOMA is a web-based resource providing browsable orthology predictions for Drosophila species, built on the OMA inference framework. It enables users to explore and download orthology data through a feature-rich web interface.
Browser to explore -omics variation across high-quality reference genomes from natural populations of drosophila melanogaster.
Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
DRPBind allows the prediction of DNA, RNA and Protein binding residues in intrinsically disordered proteins.
Deep Regression Pair Learning (DRPL) is a deep network is proposed for multi-focus image fusion
Deep Regression Picker Network (DRPnet) is a tool for automated particle picking in cryo-electron micrographs using deep regression. Identification and selection of protein particles in cryo-electron micrographs is an important step in single particle analysis. In this study, we developed a deep learning-based particle picking network to automatically detect particle centers from cryoEM micrographs. This is a challenging task due to the nature of cryoEM data, having low signal-to-noise ratios with variable particle sizes, shapes, distributions, grayscale variations as well as other undesirable artifacts.
Drug resistance prediction for Mycobacterium tuberculosis with reference graphs.
Learning Automated COVID-19 Infection Segmentation From Digitally Reconstructed Radiographs.
The Dundee Resource for Sequence Analysis and Structure Prediction is a collection of services provided by the Barton Group. The Dundee Resource includes services such as Jpred, JABAWS, AACon.
Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP)
DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.
Get data resource entries complete text.
A constructing a bilingual website with validated database for Herb and Western medicine interactions using Ginseng, Ginkgo and Dong Quai as examples.
Multifunctional platform for exploring chemical space as it relates to biological targets, and may be useful at several steps along the drug development pipeline including target discovery, structure–activity relationship, and lead compound identification studies.
Free database unifying popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. You can flag, comment and update relations, import new drug-gene relations valuable for a specific project. Gene orthology and similarity info is matched to certain entries assisting the prediction of new unreported drug-gene associations. Available links to the original source of the reported relation.
Drug2ways is a Python package for reasoning over paths on large-scale biological networks for drug discovery.
Identifying chemogenetic interactions from CRISPR screens with drugZ | DrugZ software from the Hart Lab | Critically, the "gene" column must be the first non-index column in the file, and the column headers are used on the command line. For example, to execute DrugZ analyzing just the A and B replicates of this file, the command line would be:
Unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14,000 protein or drug target sequences are linked to these drug entries.
DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online.
A platform for evidence-based drug annotation for genetic variants in cancer
BLAST search against structural domains stored in DrugEBIlity database.
A database triangulating between drugs, genes and pharmacogenomics biomarkers in regulatory agencies-approved drugs
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
Prediction of druggable proteins using machine learning and functional enrichment analysis. Machine Learning for druggable protein classifiers.
Molecular atlas and pharma-information of all drugs.
Drugmonizome is a tool for the integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.
Drugmonizome-ML is a tool for creating a custom machine learning pipeline on top of the Drugmonizome drug set libraries and SEP-L1000 phenotypic datasets in order to predict novel indications or attributes for existing drugs and understudied small molecules.
DrugnomeAI is an ensemble machine-learning framework for predicting druggability of candidate drug targets.
DrugOrchestra is a multi-task learning neural model used for jointly training tasks of drug target prediction, drug response prediction, drug side effect prediction. It is proven to be better compared to single-task learning (training only one task) under the same training conditions.
Novel insights and opportunities for drug discovery revealed by DRUGpy.
DrugRep is a computer-aided drug discovery online tool for virtual screening of drugs, particularly for drug repurposing.
DrugRepV is a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses.
DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.
A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.
DrugSimDB is a comprehensive database of multi-modal drug similarity measures by integrating variety of heterogenous datasets.
DrugSniper is a tool to exploit loss-of-function screens, identifies CREBBP as a predictive biomarker of VOLASERTIB in small cell lung carcinoma.
DrugSpaceX is a virtual compound library with outstanding characteristics for its structural novelty, diversity and large three-dimensional chemical space coverage, based on expert-defined transformation of the approved drug molecules.
Package for drug taxonomy identification and explainable feature extraction.
Discovery and Development of Safe-in-Man Broad-Spectrum Antiviral Agents.
An integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs).
This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user.
DRUIDom (DRUg Interacting Domain prediction): a computational method for predicting new drug/compound - target protein interactions for drug discovery and repurposing, via mapping ligands to structural domains.
DruMAP, a drug metabolism and pharmacokinetics (DMPK) analysis platform, consists of a database for DMPK parameters and programs that can predict many DMPK parameters from the chemical structure of a compound. The DruMAP database contains data of DMPK parameters from curated public data and newly acquired experimental data obtained under unified conditions. It also contains predicted data using our prediction programs. Users can simultaneously predict several DMPK parameters for novel compounds.
DRUMMER is designed to identify RNA modifications at nucleotide-level resolution on distinct transcript isoforms through the comparative analysis of basecall errors in Nanopore direct RNA sequencing (DRS) datasets.
A software package for drug repurposing in cancer via a subpathway crosstalk network.
Efficient genome assembly of known eukaryotic viruses from metagenomes.
Robust foreground detection in somatic copy number data. Irons out wrinkles in noisy coverage data using robust PCA. Robust PCA based method to de-noise genomic coverage data. devtools::install_github('mskilab/dryclean'). Install dependent packages and latest Bioconductor (if you haven't already). dryclean is a robust principal component analysis (rPCA) based method. dryclean uses a panel of normal (PON) samples to learn the landscape of both biological and technical noise in read depth data. dryclean then uses this landscape significantly reduce noise and artifacts in the signal for tumor samples. The input to the algorithm is GC amd mappability corrected read depth data from fragCounter that can be found at: https://github.com/mskilab/fragCounter
DRYGIN (Data Repository of Yeast Genetic Interactions)-a web database system that provides a central platform for yeast genetic network analysis and visualization. DRYGIN searches SGA interactions and integrates other data sources, in order to associate the genetic interactions with pathway information, protein complexes, other binary genetic and physical interactions, and Gene Ontology functional annotation.
DryMass is a Python library and a command-line tool for manipulating and analyzing quantitative phase microscopy images of cell-sized objects.
Dual-Supervised Mixture of Gaussian Mixture Models for Uncertainty Inference in Image Recognition
DS4H Image Alignment (DS4H-IA) is an open-source ImageJ/Fiji plugin designed for aligning multimodality, immunohistochemistry, and immunofluorescence microscopy images with a focus on user-friendliness. It provides a solution for image registration with readily available source code, standalone applications, video tutorials, documentation, and sample datasets.
DSaaS (Data Science as a Service) is an easy-to-use cloud platform well suited for hospital structures, where healthcare operators might not have specific competences in using programming languages but still, they do need to analyze data as a continuous process. It is able to predict patients risk to contract a multidrug resistant urinary tract infection (MDR UTI) after hospitalization.
Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction.
Automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology.
Dsb is an R package for normalizing and denoising CITE-seq protein data. Used for normalizing and denoising protein expression data from droplet-based single cell profiling.
A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing. DSBS analyzer is a pipeline to analyzing Double Strand Bisulfite Sequencing data, which could simultaneously identify SNVs and evaluate DNA methylation levels in a single base resolution.
A computational tool to infer cell-cell communication networks in the developing and aging brain.
Takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. It can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.
DSCMF is a tool for the prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization.
DSCN (double-target selection guided by CRISPR screening and network), a method that matches expression levels in patients and gene essentialities in cell lines through spectral-clustered protein-protein interaction (PPI) network.
dSCOPE (detecting Sequence Critical fOr Phase sEparation) is a web server developed for detecting sequences critical for phase separation related proteins.
DscoreApp is a Shiny web application for the computation of the Implicit Association Test D-Score.
A disorders of sex development atlas for reproductive endocrinology-related gene discovery in integrative omics platforms.
DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
DSFworld is a web application for the method Differential Scanning Fluorimetry (DSF) that enables rapid determination of a protein’s apparent melting temperature (Tma).
A tool for predicting frequencies of drug side effects by graph attention networks.
This program aims to identify differentially spliced genes from two groups of RNA-seq samples.
DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.
R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided.
K-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k 32. This software supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. It can count k-mers of large Illumina datasets on laptops and desktop computers.
Software of content-based exploration and retrieval method for whole metagenome sequencing samples.
Diving into high-throughput DSMZ cell line data.
Shape string predictor for protein sequences. It provides both predicted shape string and sequence-shape string profile for each query sequence allowing for comparison of protein structure or evolution in shape string space.
DSPLMF is a method for Cancer drug sensitivity prediction using a novel regularization approach in Logistic Matrix Factorization.
dSPRINT is a machine learning framework for predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. The predictor can run on any human Pfam protein domain, and return per-position predictions of interaction-sites for five different ligand types: DNA, RNA, ion, peptide, and small molecule.
Modeling the effect of RNA secondary structure on double stranded RNA-protein binding.
Compression algorithm for genomic data in FASTQ format
A sequence-based solubility predictor created with dilated squeeze excitation residual networks.
in silico identification of dsRNA regions using long-read RNA-seq data.
R library that performs differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). Its core is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
NIAGADS is a data storage site and sharing service that distributes genetics and genomics data from Alzheimer’s disease studies. The linked publication investigates racial/ethnic representation in AD genetics research and its statistical power.
DSSP secondary structure database . It produces secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated tool for analyzing and annotating RNA tertiary structures.
Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD.
dsSwissKnife is an R package that enables several powerful analyses to be performed on federated datasets.
DStabilize is a server to generate enantiomers of peptides and proteins.
DSTG is a tool for deconvoluting spatial transcriptomics data through graph-based artificial intelligence.
Institut de Pharmacologie Moléculaire et Cellulaire
DSW@IFB is the support service for the development of data management plans in life sciences hosted by the French Bioinformatics Institute (IFB / ELIXIR-FR). It is based on an instance of the Data Stewardship Wizard<https://ds-wizard.org/> (DSW) tool, a DMP support tool developed by the ELIXIR infrastructure. Access to the DSW@IFB service is free. ELIXIR-FR develops, in collaboration with the other French research infrastructures in Life Sciences, customised DMP models.
Considering pathological genetic variants within the context of the human interactome network can help understanding the intricate genotype-to-phenotype relationships behind human diseases. It allows, for instance, to distinguish between changes that totally suppress a gene product (i.e. node removal) from the ones that might affect only one of its functions, modulating the way in which the protein interacts with its partners (i.e. edge-specific or edgetic1). dSysMap is a resource for the systematic mapping of disease-related missense mutations on the structurally annotated binary human interactome from Interactome3D.
Dynamic Transcriptome Analysis can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis and decay rates from individual microarray or RNAseq measurements.
Small Dataset Curator and Small Dataset Modeler. Integration of Data Curation, Exhaustive Double Cross-Validation, and a Set of Optimal Model Selection Techniques | DTC lab - Software Tools - DTC lab is working in the field of molecular modelling mainly using different QSAR methodologies in various diverse area such as drug designing, toxicity, anti-oxidant studies etc
DTF is a deep tensor factorization for predicting anticancer drug synergy.
DTFLOW is a tool for inferring and visualizing dynamic cellular trajectories from single-cell data.
DTI-MLCD is a tool for predicting drug-target interactions using multi-label learning with community detection method. It can be used for identifying drug-target interactions (DTIs) is an important step for drug discovery and drug repositioning.
DTI-Voodoo is a computational method that combines molecular features and ontology-encoded phenotypic effects of drugs with protein protein interaction networks, and uses a graph neural networks to predict drug-target interactions.
End-to-end drug-target binding affinity prediction with transformers.
Desktop Molecular Modeller (DTMM) Version 4.2 is a simple-to-use molecular modelling program that enables you to perform powerful molecular synthesis, editing, energy minimizations, and display.
dtoolAI is a library for supporting reproducible deep learning.
DTranNER is a tool for biomedical named entity recognition with deep learning-based label-label transition model.
DTSR method of fMRI reconstruction by imposing double temporal sparsity
A simulation framework for modelling waterborne spread of highly infectious pathogens in marine aquaculture.
A web-based tool to assess the dual-use potential of life science research. The aim of the tool is to provide a clear and practical dual-use risk assessment of research concerned and to create dual-use awareness amongst life-science researchers, as explicitly stated in the WHO Benchmarks for International Health Regulations Capacities.
A dual graph convolutional network model to predict cancer drug response. It takes chemical structure information of a drug and gene features of a cancer sample as inputs and outputs IC50.
This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes.
dualmarker is a flexible toolset/R package for exploratory analysis of combinatorial dual biomarkers for clinical efficacy. Dualmarker is designed for data exploration and hypothesis generation for dual biomarkers. It provides intuitive visualizations and extensive assessment of two marker combinations using logistic regression model for binary outcome (response analysis) and Cox regression for time-to-event outcome (survival analysis).
DualSeqDB is a host-pathogen dual RNA sequencing database for infection processes.
Dual Encoding Visual Dialogue (DualVD) is a library, which is able to adaptively select question-relevant information from the visual and semantic views in a hierarchical mode.
Software suite that will help bioinformaticians to analyze genomes AND phenomic experiments. The final purpose of the program is to combine the genomic informations (encoded as KEGG pathways) with the results of phenomic experiments (Phenotype Microarrays) and highlight the genes that may be responsible for phenotypic variations. It's written in python and works as a command line tool for Unix environments.
Web server for an integrated computational approach for studying missense mutations in proteins.
SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing.
A Semantic Search Engine Leveraging Peer-Reviewed Literature to Span Biomedical Data Repositories. Dug applies semantic web and knowledge graph methods to improve the FAIR-ness of research data.
This is a deep-learning-based pattern unmixing pipeline for protein subcellular localization to quantitatively estimate the fractions of proteins localizing in different subcellular compartments from immunofluorescence images.
Dune is an R Package that provides a parameter-free method for optimizing the trade-off between the resolutionof the clusters and their replicability across datasets. Dune method takes as input a set of clustering results on a dataset, and iteratively merges clusters within those clusterings in order to maximize their concordance.
A Web Application for Uncertainty Estimation in Skin Cancer Detection with Deep Neural Networks.
Software toolbox for forward modeling in bioelectromagnetism.
Meta-analysis has become a popular approach for high-throughput genomic data analysis because it can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often-encountered problem. Not removing duplicates would make study results questionable. We developed a BioConductor package that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.
Duplication rate quality control for RNA-Seq datasets.
Dupre is able to estimate the duplicate rate of a sequencing library at a given sequencing depth N, when the occupancy vector of a (small) subsample is known.
DupScan is a database for visualizing and predicting vertebrate synteny and genome duplication.
dv-trio is a family-based variant calling pipeline using DeepVariant. It provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants.
Diagnostic Variant Database (DVD) is a nation-wide human genomic variant database launched by Dutch University Medical Centers. Its purpose is to share all genetic variants detected in the course of next-generation sequencing (NGS) applications between collaborators. It helps medical researchers to distinguish between functionally relevant and benign genetic variants. DVD also allows users to contact the researcher who originally identified a particular genetic mutation.
DVDeconv is an open-source MATLAB toolbox for depth-variant asymmetric deconvolution of fluorescence micrographs.
A decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations.
Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM. DXM performs a local deconvolution of DNA methylation data for one or more regions of the genome.
Dopamine Receptors Interaction Profile is a resource for understanding the binding specificity of G-Protein Coupled Receptors (GPCR) toward G-proteins and arrestins in the case of dopamine.
A neuroimaging module for dynamic connectome mapping.
Adaptable gene-specific dye bias correction for two-channel DNA microarrays.
First of its kind dye-sensitized solar cell database, aims to provide users with up-to-date information from publications on the molecular structures of the dyes, experimental details and reported measurements (efficiencies and spectral properties) and thereby facilitate a comprehensive and critical evaluation of the data.
A dynamic nomogram for predicting the risk of asthma.
Dynamic cancer drivers A causal approach for cancer driver discovery based on bio pathological trajectories.
A web application for dynamically calculating the codon usage bias in bacterial genomes.
A web-based nomogram for accurately predicting probabilities of overall survival in elderly patients with chondrosarcoma (CHS), which will contribute to personalized survival assessment and clinical management.
Tool for performing dynamic risk prediction using a landmark supermodel for survival data under competing risks.
An open-source GUI program coupled with MCNP for modelling relative dynamic movement of radioactive source and ORNL phantom in 3-dimensional radiation field.
Dynamic Proteomics database contains information on the position and amounts of endogenous proteins in individual living human cells. This is based on the Library of Annotated Reporter Cell-clones (LARC). The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition.
Dynamic visualization of high-dimensional data.
DynaMight is a software tool that estimates continuous space of conformations in a cryo-EM dataset by learning three-dimensional deformations of a Gaussian pseudo-atomic model, improving reconstruction of the consensus structure.
Protein backbone dynamics prediction from sequence.
DYNAMITE is a phylogenetic tool for identification of dynamic transmission epicenters. DYNAMITE takes a tree (scaled in substitutions/site) in newick or nexus format with support values at the nodes.
A Dynamic Programming Approach to Segment ONT Signals. Dynamont is a segmentation/resquiggling tool for ONT signals.
An exploratory data visualization software for mapping movement in relation to internal and external factors.
Implements two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. It integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability.
Inferring the dynamics of time-series phosphoproteomics.
Python package allowing the easy study of dynamics-function relationships in biomolecules.
Tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows to include restriction enzyme mapping and design of primers spanning user specified sequences.
DynaVenn is a tool for creating Venn diagrams. It can be used to determine the most significant overlap between subsets of two or three sorted (gene) lists. This approach avoids the arbitrary selection of a fixed threshold for the length of the sets.
dynBGP is a tool for the estimation of dynamic SNP-heritability with Bayesian Gaussian process models.
A set of functions to create and interact with dynamic documents and vignettes.
DynLib is spectral database containing spectras from LC-MS runs for maize organs in order to investigate the metabolome.
Development and validation of a nomogram to estimate future risk of type 2 diabetes mellitus in adults with metabolic syndrome.
Compute biomolecular systems dynamics for user-uploaded structural coordinates or PDB identifiers, by integrating two widely used elastic network models (ENMs) – the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM).
An R method for multiple imputation in R library Dynamic Modeling in R (dynr).
dynUGENE is an R package for uncertainty-aware gene regulatory network inference, simulation, and visualization.
A Novel Dysregulated Pathway Identification Analysis Method.
DysRegSig is an R package for identifying gene dysregulations and building mechanistic signatures in cancer. DysRegSig is capable of robustly exploring gene dysregulations from high-dimensional expression data with cooperativity and synergy between regulators and several other transcriptional regulation rules taken into consideration. DysRegSig also offers tools to rank dysregulated regulations and TFs, and construct mechanistic signature with gene dysregulations by using genetic algorithm.
Identifies cancer driver genes based on linear annotations of biological regions such as protein domains. e-Driver uses information on three-dimensional (3D) structures of the mutated proteins to identify specific structural features. Then, the algorithm analyzes whether these features are enriched in cancer somatic mutations and, therefore, are candidate driver genes.
A Novel mHealth System for Remote Monitoring of Symptoms in COVID-19. Application for remote monitoring of vital signs and symptoms.
E-CRISP is a computational tool to design and evaluate guide RNAs for use with CRISPR/Cas9. The web application uses fast algorithms to identify target sequences for use with mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different parameters of how CRISPR constructs can be used in experimental applications, such as knock-out and tagging experiments. E-CRISP can design guide RNAs for genomes of more than 30 organisms.
E-FTMap is a web server that expands on the original FTMap protocol to identify pharmacophore features within ligand binding sites using 119 organic probes. It helps in early-stage structure-based drug discovery by mapping binding hot spots and interactions.
Enviromic Assembly for purposes of Genomic Prediction (E-GP). Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity
Augmentation of Doppler Radar Data Using Generative Adversarial Network for Human Motion Analysis. Objectives:Human motion analysis can be applied to the diagnosis of musculoskeletal diseases, rehabilitation therapies, fall detection, and estimation of energy expenditure. To analyze human motion with micro-Doppler signatures measured by radar, a deep learning algorithm is one of the most effective approaches. Because deep learning requires a large data set, the high cost involved in measuring large amounts of human data is an intrinsic problem. The objective of this study is to augment human motion micro-Doppler data employing generative adversarial networks (GANs) to improve the accuracy of human motion classification. Methods:To test data augmentation provided by GANs, authentic data for 7 human activities were collected using micro-Doppler radar.
e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.
E-MAGMA is an eQTL-informed method to identify risk genes using genome-wide association study summary statistics.
e-MutPath is a R library for the identification of candidate cancer mutations based on edge perturbation.
E-Pedigrees is a large-scale automatic family pedigree prediction application.
E-PIX® is a record linkage tool for managing multi-million patients in research projects at a large university hospital in Germany. The Record Linkage and ID Management solution E-PIX (Enterprise Identifier Cross Referencing) applies the propabilistic Fellegi-Sunter-algorithm and the Levenshtein distance to avoid duplicate participant entries. The independent software module facilitates participant management and multisite-aggregation of medical research data.
Federated Trusted Third Party as an Approach for Privacy Preserving Record Linkage in a Large Network of University Medicines in Pandemic Research.
E-Predict compares observed hybridization patterns with theoretical energy profiles representing different species. We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications.
E-pRSA is a method for predicting the Relative Solvent Accessibility of residues in a protein chain without requiring previous knowledge of the 3-dimensional structure. E-pRSA is based on embeddings derived from protein language models.
Collection of web servers for comparative RNA structure prediction and visualisation.
E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.
an open-source, browser-based visualization suite to render complex relationships between cancer evolution data in an intuitive, interactive framework for biomedical investigators. It consists of 3 visualization tools: Timescape, Mapscape and Cellscape
Embedding of protein sequence and function improves the annotation of human pathogenic variants.
Web tool to design TALENs for genome engineering.
An interactive visual exploration platform for target-disease knowledge mapping from literature.
Evolve is a Webtool designed to model mutations in the input protein complex using Modeller.
E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.
E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy.
E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.
Web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases.
simultaneous classification and motif identification for enzyme annotation. Simultaneous Classification and Motif Identification(eCAMI). eCAMI: Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation
A novel, open-access web-based interactive contouring resource that aims to facilitate point-of-care decision support that is based on available evidence-based radiation treatment guidelines.
R package for the quantitative exploration of elastic net families for generalized linear models.
ePOSSUM analyses the effect of DNA variants on transcription factor binding sites
An online database towards comprehensive essential gene annotation for prokaryotes.
Open, sustainable research informatics and analytics platform for the IMI OncoTrack consortium.
a practical variant filtering for low-frequency variants detection in cell-free DNA. A software to identify low-frequency variants from molecular-barcoded targeted sequencing data using the ThruPLEX tag-seq (Takara Bio). Process a bam file using Conner, and detect candidate variants. Remove barcode and stem sequences from a raw bam file, and generate a new bam file. Mizuno K. et al. eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA. Sci Rep. 9, 15017 (2019)
Expression-based variant impact phenotyping to predict the function of gene variants. Expression-based variant impact phenotyping. Expression-based variant impact phenotyping (eVIP) is an approach to predict functional impacts of mutations by comparing gene expression signatures induced by wild-type vs. mutated ORFs. eVIP2 is an updated version of eVIP that can predict functional impact on the pathway level in addition to the overall functional prediction
Efficient ancient genome reconstruction.
Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method.
EAGLE is an alignment-free method and associated program to compute relative absent words (RAW) in genomic sequences using a reference sequence.
An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions | Enhancer And Gene Learning Ensemble method | EAGLE: an algorithm that utilizes small number of genomic features to predict tissue/cell type specific enhancer-gene interactions | EAGLE used all six features only derived from the enhancers and gene expression datasets, without providing more information like histone modification, methylation or other enhancer-gene (EG) detection datasets
Eagle is an R package for multi-locus association mapping on a genome-wide scale.
An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression (ASE) quantified from RNA-seq
A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool.
Information-rich genome assembler viewer with data integration capability.
An atlas of enhancer activity quantitative trait loci across cancer types.
EARN is an ensemble machine learning algorithm to predict driver genes in metastatic breast cancer.
EARRINGS is an efficient and accurate adapter trimmer that entails no a priori adapter sequences for both single- and paired-end NGS reads.
EASAL is a tool for efficient atlasing, analysis and search of molecular sssembly landscapes. It is a geometric methodology for analyzing free energy and kinetics of assembly driven by short-range pair-potentials in an implicit solvent and provides a proof-of-concept illustration of its unique capabilities. An atlas is a labeled partition of the assembly landscape into a roadmap of maximal, contiguous, nearly-equipotential-energy conformational regions or macrostates, together with their neighborhood relationships. The new methodology decouples the roadmap generation from sampling and produces: (1) a queryable atlas of local potential energy minima, their basin structure, energy barriers, and neighboring basins; (2) paths between a specified pair of basins, each path being a sequence of conformational regions or macrostates below a desired energy threshold; and (3) approximations of relative path lengths, basin volumes (configurational entropy), and path probabilities
Developed for user-friendly exploration, visualization and analysis of genome-wide single-read sequencing data. Both individual genomic loci and populations of loci can be visualized. The underlying loci can then be inspected just by selecting them in the plots. It also integrates more than 20 tools for analysis. Finally, it automatically generates legends and descriptions of the handling and can store plots together with underlying data and these descriptions as a single compact session file.
A Python program (easer.py) based in PyCogent library for the homology-based retrieval of several sequence data types from Ensembl. A Perl program (enamer.pl) for the identification of sequence descriptions.
Emending Alignments of Spliced Transcript Reads (EASTR). EASTR is a tool for detecting and eliminating spuriously spliced alignments in RNA-seq datasets. It improves the accuracy of transcriptome assembly by identifying and removing misaligned spliced alignments. The tool can process GTF, BED, and BAM files as input. EASTR can be applied to any RNA-seq dataset regardless of the alignment software used.
Easy-MODA is a web-based tool developed on the Enalos Cloud Platform that simplifies the creation of MODA documentation for materials modelling workflows, facilitating registration and improving FAIRness. It assists users in creating detailed MODA documentation even for complex models and integrates with the broader MODA guidelines.
Easy16S is designed to facilitate the exploration, visualization, and analysis of microbiome data.
Learning to Solve the Intractables From a Synthetic Dataset for Structure-Preserving Image Smoothing.
Easy353 is a tool for recovering Angiosperms353 gene set(AGS), which can filter reads from high throughput sequencing data such as RNASeq and genome skimming and capture AGS accurately and effectively with our optimized reference-guided assembler.
EasyFRAP-web is a web-based application which enables fast and interactive qualitative and quantitative analysis of Fluorecence Recovery After Photobleaching (FRAP) data. EasyFRAP-web allows large data-sets to be rapidly evaluated and normalized fluorescence recovery curves to be generated and exported. It also performs curve fitting and provides quantitative parameters (mobile fraction and recovery half time) necessary for comparison across data-sets.
EasyAmber is a comprehensive toolbox to automate the molecular dynamics simulation of proteins. EasyAmber is a set of wrapper scripts to automate the molecular dynamics routines implemented in the Amber package. The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility, and supports the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. The easyAmber software takes the molecular dynamics to the next level in terms of usability for complex processing of large volumes of data. It implements advanced MD protocols, but is highly automated and easy-to-operate to attract a broad audience. The toolbox can be used on a personal desktop station equipped with a gaming GPU-accelerator, as well as help to manage huge workloads on a powerful supercomputer.
EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
Marker-based cell-type annotation by automatically querying multiple databases.
Pipeline for prokaryotic phylogenomic analysis based on core gene sets.
A python program devised to create gene-oriented clusters of ESTs/FL-cDNAs given a genomic sequence.
EasyFlowQ is an open-source, user-friendly flow cytometry analysis GUI based on Matlab or Python. It facilitates quantitative measurements of fluorescence in single cells and is designed for both inexperienced users and advanced customization.
A versatile tool that assists quantitative and qualitative analysis of fluorescence recovery after photobleaching data. The user can handle simultaneously large data sets of raw data, visualize fluorescence recovery curves, exclude low quality data, perform data normalization, extract quantitative parameters, perform batch analysis and save the resulting data and figures for further use.
Process and analyze ecological field sampling data generated using the Fulcrum mobile application.
EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms.
Fully automated gene prediction for prokaryotes. It produces a list of predicted genes for a chosen prokaryotic genome.
A graphical user interface for automated linkage analyses.
Easymap is a user-friendly software package for rapid mapping by sequencing of point mutations and large insertions.
easyMF is a web platform for matrix factorization-based biological discovery from large-scale transcriptome data. easyMF comprises three functional modules, named Matrix Preparation, Matrix Factorization, and Deep Mining. Deep Mining includes Metagene-based Deep Mining Using Amplitude Matrix and Metagene-based Deep Mining Using Pattern Matrix.
EasyMicroPlot package for microbiome analysis tool on R platform that accomplishes the core tasks of metagenomic down-stream analysis from start to finish, specially designed by screening popular microbial analysis and visualization.
EasyOmics is an R Shiny application designed for population-scale omics data association, integration, and visualization, accessible via Docker containers. It provides a user-friendly interface for wet-lab biologists to perform various omics data analyses.
EasyParallel is a free GUI cross-platform tool that utilizes a multi-thread parallel algorithm for processing multiple iterations of STRUCTURE and NEWHYBRIDS analyses.
An easy-to-use and easy-to-extend Python framework for phenotype prediction using Bayesian optimization.
Graphical and software platform for the analysis of MS/MS data.
EasyPubPlot is a Shiny web application and associated R package designed for rapid omics data exploration and visualization. It simplifies the creation of publishable plots like scores plots, volcano plots, and heatmaps, guiding users through the process with minimal steps.
An R-package that provides advanced funcionality to perform file-level QC of single genome-wide association (GWA) data-sets, to conduct quality control across several GWA data-sets (meta-level QC) and to simplify data-handling of large-scale GWA data-sets.
This package is based on the qBase algorithms published by Hellemans et al. in 2007. The package allows you to import easily qPCR data files as described in the vignette. You can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes chosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.
Ready-to-use machine learning tool for symmetric multi-modality registration of brain MRI.
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
easySCF is a tool designed to enhance the interoperability of single-cell data between R and Python, facilitating efficient data exchange and improving analysis accuracy using a unified .h5 data format.
A user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison.
A user-friendly web-based tool for molecule library selection and structure-based virtual screening. Virtual Screening in just a few clicks. EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a know structure and tailoring a purchasable molecule library to performing and visualising docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalise docking parameters.
easyXpress is an R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler. The package is rather specific to use in the Andersen Lab and, therefore, is not available from CRAN.
Enrichment Analysis Tool for Upstream Transcription Factor of a gene set (EAT-UpTF) is a tool to conduct enrichment analysis of upstream transcription factor for a gene set of interest.
Eatomics is an R-Shiny based web application that enables interactive exploration of quantitative proteomics data generated by MaxQuant software. Eatomics enables fast exploration of differential expression and pathway analysis to researchers with limited bioinformatics knowledge. The application aids in quality control of the quantitative proteomics data, visualization, differential expression and pathway analysis. Highlights of the application are an extensive experimental setup module, the data and report generation feature and the multiple ways to interact and customize the analysis.
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
Search globally across all EMBL-EBI databases.
This software provides tools for the analysis of replicated/unreplicated microarray data.
Analyze groups of proteins or entire proteomes for the presence of eMOTIFs in batch fashion.
EBCall is a software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.
An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level.
Web resource targeted at metagenomic researchers.
Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)
High-performance, full-featured text searches across all EMBL-EBI databases or in selected databases available from EMBL-EBI.
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.
R package which provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, It offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
eBird gathers knowledge from birdwatchers in the form of checklists of birds, maps, audio recordings .
eBLOCKS is a database of 80,000 conserved protein regions from 20,000 aligned protein families assembled using PSI-BLAST. eBLOCKs lets you compare new proteins to this database of conserved sequences using either eMOTIFs or eMATRICES made from eBLOCKs.
The 2014 Ebola epidemic in West Africa has stirred international response and renewed efforts to develop effective preventative and treatment options. In response to a request for help from vaccine researchers, the UCSC Ebola Genome Browser was built with viral sequences from previous outbreaks as well as the 2014 outbreak. This site also provides related tools and information that can be used to further the understanding of Ebola.
Ebolabase is a comprehensive source for ebola-human interactions has been developed. Ebolabase contains experimentally verified entries of ebola-human interactions. The interactions are visualized as network images. This study provides the information to understand the ebola pathogenesis and also to identify the re-purposing drugs.
Provides a complete, quality checked and regularly updated list of oligonucleotides for the Ebola virus. The database describes the genetic diversity across the Ebola genome to facilitate the design of accurate diagnostic methods and therapeutic approaches. The database provides different measures of sequence conservation for each target region obtained from multiple sequence alignments, allowing the selection of the most conserved oligonucleotides.
EBOLApred is a machine learning-based web application for predicting molecules capable of inhibiting the activities of glycoprotein (GP) and the matrix protein (VP40) of the Ebola virus.
Perseus plugin for differential protein abundance analysis of labeling-based and label-free quantitative proteomics data
Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.
Differential Expression analysis at both gene and isoform level using RNA-seq data.
This package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). It provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.
EBST is an evolutionary multi-objective optimization-based tool for discovering potential biomarkers in ovarian cancer.
A suite of tools for investigating EBV-associated human gastric carcinogenesis.
ebwt2InDel is a tool for finding SNPs and InDels from the BWT of a FASTA read set.
A Icy plug-in that enables to align multidimensional images in 2D or 3D, rigidly or with warping, whatever the difference in scale.
EC-PGMGR is a tool for ensemble clustering based on probability graphical model with graph regularization for Single-Cell RNA-seq Data.
Eucalyptus interactive biotic stress investigator (eCALIBRATOR) is a comparative tool to identify key genes and pathways for eucalyptus defense against biotic stressors.
High-quality database for exploration and characterization of extrachromosomal circular DNAs in cancer.
Parallelized GPU implementation of Ensemble Classifier Chains.
Comprehensive repository for eccDNA-mediated chromatin contacts in multi-species.
The Esophageal Cancer Clinical Data Interactive Analysis (ECCDIA) is an interactive web tool for the comprehensive analysis of clinical and survival data of esophageal cancer patients.
eccDNABenchmarking is a resource for the comparative analysis of methodologies for detecting extrachromosomal circular DNA (eccDNA). It evaluates the performance of software pipelines and experimental methods through simulated and real sequencing datasets.
A comprehensive resource of eccDNA catalog.
An integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data.
A database of extrachromosomal circular DNA profiles in human cancers.
Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.
English-Chinese Cancer Parallel Corpus (ECParaCorp) is a database involving information of 6 cancers in three different themes: cancer prevention, cancer screening and cancer treatment.
The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA from paired-end read data of amplified circular DNA.
ECDB, a manually curated database is designed and developed to provide a comprehensive resource of genes deregulated in Endometrial cancer.
Track the Pandemic COVID-19 with MATLAB Helper with use of the dataset from ECDC Europa
ECFS-DEA is an ensemble classifier-based feature selection tool for differential expression analysis on expression profiles.
ECGanalysis is a MATLAB-based tool for analyzing electrocardiogram data from freely moving mice. The protocol provides a step-by-step guide for equipment manufacturing, electrode implantation, and data processing to accurately detect heartbeats and calculate heart rate.
ECG-GPT is an AI-powered tool that generates diagnostic reports from 12-lead ECG images. The model has been extensively validated across geographically diverse populations and demonstrates a scalable and accessible strategy for automated ECG analysis.
This server allows user to analysis the expression data (Microarray Data) where it calculate correlation coefficient between level of gene expression and nucleotides composition of genes.
Electrocardiogram-based deep learning improves outcome prediction following cardiac resynchronization therapy
Echidna is integrated simulations of single-cell immune receptor repertoires and transcriptomes. Single-cell sequencing now enables the recovery of full-length immune repertoires [B cell receptor (BCR) and T cell receptor (TCR) repertoires], in addition to gene expression information. The feature-rich datasets produced from such experiments require extensive and diverse computational analyses, each of which can significantly influence the downstream immunological interpretations, such as clonal selection and expansion. Simulations produce validated standard datasets, where the underlying generative model can be precisely defined and furthermore perturbed to investigate specific questions of interest. Currently, there is no tool that can be used to simulate a comprehensive ground truth single-cell dataset that incorporates both immune receptor repertoires and gene expression.
Leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.
EchinoDB is a database consisting of amino acid sequence othoclusters from 42 echinoderm transcriptomes. We sampled taxa to span the deepest divergences within each of the 5 extant echinoderm classes. Data can be searched by keywords such as annotation and database identifiers from the Strongylocentrotus purpuratus reference protein set at NCBI.
Suite containing tools in the field of chromatography.
Reference-free short read error correction from diploid genomes, with explicit modeling of heterozygous sites.
An Application for Detection and Analysis of Oscillators Identifies Metabolic Regulation on Genome-Wide Circadian Output | An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators | Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO) | Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> | This is the first step in the PAICE (Pipeline for Amplitude Integration of Circadian Exploration) Suite! This suite of tools provides high-throughput applications for circadian, ultradian, and infradian rhythms | ECHO (Extended Circadian Harmonic Oscillators) is an R-powered application designed to find and visualize circadian rhythms from your data using extended harmonic oscillators | Use and First-Time Set-Up Instructions
Extended Circadian Harmonic Oscillators (ECHO)
Echo-SyncNet is a tool for self-supervised cardiac view synchronization in echocardiography (ECG). Echo-SyncNet is an encoder style CNN trained to produced low dimensional and feature-rich embedding sequences cardiac ultrasound videos.
A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.
Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
Compressed variant representation for rapid annotation and filtering of SNPs and indels.
Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins.
Extended Connectivity Interaction Features (ECIF) to describe protein–ligand complexes and build machine-learning scoring functions with improved predictions of binding affinity. ECIF are a set of protein−ligand atom-type pair counts that take into account each atom’s connectivity to describe it and thus define the pair types. ECIF were used to build different machine-learning models to predict protein–ligand affinities (pKd/pKi).
ECJ is a research EC system written in Java. It was designed to be highly flexible, with nearly all classes (and all of their settings) dynamically determined at runtime by a user-provided parameter file. All structures in the system are arranged to be easily modifiable. Even so, the system was designed with an eye toward efficiency.
A set of three programs (preproc, eclipse2 and eclipse3) which analyze genetic marker data for genotyping and/or pedigree errors. Using the same preprocessing program (preproc) eclipse2 analyzes data on pairs of individuals, while eclipse3 analyzes data jointly of trios.
ECMPride is a flexible and scalable tool for predicting extracellular matrix (ECM) proteins. ECMPride can directly perform ECM prediction by taking UniProt IDs in CSV file format as input.
ECMpy 2.0 is a Python package that automates the construction and analysis of enzyme-constrained models (ecModels) for microorganisms, significantly improving upon traditional genome-scale metabolic models (GEMs). It streamlines parameter retrieval and integrates algorithms for metabolic engineering target discovery.
With this tool you can calculate Elementary Conversion Modes (ECMs) from metabolic networks. Combinations of ECMs form all metabolic influence an organism can exert on its environment.
The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions.
A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.
A scientific database for the bacterium Escherichia coli K-12 MG1655. This project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
A hierarchical Bayesian model to combine stomach, biotracer, and literature data into diet matrix estimation.
Interactive Apps for Teaching Theoretical Models in Ecology and Evolutionary Biology.
Information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies.
EcoliGD is an online tool for designing artificial Escherichia coli genome and viewing function related information of the genome Escherichia coli str. K-12 substr. MG1655
Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.
eCOMPASS (evaluative comparison of multiple protein alignments by statistical score) addresses this problem using a statistical measure of relative alignment quality based on direct coupling analysis (DCA): to maintain protein structural integrity over evolutionary time, substitutions at one residue position typically result in compensating substitutions at other positions. eCOMPASS computes the statistical significance of the congruence between high scoring directly coupled pairs and 3D contacts in corresponding structures, which depends upon properly aligned homologous residues.
ECONTACT (Energetic CONTributions of Amino acid residues and its possible Cross-Talk) is an approach to identify potential cross-talks between amino acid residues of protein pocket involved in ligand binding. This approach utilizes per-residue energy terms derived from multiple protein-ligand complexes as variables for principal component analysis (PCA) and identifies top cross-talks which can be tested in any protein-ligand complex.
> HOMEPAGE MISSING! | Improved ensemble convolutional neural networks for RNA binding protein prediction directly from sequence | RNA binding proteins (RBPs) determine RNA process from synthesis to decay, which play a key role in RNA transport, translation and degradation. Therefore, exploring RBPs' function from the amino acid sequence using computational methods has become one of the momentous topics in genome annotation. However, there still have some challenges: (1) shallow feature: Although the sequence determines structure is self-evident, it is difficult to analyze the essential features from simple sequence. (2) Poorly understand: feature-based prediction methods mainly emphasize feature extraction, while in-depth understanding of protein mysteries limits the application of feature engineering. (3) Feature fusion: multi-feature fusion is often used, but the features are not well integrated
EcoPLOT is an interactive web-application for the analysis of multivariate-biogeochemical datasets.
EcoSP database is an integrated repository of bacterial O-antigens and K-antigens (Escherichia coli), which collects comprehensive information, including serotypes, coding region sequences, glycosyltransferases, structures, and biosynthetic pathways of K-/O- antigens.
An R-package to easily use Transfer Learning for Ecological Studies. A plankton case study.
The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.
Enzyme commission number prediction and benchmarking with hierarchical dual-core multitask learning framework.
This repository presents an objective, quantifiable method for assessing atopic dermatitis (AD) severity.
The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond
Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies. EcTracker possesses two distinct modules i.e. CellEnrich and TissueEnrich, to allow detection of cell-type or tissue-specific genes in the user-supplemented scRNA-sequencing dataset.
Ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. (Galaxy Version 1.0.0)
ECuADOR is a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines.
A web-based tool to support researchers in the planning of animal experiments. It helps researches to improve the study design, analysis and reporting of the findings to decrease the number of irreproducible research.
EdaFoldAA is a fragment assembly based de novo protein structure prediction method that uses an Estimation of Distribution Algorithm for high efficiency conformational sampling.
e!DAL is a lightweight software framework for publishing and sharing research data. Its main features are version tracking, metadata management, information retrieval, journal and founding agency proven registration of persistent identifiers (DOI), an embedded HTTP(S) server for public data access, access as a network file system, and a scalable storage backend.
The EDAM Browser is a client-side web-based visualization javascript widget of the EDAM ontology. The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.
Find EDAM ontology terms by has_input relation.
Find EDAM ontology terms by has_output relation.
Find EDAM ontology terms by is_format_of relation.
Find EDAM ontology terms by is_identifier_of relation.
Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
Extension of GDC data analysis, visualization, and exploration tools.
Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
The European & Developing Countries Clinical Trials Partnership (EDCTP) Knowledge Hub.
This tool can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance.
Eddymotion is an open-source framework for volume-to-volume artifact estimation in neuroimaging, inspired by FSL’s eddy. It offers an alternative to FSL's eddy without commercial limitations and generalizes beyond eddy current distortions of diffusion MRI.
A program for assembling de novo bacterial genomes from short reads produced by Illumina sequencing platform.
A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia
A database of Disease-Gene Associations with annotated Relationships among genes.
The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" - was developed.
Software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology.
Estimate gene expression from prokaryotic RNA-seq.It uses Bowtie2 for alignment but, unlike TopHat and Cufflinks, does not allow spliced alignments. It also handles overlapping genes, a common phenomenon in bacteria that is largely absent in eukaryotes.
We incorporate gradient information and probability scores from a classifier to construct ESF.
Robust Edge-Stop Functions for Edge-Based Active Contour Models in Medical Image Segmentation
A Web Platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.
Platform for deep reinforcement learning based pairwise DNA sequence alignment compatible with embedded edge devices.
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.
Efficient Detection of Hydrogen Bonds (EDHB) is a tool that systematically detects hydrogen bonds based on the nearest neighbors algorithm. EDHB classifies inter- and intramolecular hydrogen bonds as well as hydrogen bond networks.
Easily interpretable electron density score for individual atoms. It quantifies the electron density support of each single atom by computing a weighted sum over an oversampled electron density grid in the proximity of the atom. Atomic EDIA values can also be combined with the help of the power mean to compute EDIA_m, an electron density score for small molecules, fragments, or residues.
The Exome Database of Interspersed Repeats (EDIR) was developed to provide an overview of the positions of repetitive structures within the human genome composed of interspersed repeats encompassing a coding sequence.
Entrez Direct (EDirect) is a command-line tool for Entrez databases. EDirect connects to Entrez through the Entrez Programming Utilities interface. It supports searching by indexed terms, looking up precomputed neighbors or links, filtering results by date or category, and downloading record summaries or reports.
Extended Dimension Iterative Signature Algorithm is a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules,Its samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality.
EditGDS is a visual tool for browsing and editing Genomic Data Structure (GDS) files
eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics. Exome Disease Variant analysis (eDiVA),. is a variant annotation and prioritization pipleine which. You will need to run git clone https://github.com/mbosio85/ediva.git to get eDiVA. No special compilinig is needed, eDiVA can work as a standalone application or using Docker containers.
EDLMFC is an ensemble deep learning with multi-scale feature combination for ncRNA-protein interaction prediction.
An R program for comprehensive DMR (differentially methylated regions) analysis based on bimodal normal distribution model and cost function for regional methylation analysis.
Extremely-Downsampled Network (EDN), which employs an extreme downsampling technique to effectively learn a global view of the whole image, leading to accurate salient object localization.
eDNAFlow is a fully automated pipeline that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and non-curated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. As part of eDNAFlow, we also present an in-house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning Lowest Common Ancestor (LCA). This pipeline is based on Nextflow and Singularity which enables a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters.
A machine learning tool that accurately predicts qPCR cross-amplification.
EDock-ML (Ensemble Docking With Machine Learning) is a web server for using ensemble docking with machine learning to aid drug discovery.
A comprehensive and comparative multi-omics database for animal evo-devo.
A data transformation method which takes into account the special property of scale non-invariance with a breakpoint at 1 of the Euclidean distance.
The electrodiffusive Pinsky-Rinzel (edPR) model is multicompartmental neuron model that accounts for electrodiffusive ion concentration dynamics in a way that ensures a biophysically consistent relationship between ion concentrations, electrical charge, and electrical potentials in both the intra- and extracellular space.
A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.
Electron density server at Uppsala university
Database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition is demonstrated by making use of small subgroups of the descriptors.
EEfinder is a tool for identifying bacterial and viral endogenized elements in eukaryotic genomes. It automates several steps in the process, improving reproducibility and facilitating comparative analysis.
EEG-Beats is a matlab toolbox to analyze heart rate variability (HRV) from EKG measured with an EEG Sensor. This MATLAB toolbox extracts heartbeat peaks and interbeat interval measures from a single channel of EEG that has been recorded by placing an EEG sensor on the upper portion of the chest.
EEG-DTI is an end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction.
This package evaluates cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. It performs DE analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences.
A benchmark dataset, that is suited for training and testing deep learning-based EEG denoising models, as well as for comparing the performance across different models.
EEGNET is software designed to enclose the different steps from EEG signal preprocessing to brain network visualization.
Calculates partial atomic charges for small organic molecules, drug-like molecules. The tool is deprecated, we recommend the use of AtomicChargeCalculator.
Modular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools. Containerized, currently supports input datasets in CSV, JSON, XLSX.
eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.
R package offering a scenario tool beyond forestry.
Retrieves Genes in the requested format from a list of one or more unique identifiers.
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
Retrieves sequences in requested format from a list of one or more unique identifiers.
Get taxonomy information given taxonomy ID.
R package to predict candidate RxLR and CRN effectors in oomycetes using motif searches.
Effective is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identification of eukaryotic-like protein domains and the recognition of signal peptides in amino acid sequences. The Effective web portal provides user-friendly tools for browsing and retrieving comprehensive precalculated predictions for whole bacterial genomes as well as for the interactive prediction of effectors in user-provided protein sequences.
Division of Computational Systems Biology, University of Vienna
Tools for combining structural MRI (tractography/connectome) to functional MRI https://doi.org/10.1016/j.neuroimage.2021.118288
Predictive validity of a novel non-invasive estimation of effective shunt fraction in critically ill patients
Prediction of Type-III secreted proteins by recognition of chaperone-binding sites.
Prediction of intact bacterial protein secretion systems and putative secreted proteins.
Prediction of putative secreted proteins based on eukaryotic-like domains (ELD).
Prediction of intact secretion systems III, IV and VI in bacterial genomes by using a Support Vector Machine (SVM) approach.
Prediction of putative Type-III secreted proteins.
Prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks.
Public math open-source project in Java & MATLAB.
Efficient Approximative Multiplication of Square Matrices
Efficient B-mode Ultrasound Image Reconstruction from Sub-sampled RF Data using Deep Learning.
Efficient B-mode Ultrasound Image Reconstruction Using CNN
EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.
EFMrep provides an extended model of EuroForMix by allowing different model parameters to be assigned to each DNA profile involved in the analysis, rather than applying global model parameters to all.
Drug-target interaction prediction based on an efficient fusion of multi-source data.
An ensemble feature selection tool implemented as R-package and web-application.
European genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.
The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.
An image explainer that automizes image segmentation. Ensemble-based Genetic Algorithm Explainer (EGAE) for melanoma cancer detection that automatically detects and presents the informative sections of the image to the user.
EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.
Drug-drug interaction extraction and generation with fusion of enriched entity and sentence information.
EGFRIndb is a literature curated database of 4581 small molecule inhibitors that have shown activity against either epidermal growth factor receptor isoforms (EGFR, ErbB2, ErbB4) or mutants of EGFR-TK domain (L858R, T790M, double mutant).
EGG is a software tool developed to estimate the accuracy of predicted multimeric protein models. It uses deep energy-based models and graph neural networks, achieving promising results against other predictors in CASP15 evaluations.
A python package for population genetics and genomics.
eggNOG is a database of nested orthologous gene groups (NOGs) inferred using unsupervised clustering applied to >5,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. eggNOG provides orthologous group assignments at 379 different taxonomic levels as well as multiple sequence alignments, maximum-likelihood trees and broad functional annotations for each group accessible via a web interface or through bulk download.
For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.
EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.
EGGTART is a tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP.
EGIO (Exon Group Ideogram based detection of Orthologous exons and Orthologous isoforms) is aimed to detect orthologous exons and isoforms within pre-defined orthologous gene pairs.
Encyclopedia of microbiota regulated genes.
Leveraging Scaffold Information to Predict Protein-ligand Binding Affinity with an Empirical Graph Neural Network.
EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI.
EGPred implements a new strategy where the specificity is maintained while the sensitivity is increased on combining ab initio predictions with BLASTX exons that are filtered using criteria such as length of HSP alignment, percent identity, score, expectation value, and similarity to intron sequences.
eGreenhouse is a lightweight and low-cost greenhouse sensor package integrated with the OPEnS HyperRail.
EGRET is a deep learning based method for Protein-protein interaction site prediction, where we have introduced a novel edge aggregated graph attention network to effectively leverage the structural information.
egs_brachy is an egs++ application for rapid brachytherapy calculations for both photon and electron sources.
This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.
EgyGene GelAnalyzer4 is a powerful image analysis software for one-dimensional gel electrophoresis.
An R package for the preparation and enrichment of health datasets for analysis. Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Database and analysis platform for pathogenic E. coli transcriptional gene regulatory networks. The database contains the known regulatory network of E. coli K-12 extracted from RegulonDB. In addition, it provides inter-species transferred gene regulatory interactions for 16 pathogenic E. coli strains.
A tool for automated image analysis of spherical bacteria based on cell cycle progression.
A streamlined pipeline for automated electronic health records standardisation and preprocessing to predict clinical outcomes.
ehrapy is an open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data. It incorporates a series of analytical steps and facilitates various analyses, including survival analysis and causal inference.
Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. A Python package for extracting and scoring reaction templates based on extended Hasse diagrams.
Functions to delineate temporal dataset shifts in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds, uncovering the patterns of the data latent temporal variability. EHRtemporalVariability is particularly suitable for multi-modal data and categorical variables with a high number of values, common features of biomedical data where traditional statistical process control or time-series methods may not be appropriate. EHRtemporalVariability allows you to explore and identify dataset shifts through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots. An additional EHRtemporalVariability Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding.
eHSCPr is a tool for predicting the early stages of HSCs development.
The eICU Collaborative Research Database is a freely available, multi-center database used for critical care research. It enables researchers to analyze patient data, as evidenced by its use in identifying a U-shaped correlation between lymphocyte count and hospital mortality.
eido is the official Python package for validating Portable Encapsulated Projects or PEPs in Python.
EigenDel is a tool for detecting genomic deletions from high-throughput sequence data with unsupervised learning.
Combindes functionality from population genetics methods (Patterson et al. 2006) and the EIGENSTRAT correection method (Price et al. 2006). The EIGENSTRAT methods uses principal component analysis to model ancestry differences between cases and controls along continuous axes of variation. The resulting correction is specific to a candidate markers variation in frequency across ancestral populations, minimizing spurious associations while maximising power to detect true associations.
Find inverted repeats in nucleotide sequences.
Enhanced image prior for unsupervised remoting sensing super-resolution.
This package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms.
EIT-MESHER is C++ software, based on the CGAL library, which generates high quality Finite Element Model tetrahedral meshes from binary masks of 3D volume segmentations. Originally developed for biomedical applications in Electrical Impedance Tomography (EIT) to address the need for custom, non-linear refinement in certain areas (e.g. around electrodes), EIT-MESHER can also be used in other fields where custom FEM refinement is required, such as Diffuse Optical Tomography (DOT).
An explainable LSTM network for RNA-associated multi-compartment localization prediction.
DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.
A Novel App for Insights into Laboratory Data of Clinical Trials.
Illumina's algorithm for whole genome or reads alignments to a reference genome.
ELaSTIC is a software suite for a rapid identification and clustering of similar sequences from large-scale biological sequence collections. At its core is an efficient MinHash-based strategy to detect similar sequence pairs without aligning all sequences against each other.
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective.
Evaluation of an Open Source Registration Package for Automatic Contour Propagation in Online Adaptive Intensity-Modulated Proton Therapy of Prostate Cancer. Home : About : FAQ : wiki : Download : News : Legal stuff : Documentation. Welcome to elastix : a toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. Nowadays elastix is accompanied by SimpleElastix , making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.
Repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.
The ElastoGUI application is a graphical user interface dedicated to analyze shear wave imaging data in images or clips recorded using specialized ultrasounds. The ElastoGUI application allow drawing forms of different shape (i.e., polygons, rectangles or circles) and size in a desired ultrasound frame, and then batch process the delimited color map region(s) in all frames that correspond to the shear wave imaging (SWE) rate in all imported files. From the delimited color map region(s) in frames, the ElastoGUI application processes young modulus (maximal value, mean and standard deviation), shear modulus (mean and standard deviation), shear wave velocity (mean and standard deviation) and form surface area. Drawing tools enable editing form shape and size across frames and files, but also enable keeping the exact same forms between files. Acquisition and Analyze software for elastography data recorded with Aixplorer® ultrasounds.
FC test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance. It provides the same consistency as fold testing in cross platform analysis and has lower FP and FN rates than standard fold testing. It provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.
A large eldercare-oriented BEnchmark database of SSVEP-BCI for The Aging population (eldBETA)
ELECTOR (EvaLuation of Error Correction Tools for lOng Reads) is a program that enables the testing of different hybrid and non hybrid long read correction tools.
In this code, using EIDORS Electrical Impedance Tomographic Image Reconstruction is demonstrated.
Electrical Impedance Tomography Image Reconstruction using MATLAB based freeware EIDORS
Comparison of analytical and numerical geometric factors for surface-borehole configuration.
Electrical resistivity tomography Geometric Factors
A script for numerical simulation of electroactive hydrogels for cartilage-tissue engineering
Electroactive hydrogel cartilage-tissue simulation
Accepts 1 channel EMG and finds number, amplitude, maximum, and duration of contraction periods.
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest, useful for detecting mis-priming events.
A supervised machine learning approach for label harmonization and annotation of single cell RNA-seq data.
An enhanced tool for detection and curation of core promoter elements.
Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language.
ELEPHANT is an interactive platform for cell tracking in 4D that seamlessly integrates annotation, deep learning, and proofreading.
An Ensemble Learning Framework for Detecting Protein Complexes From PPI Networks.
Elfin is suite of tools that helps protein designers build structures by using smaller proteins as building blocks.
Eliater is a Python package for estimating the effect of a perturbation on a downstream molecule in a biomolecular network. It takes a network, observational data, and the perturbation as input and provides quantitative effect estimates, as demonstrated by a case study on the Escherichia coli transcriptional regulatory network.
The ELIHKSIR (Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators) web application offers insights about the probability of protein interaction specificity in two-component systems. The knowledge reported on this website is gained through statistical inference from genomic data.
pyradiomics is a Python package for extracting radiomics features from medical images. The package was used in a study predicting local control of brain metastases after stereotactic radiotherapy by integrating radiomics and deep learning features with clinical characteristics.
Enhanced Ligand Exploration and Interaction Recognition Algorithm (ELIXIR-A). ELIXIR-A, a plugin in VMD, can find similarities in the active site of the receptor under study compared to other receptors.
ELIXIR-SI eLearning Platform (EeLP) is a learning management system (LMS) continuously administered and maintained by ELIXIR Slovenia. EeLP is an open educational resource that enables all-in-one-place access to materials, tools and services for any ELIXIR-related course.
University of Ljubljana, Faculty of Medicine
EllipTrack is a global-local cell-tracking pipeline for 2D Fluorescence Time-Lapse Microscopy. EllipTrack is a global-local hybrid cell tracker optimized for tracking modern large-scale movies. EllipTrack introduces a local track correction module.
Tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.
ELMA - MRI tissue classification software for setting up electric field FEM simulations in Comsol Multiphysics
This tool is designed to use DNA methylation and gene expression from a large number of samples to infer a regulatory element landscape and transcription factor network in primary tissues.
Fast and Accurate Correction of Optical Mapping Data via Spaced Seeds | Elmeri is a program to correct errors in raw optical map data (Rmaps) | L. Salmela, K. Mukherjee, S.J. Puglisi, M.D. Muggli, and C. Boucher: Fast and accurate correction of optical mapping data with spaced seeds
Map ELM predictions of a query sequence to known annotated ELM instances.
Mapping of ELM (Eucaryotic Linear Motifs) motifs to a query sequence.
A website to browse miRNA target predictions from the ElMMo algorithm
ELMSI is a method for the detection of micro-satellite instability events based on the next generation sequencing technology. ELMSI can estimate the specific length distributions and states of micro-satellite regions from a mixed tumor sample paired with a control one. It first estimated the purity of the tumor sample based on the read counts of the filtered SNVs loci. Then, the algorithm identified the length distributions and the states of short micro-satellites by adding the Maximum Likelihood Estimation (MLE) step to the existing algorithm.
Tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.
Preference rating for visual stimuli based on Elo ratings.
ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.
Enzymatic link prediction (ELP) is a tool for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph.
ELPGV is an ensemble learning method for predicting genetic values, combining predictions from various methods like GBLUP and BayesA to improve accuracy. It is implemented in R and available on GitHub with a user manual and example datasets.
Is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.
Finding Time-Dependent Associations in Time Series Datasets.
Ensemble learning-based approach (ELSSI): parallel SNP-SNP interactions detection by ensemble multi-type detectors.
ElTetrado is a tool for identification and classification of tetrads and quadruplexes in DNA/RNA 3D structures. The application analyzes base pairing patterns of DNA/RNA 3D structures to find and classify tetrads and quadruplexes.
Exploration of metagenome assemblies with an interactive visualization tool
Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach.
EM-stellar is a platform that can be used to benchmark the performance of a range of state-of-the-art Deep Learning methods on user-provided datasets.
Freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages, allowing data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, data can be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.
A scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. he suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography.
A digital atlas of mouse embryonic development consisting of a database of the anatomical structures that are found at different stages of mouse embryo development, and a set of 3D volumetric digital embryo models at different stages of mouse development. It creates interactive three-dimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names.
creation of genbank files from Eggnog-mapper annotation outputs
Expectation-Maximization algorithm for Allele Specific Expression.
Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models.
A recommender system for biomedical literature based on supervised learning.
A comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.
EmbedGEM is a framework to systematically evaluate the utility of embeddings in genetic discovery, focusing on heritability and disease relevance. It provides methods for comparing embeddings and multivariate traits in both synthetic and real-world datasets.
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning.
EmbedSeg, an embedding-based instance segmentation method designed to segment instances of desired objects visible in 2D or 3D biomedical image data.
Fast, precise and flexible way to produce visualizations from flow and mass cytometry data. Based on FlowSOM.
EMBER is a tool for multi-label prediction of kinase-substrate phosphorylation events through deep learning.
Frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence with one mutation through sequencing errors.
Software to convert GFF3 and fasta to legal EMBL format suitable for ENA submission.
A modified version of EMBLRead for Reading a EMBL file into a Matlab structure much faster
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
Check for more recent updates to EMBOSS.
Report the current EMBOSS db version number.
Using deep learning to link embryonic phenotypes to signaling pathways.
A method for identifying G-protein coupled receptors based on word embedding and wordbooks.
The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
An ensemble multiscale deep learning predictor (EMDLP) to identify RNA methylation sites in NLP and DL way.
emDNA is a C++ software for minimizing the energy of DNA or DNA+proteins complexes. It can handle various geometrical constraints (e.g. fixed end-to-end distance and/or rotation) and can be used to simulate opened or closed DNA fragments.
Algorithm used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Traditional methods use significance tests based on summary statistics of the distributions. This approach lacks power to identify differences between groups with high levels of intra-group heterogeneity. The algorithm transforms one distribution into another, providing the overall difference in shape between two distributions.
Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, this missing metadata may be found in the narrative of publications describing the research. This respository offers a new metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, and Europe PMC annotations API.
EMERALD METAGENOMICS ANNOTATIONS PIPELINE
The Extreme-scale Model Exploration with Swift (EMEWS) framework enables the direct integration of multi-language model exploration (ME) algorithms while scaling dynamic computational experiments to very large numbers (millions) of models on all major HPC platforms. EMEWS has been designed for any "black box" application code, such as agent-based and microsimulation models or training of machine learning models, that require multiple runs as part of heuristic model explorations. One of the main goals of EMEWS is to democratize the use of large-scale computing resources by making them accessible to more researchers in many more science domains. EMEWS is built on the Swift/T parallel scripting language.
Extensible Matrix Factorization (EMF) is an flexible method for imputing genetic interactions with cross-species and side information.
EMF-Portal is a comprehensive, systematically curated database and literature search platform from RWTH Aachen University, summarizing research data on the effects of electromagnetic fields (EMF) on animals and plants, available in both English and German. It offers search capabilities and information on limits and regulations.
EMGB is a CWL-based workflow for metagenomics analyses including a web-based interface for filtering ind querying analysis results
Finds the "on" and "off" indicies of a single raw surface EMG burst (muscle contraction).
Accurate automated hole masking algorithm for single-particle cryo-EM image processing.
EMhub is a web platform designed to manage users, instruments, bookings, and projects in scientific facilities, initially for cryoEM but adaptable for other data-generating centers. It allows for on-the-fly data processing and integrates with external processes via a REST API.
EMIRGE (Expectation-Maximization Iterative Reconstruction of Genes from the Environment) reconstructs full length ribosomal genes from short read sequencing data. In the process, it also provides estimates of the sequences' abundances. EMIRGE uses a modification of the EM algorithm to iterate between estimating the expected value of the abundance of all SSU sequences present in a sample and estimating the probabilities for each read that a specific sequence generated that read. At the end of each iteration, those probabilities are used to re-calculate (correct) a consensus sequence for each reference SSU sequence, and the mapping is repeated, followed by the estimations of probabilities. The iterations should usually stop when the reference sequences no longer change from one iteration to the next. Practically, 40-80 iterations is usually sufficient for many samples. Right now EMIRGE uses Bowtie alignments internally, though in theory a different mapper could be used.
emiRIT is a text-mining based database for microRNA information.
EmiRPred: A webserver to predict exosomal and non-exosomal miRNA
An ensemble machine learning-based integration algorithm for metastasis prediction and risk stratification in intrahepatic cholangiocarcinoma.
Genotype imputation has become standard practice in modern genetic studies. As sequencing-based reference panels continue to grow, increasingly more markers are being well or better imputed but at the same time, even more markers with relatively low minor allele frequency are being imputed with low imputation quality. Here, we propose new methods that incorporate imputation uncertainty for downstream association analysis, with improved power and/or computational efficiency.
Multiple sequence alignment (ClustalW wrapper).
EMMA-CAD a web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors
MAGE-compliant software platform for the evaluation of microarry experiment data sets resulting from genome-wide transcriptomics studies. It allows to access the raw transcriptome data sets and provides automated and extensible analysis and visualization pipelines, including but not limited to the normalization of single and multiple microarrays and statistical tests for inferring differentially expressed genes.
A MAGE-compliant system for the collaborative analysis and integration of microarray data.
A new method for computing multiple sequence alignments given a constraint subset alignment.
Efficient Mixed-Model Association eXpedited is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the efficiency obtained by the EMMA algorithm, EMMAX takes advantage of the fact that each locus explains only a small fraction of complex traits allowing the avoidance of repetitive variance component estimation procedures.
emmtyper is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly. By default, we use the U.S. Centers for Disease Control and Prevention trimmed emm subtype database, which can be found here (https://www2a.cdc.gov/ncidod/biotech/strepblast.asp). The database is curated by Dr. Velusamy Srinivasan. Inner workings The difficulty in performing M-typing is that there is a single gene of interest (emm), but two other homologue genes (enn and mrp), often referred to as emm-like. The homologue genes may or may not occur in the isolate of interest. When performing emm-typing from an assembly, we can distinguish betweeen one or more clusters of matches on the contigs. The best match for each of the clusters identified is then parsed from the BLAST results. Where possible, we try to distinguish between matches to the emm gene, and matches to one of the emm-like genes.
EMNUSS is a deep learning framework for secondary structure annotation in cryo-EM maps.
A database of comparative structure models of drug-target interactions from the Binding Database. Computational Systems Biology Group. A database of 200,005 comparative models of drug-bound proteins based on 1,391,403 interaction data obtained from the Binding Database. Complex models in eModel-BDB were generated with a collection of the state-of-the-art techniques, including protein meta-threading, template-based structure modeling, refinement and binding site detection, and ligand similarity-based docking.
Search protein sequences by digest fragment molecular weight.
The Electron Microscopy Public Image Archive.
Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.
EmpPrior facilitates the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics.
The Empusa code generator: bridging the gap between the intended and the actual content of RDF resources
a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures. resource for metastatic research.
EMU is a tool for large-scale inference of population structure in presence of missingness using EM-PCA.
Single-nucleotide variant caller based on expectation maximization.
Emory Genetics Laboratory's (EGL) Variant Classification Catalog contains variants of the gene of interest that has been seen and analysed by EGL Genetics.
A globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data.
Sequence similarity search to retrieve sequence and associated records from ENA.
EnAET: Self-Trained Ensemble AutoEncoding Transformations forSemi-Supervised Learning. Deep neural networks have been successfully applied to many real-world applications.
An encoder for nanopore FASTQ files. ENANO is a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files. We tested ENANO and current state-of-the-art compressors on several publicly available nanopore datasets. The results show that our algorithm consistently achieves the best compression performance on every nanopore dataset, while being computationally efficient in terms of speed and memory requirements when compared to existing alternatives.
Manually curated database of experimentally supported endocrine system disease and lncRNA associations.
encG-reg is a regression approach that detects relatives in genomic data using encryption, avoiding privacy concerns while maintaining accuracy. The software was tested across a large dataset of 54,092 GWAS samples and demonstrated comparable results to established methods.
This is the ENCODE-DCC RNA-sequencing pipeline. The scope of the pipeline is to align reads, generate signal tracks, and quantify genes and isoforms.
It has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data.
This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.
Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data. Single-cell RNA sequencing enables us to characterize the cellular heterogeneity in single cell resolution with the help of cell type identification algorithms. However, the noise inherent in single-cell RNA-sequencing data severely disturbs the accuracy of cell clustering, marker identification and visualization. We propose that clustering based on feature density profiles can distinguish informative features from noise. We named such strategy as 'entropy subspace' separation and designed a cell clustering algorithm called ENtropy subspace separation-based Clustering for nOise REduction (ENCORE) by integrating the 'entropy subspace' separation strategy with a consensus clustering method. We demonstrate that ENCORE performs superiorly on cell clustering and generates high-resolution visualization across 12 standard datasets
Web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations.
EnCurv method for maintaining membrane curvature in MD simulations.
ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.
Cell type deconvolution of spatially resolved transcriptomics data via ensemble learning.
EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
Dynamic Analysis for Detecting Endianness Bugs. Endicheck is a Valgrind tool to help you detect missing byte-swaps in your program. It is recommended to use --prefix to install into other-than-default location, since you typically do not want to replace your system's installation of Valgrind. Endicheck still contains all the original Valgrind tools, like MemCheck, but it might not contain all the latest updates or distribution patches.
Ensemble deep learning-based tool for identifying therapeutic peptides with low hemolytic activity.
a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) transcriptomics data (Pubmed).
Deep Super-Resolution for Capsule Endoscopy.
A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions. EndometDB web frontend works as the input/output layer for the EndometDB, providing user's query for the backend and plotting it after backend has finished processing it. An extensive collection of human samples and data from patients, that aids in the research for better diagnosis or cure for endometriosis.
Comprehensive genome-wide experimentally validated endogenous G-quadruplex database.
Interpreting tree ensemble machine learning models with endoR.
Gene tree and species tree reconciliation with endosymbiotic gene transfer.
A package for the temporal refinement of endometrial biopsies using an initial timing value as provided via urinary ovulation test and the measurement of expression for a panel of time-sensitive genes
Directing Protein Design Choices by Per-Residue Energy Breakdown Analysis with an Interactive Web Application.
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.
The ENsemble Fusion (EnFusion) repo contains a Dockerfile to build a Docker Image that can overlap outputs from 7 fusion detection algorithms, to identify high confidence fusion events.
A Supervised Ensemble Learning Method for Recovery of Large-scale Gene Regulatory Networks.
Enhancer-FRL, a two-layer predictor proposed for identifying enhancers (enhancers or non-enhancers) and their activities (strong and weak) using the feature representation learning scheme.
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome.
LOVD for GDPD1 is a database and web application providing variant information for the Glycerophosphodiester Phosphodiesterase Domain Containing 1 (GDPD1) gene, used to identify and characterize structural variants linked to retinitis pigmentosa type 17. The platform facilitates data submission and analysis for researchers and clinicians.
A Bi-LSTM and Attention-Based Deep Learning Method for Enhancer Recognition.
A novel deep learning framework for identifying cell-specific enhancers.
An updated resource with enhancer annotation in 586 tissue/cell types across nine species. an updated resource with typical enhancer annotation in 600 tissue/cell types across nine species.
A database of enhancer mediated feed-forward loops for human and mouse.
Learning fine-resolution Hi-C contact maps using a generative adversarial framework.
Enhort is a platform for deep analysis of genomic positions.
A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering.
Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets. The ENIGMA TOOLBOX is an open source repository for the sharing of neuroimaging and genetics data, analytical codes, and visualization tools that are 100% ENIGMA-friendly and -focused. The ENIGMA Consortium brings together researchers in imaging genomics to understand brain structure, function, and disease, based on brain imaging and genetic data. We welcome brain researchers, imagers, geneticists, methods developers, and others interested in cracking the neuro-genetic code!.
ENKIE is a Python package that predicts enzyme kinetic parameter values and their uncertainties in metabolic networks using Bayesian Multilevel Models. The tool's code and package are available on GitLab and PyPI, with a peer-reviewed publication describing its methods and performance.
Molecular Dynamics Simulations of Protein-Ligand Systems Made Accessible. Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems. To acknowledge the use of the Enlighten2 plugin and/or protocols, please cite the following publication:. Download PyMOL plugin PyMOL plugin GitHub page Python package GitHub page. Enlighten2 allows to easily prepare and run molecular dynamics simulations of protein-ligand systems. It requires no installation or knowledge of computational chemistry software and can be run on any machine (Windows, Mac or Linux) that has PyMOL and Docker installed. It consists of three main parts:.
Simple tool based on the iterative mapping of sequence reads at contig edges, capable to extend the genomic contigs deriving from high-throughput sequencing, especially those deriving by Newbler-like assemblies. Testing it on a set of de novo draft genomes led to the closure of up to 20% of the gaps originally present. It is cross-platform and most of the steps of its pipeline are parallelizable, making easy and fast to improve a draft genome resulting from a de novo assembly.
EnMCB is an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models.
This package provides an efficient data pre-processing tool designed to reduce background noise and improve signal for DNA methylation estimation from Illumina Methylation BeadChip array measurements. It is a model based background correction method that can significantly improve accuracy and reproducibility of methylation measures.
ENNGene is an application that simplifies the local training of custom Convolutional Neural Network models on Genomic data via an easy to use Graphical User Interface.
enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.
ENQUIRE (Expanding Networks by Querying Unexpectedly Inter-Related Entities) offers an alternative to manual literature curation and database mining to study complex biomedical phenomena. ENQUIRE generates a co-occurrence network of genes and biomedical ontologies (MeSH) using a corpus of publications as input. The algorithm iteratively reconstructs and expands the network by generating PubMed queries from significant interrelations, until it obtains an interconnected network of genes and MeSH relevant to the input corpus.
Custom-made pipeline for matching and validating specific products, i.e., a specific brand of whole milk, to generic products, "full milk", and enriching the generic product with information from food databases.
A Global Weighted Model for Disease Ontology Enrichment Analysis. EnrichDO was based on the latest annotations of the human genome with DO terms, and double weighted the annotated genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between the parent and its children, less significant nodes were dynamically down-weighted.
Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement Enriched heatmap by ComplexHeatmap package.
A Python library providing two methods to perform enrichment analysis, such as gene set enrichment analysis in bioinformatics.
This package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
A Cytoscape plugin for functional enrichment visualization. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the ""enrichment map""). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. It also enables the comparison of two different enrichment results in the same map.
The enrichMiR R package implements various tests to identify miRNAs whose targets are enriched among genesets of interest or a differential expression signature.
Visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on 'ggplot2' graphics.
Integrative web-based and mobile gene-list enrichment analysis tool that includes over 30 gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library Data Driven Documents (D3).
Bridging enrichment analysis across multiple libraries.
Twitter bot tracking tweets about human genes. EnrichrBot performs six tasks, each task is scheduled as a cron job.
eNRSA is an enhanced version of NRSA for analyzing nascent transcription profiles generated by PRO-seq, GRO-seq, (m)NET-seq, and Butt-seq data.
A method for virtual screening based on ensemble learning.
Machine learning-based chemical binding similarity using evolutionary relationships of target genes | ensemble evolutionary chemical binding similarity | Scripts to run ensemble evolutionary chemical binding similarity (ensECBS)
Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution.
Genome databases for vertebrates genomes.
Ongoing integration of public SARS-CoV-2 data. Browse Coronavirus RNA families, including 5' and 3' UTRs, as well as frameshifting stimulation element, s2m RNA, and packaging signal. In response to the SARS-CoV-2 outbreak, Rfam produced a special release 14.2. that includes new and updated Coronavirus families. Read more in a blog post or download the data. The complete genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate Wuhan-Hu-1, cause of the disease COVID-19. The Ensembl/GENCODE human protein-coding gene set linked to COVID-19 can be found at Human Covid-19 Gene Annotation.
Test: convert json OpenAPI to json Biotools
Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).
Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.
A system for the annotation, analysis and display of vertebrate genomes and for bacteria, protists, fungi, plants and invertebrate metazoa.
Searches Ensembl Bacteria sequences using WU-BLAST.
Ensembl Genomes Bacteria ID history converter
Searches Ensembl Bacteria sequences using Exonerate.
Ensembl Genomes Bacteria sequence search
Ensembl Genomes Fungi assembly converter
Searches Ensembl Fungi sequences using Exonerate.
Get a subset of data from a BAM | VCF file.
Ensembl Genomes Fungi ID history converter
Ensembl Genomes Metazoa assembly converter
Searches Ensembl Metazoa sequences using Exonerate.
Ensembl Genomes Metazoa ID history converter
Ensembl Genomes Plants assembly converter
Search Ensembl Plants sequences with WU-BLAST.
Ensembl Genomes Plants ID history converter
Search Ensembl Plants sequences with Exonerate.
Ensembl Genomes Protists assembly converter
Searches Ensembl Protists sequences using WU-BLAST.
Ensembl Genomes Protists ID history converter
Searches Ensembl Protists sequences using Exonerate.
Ensembl Genomes Protists sequence search
Analysis of finished and draft mouse genomic clone sequences.
The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).
Sequence similarity searching against genomic, cds, cdna and protein sequence. BLAT is available for genomic sequence and WU-Blast is used for BLASTing.
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the package provides also a filter framework allowing to retrieve annotations for specific entries.
This library provides capabilities for querying Ensembl MySQL databases and for "administering" them. It is compatible with a range of Ensembl releases.
An ensemble machine learning algorithm composed of a random forest (RF), a support vector machine (SVM), and extreme gradient boosting (XGB), with the aim of integrating diverse heterogeneous algorithms to enhance the robustness of the final predictive model.
Ensemble NMF (Non-negative Matrix Factorization ) is a software for clustering and visualising protein interaction networks.
EnsembleClust enables fast and accurate clustering of ncRNAs.
EnsembleFam: Towards a more accurate protein function prediction in twilight zone
EnsembleFlex: Protein Structure Ensemble Analysis made easy - EnsembleFlex is a tool designed to perform dual-scale flexibility analysis of protein structure ensembles, encompassing both backbone and side-chain dynamics, in an easy, streamlined and reproducible way. It offers a user-friendly, no-coding graphical interface as well as a code-based option. It complements experimental ensemble data analysis with predictive methods based on elastic network models.
An ensemble biclustering approach for querying gene expression compendia with experimental lists.
Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
Ensembler is a python package that allows fast and easy access to one and two-dimensional model systems simulations. It enables method development using small test systems and to deepen the understanding of a broad spectrum of molecular dynamics (MD) methods, starting from basic techniques to enhanced sampling and free energy calculations. It is easy to install, fast, increases shareability, comparability, and reproducibility of scientific code developments. Here, we provide insights into the package's implementation, usage, and an application example for free energy calculation.
Ensemble deep learning model for splice site prediction.
Query-based biclustering techniques allow interrogating a gene expression compendium with a given gene or gene list. They do so by searching for genes in the compendium that have a profile close to the average expression profile of the genes in this query-list. As it can often not be guaranteed that the genes in a long query-list will all be mutually coexpressed, it is advisable to use each gene separately as a query.
Fast, flexible and high-throughput querying of Ensembl LD API endpoints in R.
Query the Ensembl Variant Effect Predictor via the perl API.
Transformer-based ensemble framework for the prediction of protein-protein interaction sites.
The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Our Ensete Knowledge Base is a repository of information, sharing knowledge on Ensete (Ethiopian banana, sometimes called false banana).
Software program for omics sample outlier detection.
ENT is a highly scalable genotype phasing algorithm based on entropy minimization. ENT is capable of phasing both unrelated and related genotypes coming from complex pedigrees.
ENTAIL, for the prediction of fibril deposits involved in the amyloidoses. It was developed using over than 4000 molecular descriptors.
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified (Arumugam, Raes et al. Nature 2011). Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained.
Entourage is an open-source, command-line program designed for short-read assembly, virus identification, and intrasample sequence variation profiling, streamlining virome investigation through a single workflow.
Retrieve sequence entries from flatfile databases and files.
NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.
NCBI’s database for gene-specific information. It maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.
A collection of related protein sequences (clusters) consists of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses.
Rows of two matrices are compared for Shannon entropy, coefficient of variation, and expression. P-values can be requested for all metrics.
An open-source toolkit for entropic time-series analysis.
Accurate Monoisotopic Mass Determination Based On Isotopic Envelope.
Batch fine structure, profile and centroid calculation with resolution settings provided.
End-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways.
Tools to retrieve data from ENVISION, the database for annotation, visualization and integrated discovery portal.
a software to interplay enviromics and quantitative genomics in agriculture.
Enzkin is a MATLAB tool to estimate the Michaelis-Menten kinetic parameters
Automatic Assembly and Calibration of Models of Enzymatic Reactions Based on Ordinary Differential Equations.
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network.
Substrate specificity prediction tool of plant acyl-ACP thioesterases based on Ensemble Learning.
A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
Web service which integrates publicly available information about enzymes, such as small-molecule chemistry, biochemical pathways and drug compounds.
The EnzymeDetector database offers a comparative and integrative approach to find enzymatic annotations. The most comprehensive databases for protein and genome annotation, namely manually annotated data and text mining data from BRENDA, UniProt, KEGG, PATRIC, and NCBI's RefSeq, are integrated to have a vast view on the organism of interest. The data are complemented with self-performed annotation methods, i.e. BLAST vs. all enzyme annotations from Swiss-Prot and BrEPS enzyme pattern recognition.
EnzymeMiner identifies putative members of enzyme families or subfamilies and facilitates the selection of promising targets for experimental characterization. Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.
EnzymeML is a free and open standard based XML markup interchange format for enzyme kinetics.
EnzyMine:Addition of chemical structural information in enzymatic reactions has proven to be significant for accurate enzyme function prediction. a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature. .
barley gene and transcript abundance database. EoRNA is a Barley Expression Database that displays gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes.
The described pipeline is aimed to replicate data stored at EGA generated by the GoNL consortium
Identification of the core region of a eukaryotic gene promoter.
EP3 is an ensemble predictor that accurately identifies type III secreted effectors
EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.
EPAD is an innovative position-specific distance-dependent statistical potential for protein structure and functional study. EPAD has different energy profiles for the same type of atom pairs, depending on their sequence positions.
Efficient 3D Point Cloud Feature Learning for Large-Scale Place Recognition (EPC-Net)
EPCES (Epitopes ConsEnsus Scoring) is a new antigen Epitope Prediction method from six different scoring functions – residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition.
An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
Model for identifying DNA-RNA binding sites in disease-related proteins.
Ectopic Pregnancy Expression Knowledgebase (EPEK), that involves manual compilation and curation of expression profiles of EP in humans from published articles.
Find PEST motifs as potential proteolytic cleavage sites.
Electronic Pharmacogenomics Assistant (ePGA) - browsing pharmacogenomics knowledge on gene-drug-phenotype associations and matching individual genotype-profiles with gene haplotypes and infering the corresponding diplotype and phenotype profiles.
A Versatile Library of e-Pharmacophores to Address Small-Molecule (Poly-)Pharmacology.
epiGenomic Efficient Correlator (epiGeEC) tool to enable genome-wide comparisons of very large numbers of public epigenomic datasets.
Epigenomics Single Cell Analysis in Python.
Web application for visualizing chromosome conformation capture data in the context of genetic epidemiology.
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
Enrichment analyses on epigenomic data in a fast and user-friendly way.
A Tool for Assembling, Searching, and Classifying B-Cell Epitopes
EPIC is a R package and Shiny app to estimate the proportions of different cell types from bulk gene expression data.
EpiCarousel is a Python package designed for memory- and time-efficient identification of metacells in large-scale single-cell chromatin accessibility data. It utilizes lazy loading, parallel processing, and community detection methods to analyze atlas-level datasets.
EPicker is an exemplar-based continual learning approach for knowledge accumulation in cryoEM particle picking.
EpiClass is a Optimizing and predicting performance of DNA methylation biomarkers using sequence methylation density information. EpiClass is a software program to distinguish case samples from control samples using methylation density profiles of each sample.
Epiclomal is a method for probabilistic clustering of sparse single-cell DNA methylation data.
EPICO / BLUEPRINT Data Analysis Portal, data loading scripts and API
epiCOLOC is a web-based tool with built-in large-scale and context-dependent epigenomics annotations.
R package for the comparison and quality control of epigenomic peak files.
Handling, visualisation and analysis of epidemiological contacts. Represent epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
EpiConv is an algorithm of clustering scATAC-seq data and correcting batch effects.
A framework for linking online social media in epidemiological cohorts.
Provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock. Future work will providedata tracks for these information sources and will ID tissue specific regulation information that is helpful in dissecting QTL.
epidecodeR is an R package designed to analyze the impact of epigenetic and epitranscriptomic modifications on gene dysregulation. It integrates various modification data types and dysregulated gene lists to identify the relationship between modification degrees and gene expression shifts.
Matlab Toolbox for epidemic management using partially observable decision process framework for action selection
It infers the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.
EpiDope is a deep neural network for linear B-cell epitope prediction.
EpiFactors is a database for epigenetic factors such as histones, protamines, other proteins and lncRNAs. It compiles functional information about human and mouse epigenetic regulators, their complexes, and expression in multiple cell types to facilitate the work of researchers in the field of epigenetics.
Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves. Main functions: epiFilter (or epiFilterSm) performs forward filtering to generate causal R estimates; epiSmooth performs backward smoothing to generate R estimates that use all possible information and recursPredict provides one-step-ahead predictions.
An R package for risk assessment of travel-related spread of disease | ☣✈️ Risk assessment of travel-related disease spread | Predicting Disease Spread from Flow Data | Welcome to the epiflows package! | epiflows is a package for predicting and visualising spread of infectious diseases based on flows between geographical locations, e.g., countries. epiflows provides functions for calculating spread estimates, handling flow data, and visualization
Extracting patterns and identifying co-expressed genes from RNA-Seq data.
epiGBS2 is an improved protocol and automated snakemake workflow for highly multiplexed reduced representation bisulfite sequencing.
EpiGEN is an epistasis simulation pipeline written in Python. It supports epistasis models of arbitrary size, which can be specified either extensionally or via parametrized risk models. Moreover, the user can specify the minor allele frequencies (MAFs) of both noise and disease SNPs, and provide a biased target distribution for the generated phenotypes to simulate observation bias.
EpigenCentral provides online analyses of epigenetic patterns related to diseases, intended for the broad biomedical community and clinical practitioners. Epigenetic disruptions play a key role in many congenital diseases, such as neurodevelopmental syndromes involving autism and intellectual disabilities.
Epigenetic Pacemaker is a fast conditional expectation maximization algorithm for modeling epigenetic state written in Python.
Epigenetic Target Profiler is a web server to predict epigenetic targets of small molecules. The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for different targets, which involves an under-representation of epigenetic targets, and despite the increasing importance of epigenetic targets in drug discovery, there are no open tools for epigenetic target prediction. In this work, we introduce Epigenetic Target Profiler (ETP), a freely accessible and easy-to-use web application for the prediction of epigenetic targets of small molecules. For a query compound, ETP predicts its bioactivity profile over a panel of 55 different epigenetic targets
R package for estimating epigenetic age from Illumina DNA methylation microarray data. THE WID_clocks function uses a methylation beta matrix and returns the WID general, epithelial and immune clocks. It also returns the WID-relative-epithelial-age (WID_rea) and WID-relative-immune-age (WID_ria) (∆WID epithelial or WID immune and WID general clock). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02603-3
A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.
Enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest, and its searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, it can predict the status of genomic regions that were not included in the input dataset.
An open-source platform to quantify epithelial organization | EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any computational or natural tessellation | The EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any made by computational or natural tessellation
EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments this with a wealth of additional data from other bioinformatic sources. EpiGraphDB aims to support appropriate application and interpretation of causal inference in systematic automated analyses of many phenotypes.
epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis.
EpiInvert is an R package designed for analyzing and forecasting epidemiological time series. It provides tools for incidence curve decomposition, comparison of time series, and short-term forecasting, incorporating variational techniques.
Precise and scalable evolutionary placement with informative k-mers.
Community-based ontology tailored for semantic interoperability and text mining.
Logical modelling of Epithelial dynamics. Definition, simulation and visualisation of qualitative models for epithelial pattern formation.
Detecting high-order epistasis interactions using mixed effect conditional inference forest (epiMEIF).
EpiMetal is an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics.
A database of curated mutual regulation between miRNAs and epigenetic modifications.
Mathematical Modeling of Infectious Disease.
EpiMOLAS (Epi-genoMics OnLine Analysis System) is an intuitive web-based framework for genome-wide DNA methylation analysis.
A mathematical dashboard for the analysis of Italian COVID-19 epidemic data.
EpiMut is software for functional annotation of amino acid substitutions (AASs) in epigenetic factors that is independent from sequence alignments and homology search. It is based on the biochemical and physicochemical characteristics of amino acids and digital signal processing approach in protein sequence analysis.
The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.
A nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants.
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads.
Extension of the original Nested Effects Models (NEM). It is able to take into account double knockouts and infer more complex network signalling pathways.
Platform for Analysis and Visualization of Peptide Immunoarray Data.
Resource facilitating epitope-vaccine design against human pathogenic orthopoxviruses.
EpiRegio is a resource of Regulatory EleMents (REMs) associated to protein coding, and non-protein coding genes. For a detailed documentation, please read our documentation.
An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. EpiRomics is also designed for regulatory network analysis in order to identify enhancer and enhanceosome regions from these data.
EPISCORE is a R pacakge for cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. It is a computational algorithm that performs virtual microdissection of bulk tissue DNA methylation data at single cell-type resolution for any solid tissue. EPISCORE applies a probabilistic epigenetic model of gene regulation to a single-cell RNA-seq tissue atlas to generate a tissue-specific DNA methylation reference matrix, allowing quantification of cell-type proportions and cell-type-specific differential methylation signals in bulk tissue data.
EpiSegMix is a segmentation tool based on a hidden Markov model with flexible read count distribution types and state duration modeling, allowing for a more flexible modeling of both histone signals and segment lengths.
EPISFA is an unsupervised machine learning method for exploring gene-gene interaction in family-based data.
A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules.
Metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species.
epiTOC2 is an R-script that aims to estimate the mitotic age of a sample profiled genome-wide at the DNA methylation level. It is based on a mitotic clock model where DNA methylation errors occuring during cell-division accrue in the adult stem cell pool of a tissue, allowing tracking of the number of stem-cell divisions. epiTOC2 not only estimates the cumulative number of stem-cell divisions, but also allows the intrinsic rate of stem-cell division per stem-cell per year to be estimated if the chronological age of the sample(s) is known.
Virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly.
An interactive web application to study predicted T-cell epitopes.
Accurate Taxonomy-Aware B-Cell Linear Epitope Prediction.
Epitopedia: identifying molecular mimicry of known immune epitopes.
epitopepredict is a programmatic framework and command line tool designed to aid the process of T cell epitope prediction. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualisation and filtering of the results.
Linear Epitope Prediction Using Deep Protein Sequence Embeddings. EpitopeVec predicts linear B-cell epitopes. It takes protein sequences (FASTA format) as input and then lists the peptides (of a given amino acids length) that can be epitopes along with their respective prediction probability.
EpiVIA is joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels. EpiVIA parses each read and identifies the chimeric fragments, which are further classified into different categories based on how the read pair is aligned to the combined reference genome.
A Tool for Exploratory Data Analysis and Visualisation within Epigenome Wide Methylation Analyses (EWAS).
A proactive and automatic visual analytics system integrated with Epiviz that alleviates the burden of manually executing data analysis required to test biologically meaningful hypotheses.
A library to query and transform genomic data from indexed files
This package provides connections to the epiviz web app for interactive visualization of genomic data.
API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.
Serve data from BioConductor Objects through a WebSocket connection.
This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.
This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by BioConductor packages.
A web server for prediction, analysis and visualization of enhancer-promoter interactions.
Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.
An ecosystem for computational analysis of immunogenomics data.
Open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (blender,maya and cinema4D) to provide simultaneous access the capabilities of all of the systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease.
Epoch is an R package for the reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.
Probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.
Pick PCR primers and hybridization oligos.
eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.
Network Pruning Using Adaptive Exemplar Filters.
Extreme Pseudo-Sampler (EPS) is a feature selection and feature ranking method.
EPSD (Eukaryotic Phosphorylation Sites Database) is a well-annotated data resource of protein phosphorylation sites in eukaryotes.
EQTL prioritization using similarity measures derived from local interaction networks.
Sequence-based protein solubility prediction using multidimensional embedding.
EPSVR (Antigenic Epitopes Prediction with Support Vector Regression) is a predictor of B-cell antigenic epitopes on protein surfaces with conformational information.
EPTool is a enhancing PSSM tool for protein secondary structure prediction. In addition, EPTool equips several convenient applications, such as PSSM features calculator, and PSSM features visualization. In this paper, we propose designed EPTool, and briefly introduce its functionalities and applications. The detail accessible instructions is also provided.
EPViz is a tool to aid researchers in developing, validating, and reporting their predictive modeling outputs. A lightweight and standalone software package developed in Python, EPViz allows researchers to load a PyTorch deep learning model, apply it to the EEG, and overlay the output channel-wise or subject-level temporal predictions on top of the original time series.
An R package for the ensemble of subsets of variables for highly unbalanced binary classification.
EPypes (for event-driven piplines) is a Python library for developing data processing algorithms in a form of computational graphs and their integration with distributed systems based on publish-subscribe communication.
EPySeg is a package for segmenting 2D epithelial tissues. EPySeg also ships with a graphical user interface that allows for building, training and running deep learning models.
EQscore is a computer‐assisted image‐processing algorithm to reliably quantify erythema (across a range of skin types) in the dermatology clinical setting.
eQTL Catalogue is a compendium of uniformly processed human gene expression and splicing QTLs The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human.
eQtlBma: software to detect eQTLs by Bayesian Model Averaging. The software detects quantitative trait loci for gene expression levels ("eQTLs") jointly in multiple subgroups (e.g. multiple tissues).
eQTLHap is a comprehensive eQTL analysis tool that scans the genome for different kinds of associations. It is a haplotype-based eQTL approach identifies genetic associations not detected through conventional SNP-based methods.
eQTLMAPT is a fast and accurate eQTL mediation analysis with efficient permutation testing approaches. eQTLMAPT implements fast and accurate eQTL mediation analysis with efficient permutation procedures to control for multiple testing. eQTLMAPT provides adaptive permutation scheme which prunes the permutation process opportunely, and it models the null distribution using generalized Pareto distribution (GPD) trained from a few permutations.
Hierarchical probabilistic models for multiple gene/variant associations based on NGS data.
eQTLsingle is an R package for discovering eQTLs only with single cell RNA-seq (scRNA-seq) data, without genomic data. Discovering single-cell eQTLs from scRNA-seq data only.
eQTNMiner (expression quantitative trait nucleotide Miner) is a computational package to carry out high-resolution mapping of quantitative trait loci (QTL) for high-dimensional genomic features like gene expression, epigenetic modifications, etc… and much more.
eQTpLot is an intuitive and user-friendly R package developed for the visualization of colocalization between eQTL and GWAS data. eQTpLot takes as input standard GWAS and eQTL summary statistics, and optional pairwise LD information, to generate a series of plots visualizing colocalization, correlation, and enrichment between eQTL and GWAS signals for a given gene-trait pair.
Web-based toolbox of the Equal-Life project. With the tools gallery and a comprehensive interactive guidebook.
It is a tool for illustrating all equivalent parsimonious tandem duplication random loss (TDRL) rearrangement scenarios between two given mitochondrial gene orders where at least one of the gene orders can be rearranged into the other one by one TDRL rearrangement.
Find tandem repeats in nucleotide sequences.
Biochemical thermodynamics calculator. eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface.
Improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.
E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction.
EquiSim is an open-source articulatable statistical model of the equine distal limb.
ER-CoV is a framework backed by Artificial Intelligence (AI) that uses simple blood exams to help to perform COVID-19 screening in Emergency Rooms (ER). The focus or ER-CoV is to determine which patients are likely to be negative for the coronavirus, such that more specific exams can be prioritized for those deemed as likely positive.
ERANGE is a Python package for doing RNA-seq and ChIP-seq.
EraSOR is a python software for removing bias introduced from having overlapped samples between the base GWAS data and the target genotype data for the use in PRS analyses
ERBK (Representation learning model of bio-entities) is a representation model for biological entities by fusing structured axioms with unstructured texts.
Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.
eRDF Analyser is an interactive MATLAB GUI for reduced density function (RDF) or pair distribution function (PDF) analysis of amorphous and polycrystalline materials to study their local structure.
ERDS is a free, open-source software, designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data. It uses paired Hidden Markov models (PHMM) based on the expected distribution of read depth of short reads and the presence of heterozygous sites. ERDS is NOT good for whole exome data.
Erebus is a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules.
Producing an improve assembly in presence of a sequence belonging to a closely related organism.
ERgene is a Python library for screening endogenous reference genes.
Provides a systems-biology informatics toolkit centered on comparative genomics to capture, query and visualize sequenced genomes. Building upon the most comprehensive genomic database available anywhere integrated with the largest collection of microbial metabolic and non-metabolic pathways and using Igenbio's proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products.
ERGO Genome Analysis and Discovery System
Ergo is a C++ program for all-electron Hartree–Fock and Kohn–Sham density functional theory electronic structure calculations using Gaussian basis sets.
Software and data to support epigenomic road map adventures.
ERMer: A serverless platform for navigating, analyzing, and visualizing Escherichiacoli regulatory landscape through graph database.
ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class.
The ern R package estimates the effective reproduction number (Rt) using clinical and wastewater surveillance data. It provides a user-friendly way to assess epidemic states and the effectiveness of public health interventions.
eRNA-IDO is a computational platform for the identification, interactome discovery, and functional annotation of human enhancer RNAs. It comprises two modules, eRNA-ID and eRNA-Anno, to facilitate research on the biogenesis and functions of eRNAs.
Comprehensive database for decoding the regulatory eRNAs in human and mouse.
Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite-treated reads.
A tool for predicting coarse grain RNA tertiary structures. Create models of the tertiary structure of RNA molecules starting from the secondary structure. The resulting models contain the positions of the helices and loops in 3D.
ERODE (Evaluation and reduction of stochastic reaction networks and differential equations) is an all-in-one tool for the numerical solution, stochastic simulation, and minimization of dynamical systems with import/export options for a variety of third-party formats including SBML and Matlab.
Easy RNA Profile IdentificatioN takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.
Web server for the prediction of subtype-specific estrogen receptor antagonists.
Determine various error related performance metrics.
ErrorX is a software for automated error correction of B- and T-cell receptor NGS datasets. ErrorX uses deep learning to automatically identify bases that have a high probability of being erroneous.
Fast Python package for inferring the number of top principal components from whole genome sequencing data.
ES-ARCNN is a tool for identifying enhancers' strength by using data augmentation and residual convolutional neural network
Combining machine learning and crowd-sourcing to create a shared space for updating systematic reviews. Formerly known as trial2rev.
Evidence Surveillance Synthesis and Sharing
A web-based server for EST-SSR marker development.
framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report.
Esc (Immune escape variants in SARS-CoV-2) is a comprehensive and manually curated compendium of genetic variants in SARS-CoV-2 associated with immune escape. The data on variants and associations have been compiled from published literature as well as preprints and includes a variety of antibodies ranging from monoclonal as well as oligoclonal and convalescent plasma panels.
Open-source tool which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel.
Esophageal Squamous Cell Carcinoma Risk Assessment Tool is a tool for predicting the risk of getting esophageal squamous cell carcinoma.
Database which collects human and mouse embryonic stem cell related datasets. These datasets cover perturbation (both knock-down and overexpression) and chromatin immunoprecipitation (ChIP) experiments in embryonic stem (ES) and carcinoma (EC) cell lines. Transcription factor binding data comes from various ChIP experiments (ChIP-PET, ChIP-chip, ChIP-seq).
Escher-Trace is an interactive pathway visualization tool for on-the-fly stable isotope tracing analysis.
ESCO is an R package for the simulation of single-cell RNA sequencing data with special consideration of gene co-expression.
Escort is an R package and Shiny application designed to assist researchers in selecting optimal data processing choices for single-cell RNA sequencing trajectory inference, reducing uncertainty and improving decision-making during analysis.
Propagating gene expression in chromatin networks to illuminate active enhancers.
Web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.
Utility functions for visualization of expressionSet (or SummarizedExperiment) BioConductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.
Tool for performing comparative sequence analysis of multiple closely-related nucleotide or protein sequences.
The NEW ESID online database network. European Society for Immunodeficiencies. Exchange of ideas and information among doctors, nurses, biomedical investigators, patients and their families concerned with primary immunodeficiency diseases (PID). ESID Registry (click to go to ESID Registry login page). In 2018, the ESID Registry WP renewed its call to support national registries and individual documenting centres in your invaluable work associated with the documentation within the ESID Registry.
A computationally intelligent method to identify earthworm species (E. fetida) from digital images.
eSignal is a database of eMOTIFs and eMATRICES generated exclusively from signal transduction proteins. ESIGNAL can be used to discover signal transduction functions in new proteins.
Simple deconvolution of electrospray ionization peak lists.
Simple deconvolution and 2D peak picking of LC-MS data.
Charge state determination and molecular weight calculation for low resolution electrospray ionization data.
Machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping.
Tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.
"ESLpred2" is an improved version of our previous most popular method, ESLpred, which can predict four major localizations (cytoplasmic, mitochondrial, nuclear and extracellular) with an accuracy of 88%.
A statistical model to infer admixture events from individual genomics data.
A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels.
Curated database of biomarker genes and miRNAs associated with esophageal cancer.
NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.
Practical High-Quality Electrostatic Potential Surfaces for Drug Discovery Using a Graph-Convolutional Deep Neural Network | A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces | For generating ligand PQR files, a graph convolutional deep neural network (DNN) model, trained on ESP surfaces derived using DFT calculations for ~100,000 molecules, is used. For proteins, parametrized charges for amino acids are used, which are fully compatible with the ligand ESP surfaces generated using the DNN model
A general model to predict small molecule substrates of enzymes based on machine and deep learning.
R package for automation, exploitation and processing of DICOM files in medical physics and clinical research.
End-to-end differentiable construction of molecular mechanics force fields.
An online data-analysis platform for molecular biophysics.
ESPRES is a web application for interactive analysis of multiple pressures in aquatic ecosystems.
An algorithm for hierarchical clustering and taxonomic clustering of next generation sequencing data.
Essential component analysis of Hi-C matrices. Here we introduce essHi-C, a method to isolate the specific, or essential component of Hi-C matrices from the aspecific portion of the spectrum that is compatible with random matrices. Systematic comparisons shows that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices.
EssSubgraph is a model algorithm that integrates omics data and network data to predict essential genes.
Platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.
Align EST sequences to genomic DNA sequence.
Automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
EstimAge is a webserver hub for the computation of methylation age.
Estimate LDL cholesterol based on measured total cholesterol (TC), HDL, and triglycerides (TG).
R package to estimate and monitor the effective reproductive number.
A set of MATLAB functions for computing a smooth approximation to the precision-recall curve.
Estimating a smooth precision-recall curve
ESTIpop is an R package that estimates the parameters of continuous-time Markov branching processes (CTMBPs) with constant or time-dependent rates.
Program that performs the preprocessing for cDNA reads. The program detects all the characterstics found within a sequence viz. restriction site, cloning vector, polyA tail, library tag, polyA signal. It also predicts whether the sequence should be used for further processing or should be rejected. If accepted the region within the sequence which is high quality is also identified.
A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
ESTScan can detect coding regions (CDS) in DNA sequences, even if they are of low quality. It also detects/corrects sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. The program may miss a few translated amino acids at termini, but detects coding regions with high selectivity and sensitivity.
An Ensemble Transfer Learning Network for COVID-19 detection from lung CT-scan images.
ET-Score is a scoring function based on Extra Trees algorithm for predicting ligand-protein affinity.
Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.
Find tandem repeats in a nucleotide sequence.
Textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.
A common platform that may be used in different calibration scenarios in video based oculography.
ETCHING is ultra-fast and high-performing somatic SV detector that significantly reduces the mapping cost by filtering reads matched to pan-genome and normal k-mer sets.
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org
ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and analysis framework
Ethoflow is a computer vision and artificial intelligence-based software for automatic behavior analysis.
EthoLoop is a framework for studying the neuroethology of freely roaming animals. Combining real-time optical tracking and behavioral analysis with remote-controlled stimulus-reward boxes, this system allows direct interactions with animals in their habitat. EthoLoop continuously provides close-up views of the tracked individuals and thus allows high-resolution behavioral analysis using deep-learning methods.
Extensive Tool for Network Analysis (ETNA) is an user-firendly graphical interface for the network analysis that contains classical measures and simulation-based ones.
An open source framework that allows the automated prediction of ligand-binding free energies requiring the ligand structure as only input.
ETph is a database for enhancer and their targets in pig and human.
A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients.
EUAdb is database for COVID-19 test development that contains standardized information about Eemergency Use Authorizations-issued tests and is focused on RT-qPCR diagnostic tests, or high complexity molecular-based laboratory developed tests.
EUCAIM CDM Federated Unbalance Checker is a lightweight framework for federating data quality checks across distributed datasets. It enables local computation of key statistics (age, sex, ethnicity) and centralized aggregation to detect imbalances across nodes. Ideal for pre-testing federated analysis pipelines, it provides modular runner and aggregator scripts, with a command-line interface for seamless execution and logging, helping validate dataset representativeness before federated learning or clinical research workflows.
The EUCAIM DICOM Anonymizer anonymizes a set of DICOM files. It supports both anonymization on a case-by-case scenario, meaning one DICOM Study at a time (single-mode) or on multiple cases concurrently (batch mode). Additionally it hashes and links clinical data.
This repository provides tools for segmentation files conversion in DicomSEG
The EUCAIM Wizard Tool performs an analysis of data re-identification risks of imaging and clinical data that follow the EUCAIM CDM. It includes and uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx), by supporting a wide variety of privacy and risk models as well methods for analyzing the usefulness of output data.
Computational BioMedicine Laboratory, Foundation for Research and Technology Hellas (FORTH)
Package to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases or as unknown based on their ambiguous genus classification. It measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.
Gene prediction software for eukaryotic organisms. It is currently mainly tuned for plant and fungal genomes.
Gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.
Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.
European Hepatitis C virus database (euHCVdb)
This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction.
EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.
The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanity.
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.
Eukaryotic Pathongen Database Resources (EuPathDB)
The EuphausiiDB portal offers the possibility for users to explore an Euphausiidae transcriptom database by using “simple” and “advanced” search functions for a specific taxonomic level, a specific geographic location or project origin, and a specific annotation. Statistical interactive charts, readsets location maps and tables, and the resulting list of datasets are associated with the search functions. For each selected dataset, the user can access readset and assembly short summary pages with cross-references to external databases (EBI SRA, NCBI taxID, WORMS), which allow better traceability and homogeneity across databases, as well as the possibility of downloading all resulting files...The intention is to develop the database continually as the transcriptomes of new species are sequenced and thus provide an up-to-date reference dedicated to the diversity of euphausiids.
Search catalogue providing information about plant genetic resources collections maintained in Europe. It is based on a European network of ex situ and in situ National Inventories (NIs). Currently, it comprises information about 2.1 million germplasm accessions from more than 400 holding institutions from 43 countries. It contains both passport data and phenotypic data.
European Cooperative Programme for Plant Genetic Resources (ECPGR)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
EuroCarbDB is a repository of carbohydrate structures, experimental evidence, and carbohydrate-oriented research and analysis tools.
Archive of life sciences journal literature.
Tool that allows article authors to build a bibliography and export it to ORCID.
Anyone from at least one of the Europe PMC Funders can submit an author manuscript for inclusion in Europe PubMed Central. Publishers can also submit manuscripts on behalf of authors.
Europe PMC plus Manuscript Submission System MSS
Access to all of the publications and related information held in the Europe PMC database.
Europe PMC RESTful Web Service for Articles
INFRAFRONTIER is the European Research Infrastructure for phenotyping and archiving of model mammalian genomes. The core services of INFRAFRONTIER comprise the systemic phenotyping of mouse mutants in the participating mouse clinics, and the archiving and distribution of mouse mutant lines by the European Mouse Mutant Archive (EMMA). EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant mouse strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. The comprehensive physical and data resources of EMMA support basic biomedical and preclinical research, and the available research tools and mouse models of human disease offer the opportunity to develop a better understanding of molecular disease mechanisms and may provide the foundation for the development of diagnostic, prognostic and therapeutic strategies.
INFRAFRONTIER and the European Mouse Mutant Archive (EMMA)
This web service gives programmatic access to all of the publications and related information in Europe PubMed Central (Europe PMC).
This project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or the predicted phenotype.
Database for EV-associated DNA in human liquid biopsy samples.
The EV Antibody Database is an interactive resource aggregating and sharing antibody validation results for extracellular vesicle (EV) research. It provides detailed information on antibody sources, assay conditions, and results, including negative findings, to minimize wasted resources and reagents.
The European Variation Archive (EVA) accepts submission of, and provides access to, all types of genetic variants from any species, observed in germline or somatic sources, ranging from SNVs to large structural variants. All of our data is open access via direct query through web and/or programmatic interfaces.
Software package aimed at describing inbreeding in a population and predicting genetic contributions of breeding candidates while maximizing response to selection given a penalty on/constraining the rate of inbreeding.
EVA is a deep-learning-based program that automatically evaluates the fidelity of metabolic features generated from LC-MS experiments
Automate the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.
Non-profit organisation dedicated to the characterisation, conservation, production, distribution and characterisation of biological materials in the field of virology.
Eval is a flexible tool for analyzing the performance of gene-structure prediction programs. It provides summaries and graphical distributions for many statistics describing any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another.
A machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
R Package for Evaluating Label-Free Proteome Quantification
Tools for evolutionary accumulation and cancer progression models.
EVAnalyzer is a new open‐source plugin for Fiji, developed for automated single vesicle quantification from fluorescence microscopy images
Database for ncRNA expression in human extracellular vesicles.
An optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets.
Eventer is a standalone application for the detection of spontaneous synaptic events acquired by electrophysiology or imaging, utilizing supervised learning to classify events. It aims to increase throughput and reproducibility in neuroscience research by allowing users to train models for consistent analysis.
It identifies alternative splicing events that involve either simple or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays or sequencing data. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
Evergene is a Shiny webtool for large-scale, gene-centric analysis of primary tumors utilizing RNA-sequencing data. It allows users to perform analyses such as principal component analysis, survival analysis, and correlation analysis, and allows uploading custom data for analysis.
A text mining resource built on top of PubMed abstracts and PubMed Central full texts.
EVICAN (Expert visual cell annotation) is balanced dataset for algorithm development in cell and nucleus segmentation.
Interactive Web Platform for Exploration of Molecular Features and Response to Anti-cancer Drugs.
Search tool under development in the UKPMC project. It locates sentences that present evidence in the text of research papers. Sentences from 1.5M papers in the UPMC corpus are indexed based on linguistic analysis and NER. Initial search results take the form of questions representing the most frequent types of relevant evidence in the index. On selecting a question, the user may review details of the documents containing the evidence, including the indexed sentences.
Visual analytics tool for data enrichment in SNP-based phylogenetic trees.
EView is an on-line platform for 3D electric field simulation in electroporation-based treatments using needle-shaped electrodes. EView provides an easy way to obtain approximate estimations of the electric field distribution for arbitrary electrode positions and orientations. EView has been developed with the aim of facilitating the understanding of how the electric field distribution depends on the geometry of the electrode setup and the applied voltage.
A platform for analysis of expression, variation and identification of human virus receptors.
Network enrichment analysis with flexible definition of gene sets.
Evitar (Emerging-Virus-Targeting RNA) is a program for (1) pre-designing siRNAs/Cas13a guide RNAs against future viruses based on existing viral sequences, and (2) designing siRNAs/Cas13a guide RNAs against a single virus based on sequences of multiple strains of this virus.
eVITTA (easy Visualization and Inference Toolbox for Transcriptome Analysis) is a web-based visualization and inference toolbox for transcriptome analysis.
A web tool for prediction of experimentally validated lncRNAs by deep learning.
EVlncRNAs is a comprehensive, manually curated, high-quality and freely accessible resource of integrated sequence, structure, functional, and phenotypic information of experimentally validated long noncoding RNAs from all species.
A statistical method for predicting the effects of mutations.
EvntExtrc is a biological event extractor on biomedical literature | Context awareness and embedding for biomedical event extraction
Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology. Evolutionary Atlas of Cardiac Transcriptomes and homologous Genes. EvoACTG Evolutionary Atlas of Cardiac Transcriptomes and homologous Genes. EvoACTG is a web-repository of chamber-specific cardiac transcriptome data for 7 different vertebrate species with diverse anatomy.
Improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations.
Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow.
EvoCor is a web server for predicting functionally related genes using phylogenetic and expression profiles.
EvoDesign web server is an evolutionary profile based approach to de novo protein design. Starting from a scaffold of target protein structure, EvoDesign first identifies protein families which have similar fold from the PDB library by TM-align.
Graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies.
Evol2Circos is web application for genome synteny and collinearity analysis and its visualization in fishes.
A web interface to visualize continuous phylogeographic reconstructions.
A Comprehensive resource on Olfactory receptors
Phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multispecies data.
Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.
evolSOM is an R package that explores and visualizes the conservation or displacement of biological variables, facilitating the integration of phenotypic and genotypic attributes. It allows projection of multi-dimensional expression profiles onto interpretable two-dimensional grids.
EvoLSTM is a context-dependent models of sequence evolution using a sequence-to-sequence LSTM
Web server for displaying, managing and customizing phylogenetic trees.
Comparative genomics tool for discovering conserved DNA sequences that are shared among three or more orthologous DNAs.
EvORanker is an interactive web tool for prioritizing candidate genes using coevolution and STRING.
EvoRator employs machine-learning for prediction of residue-level evolutionary rates from protein structure. This prediction is based on various features comprising the structural information characterizing the protein.
Evolutionary reconstruction of haplotypes.
EVPsort is a database and tool for profiling and sorting small non-coding RNAs within extracellular vesicles and particles. It integrates multiple databases and tools to investigate RNA-binding proteins and downstream functional effects, offering a comprehensive resource for researchers.
A database of epigenome-wide association studies.
EWAS Open Platform is a comprehensive analysis suite that integrates EWAS Atlas, EWAS Data Hub and EWAS Toolkit for epigenome-wide association studies.
EWASex is an efficient R-package to predict sex in epigenome-wide association studies.
This tool contains Infinium Human Methylation BeadChip pipeline that can be installed and used inside the Galaxy. The pipeline steps include: raw intensity data loading .idat preprocessing, optional normalisation of the data, quality control with additional sample check. It gives the user the opportunity to perform any of these preparation and data cleaning steps, including the next highly recommended genetic variation annotation step resulting in single nucleotide polymorphism identification and removal by simply running the tool. Finally, the dataset generated through all of these steps can be used to hunt find differentially-methylated positions DMP and regions DMR with respect to a phenotype co-variate.
Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.
EwE has three main components: Ecopath – a static, mass-balanced snapshot of the system; Ecosim – a time dynamic simulation module for policy exploration; and Ecospace – a spatial and temporal dynamic module primarily designed for exploring impact and placement of protected areas. The Ecopath software package can be used to
ExaBayes is a software package for Bayesian phylogenetic tree inference. It is particularly suitable for large-scale analyses on computer clusters.
Exome aggregation consortium (ExAC) - browser framework to display large population datasets of genetic variation. The browser aggregates exome sequencing data from a wide variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.
A collaboration toolset for algorithm-aided annotation of images with annotation version control. Rest API sync with the EXACT Server https://github.com/ChristianMarzahl/Exact.
ExActR is a Shiny app that generates ecosystem extent accounts from shapefiles, enabling users to quantify land cover change over time according to the SEEA-EA framework. The application facilitates the understanding, visualisation, and tracking of changes in ecosystem assets for both scientists and stakeholders.
A multimodal explanation framework for computer-aided diagnosis of skin lesions.
Compare and search the exon-intron structure of existing gene annotations.
Set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
Finding an informative subset of a set of markers.Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. It uses a depth-first search combined with a branch-and-bound approach to search the space of marker sets of a given size.
Integrated large scale dataset facilitating Big Data analysis in chemogenomics.
Web-based application that was developed to support the exchange and long-time storage of experimental data, especially spreadsheets in general and immunoblot-related experiments in particular. It is able to parse these data from the initial experimental setup stage and to automatically generate the following spreadsheet stages in the experimental workflow.
ExceS-A is a fast, exon-centric spliced aligner and is included in the ExonMatchSolver pipeline.
A Flexible Statistical Framework for Estimating Excess Mortality.
Exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies.
EXFI is a tool for exon and splice graph prediction without a reference genome.
ExfilMS is a tool to filter mass spectrometry data in mzML.
Identifying external communication signals using single-cell transcriptomics data.
Exhaustive feature selection for classification and survival analysis.
Exposome of Human Milk across India (ExHuMId) is a curated resource and analysis of exposome of human milk across India.
Software package for detecting Identity-by-descent (IBD) segments in exome sequencing data.
This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.
ExMdb is a database of exosomal nucleic acid biomarkers and disease-gene associations curated from published literature and high-throughput datasets. It provides comprehensive data on gene-disease associations, biomarkers, and subcellular locations, along with high-throughput sequencing datasets.
EXMO (Exercise Medicine Ontology) is a reference ontology for individualized exercise prescriptions, providing a structured vocabulary of physical activity, health status, and exercise prescription terms. It aims to support personalized exercise recommendations and integrate with databases and recommendation systems.
ExMove is an open-source R toolkit for processing and exploring animal-tracking data. It facilitates data cleaning and standardization, improving reproducibility and enabling data sharing.
MATLAB program for analyzing H/D-exchange data.
ExoBCD is a comprehensive database for exosomal biomarker discovery in breast cancer.
Manually curated database of exosomal proteins, RNA, and lipids. Catalogs information from both published and unpublished exosomal studies. Currently contains info on 11,261 protein entries, 2375 mRNA entries, and 764 miRNA entries obtained from 134 exosomal studies.
ExoDIVERISTY is a tool that can be used to resolve diverse protein-DNA footprints from exonuclease based ChIP experiments such as ChIP-exo or ChIP-nexus.
Exodus is a bioinformatics pipeline aimed to quantify relative abundance of highly similar sequences.
ExoLocator is a database of protein coding exons from completed vertebrate genomes in Ensembl. Exons are organized into alignments of ortologous and paralogous sequences, and when an exon appears to be missing form a species, we look for it using our own hardware accelerated version of Smith-Waterman algorithm.
Search the Exome Variant Server for genetic variants identified in patients using a chromosome position.
Identifies copy number variation from targeted exome sequencing data.
Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.
Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built based on the MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome.
ExomePicks is a program that suggests individuals to be sequenced in a large pedigree.
ExomiRHub is a database and analytical platform designed for biologists to host, analyze, and interpret human extracellular microRNA transcriptomics data. It integrates a large collection of datasets and offers 25 analytical functions, along with tools for miRNA function and target evaluation.
A program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a VCF file and a set of phenotypes encoded using the Human Phenotype Ontology (HPO) it will annotate, filter and prioritise likely causative variants depending on the user-defined criteria.
The Exon Array Analyzer (EAA) allow to process CEL files from Affymetrix, Inc. GeneChip® Exon 1.0 ST Arrays. Various processign steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.
A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.
ExonSurfer is a web-based tool for designing high-specificity primers for qPCR, targeting exon junctions and avoiding genomic amplification. The tool includes features for specificity assessment, self-complementarity verification, and is available as a command-line tool with published source code.
Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement.
Prediction of unconventional protein secretion by exosomes.
ExoProPred is a webserver to predict exosomal proteins based on hybrid model that combines machine learning model with motif-search approach.
Exorcise is a software tool that corrects mis-annotations in CRISPR guide libraries by using exome sequencing to verify target presence and apply corrections. It improves CRISPR screen results by focusing experiments on the genome of the cell line under investigation and can be applied both during library design and post-hoc analysis.
ExOrthist is a Nextflow based pipeline to infer exon orthology groups at all evolutionary distances. As a crucial innovation, ExOrthist sequentially evaluates three features when inferring exon homologous relationships: conservation of up/downstream intron positions and phases, conservation of the exon sequence, and conservation of the up/downstream exon sequences.
ExPa (extreme pathways analysis) , a generating set for all possible steady state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix, an incidence-like matrix reflecting the network topology. ExPa compute these pathways.
expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.
Expansin Engineering Database integrates information on sequence, structure and function of expansins.
Webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics.
Automated inference of gene regulatory networks using explicit regulatory modules. This GitHub project provides the code for the network inference and model expansion procedures, along with all the related scripts used in the paper Automated Inference of Gene Regulatory Networks Using Explicit Regulatory Modules (non published).
Structure motif based alignment generation.
Simultaneous exact pattern matching and folding of RNAs.
Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools, supporting a range of life science and clinical research domains.
EXPath is a database resource that collects and utilizes expression profiles derived from microarray under various conditions to infer metabolic pathways for six model plants: Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycine max, and Medicago truncatula. Five main functions in EXPath are as follows.
An effective and interpretable pooling method for predicting DNA-protein binding.
Web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments.
This package provides a client for the BioConductor corresponding web resource, which is a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.
Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.
ExperimentSubset is an R package to manage subsets of Bioconductor Experiment objects. ExperimentSubset package enables users to perform flexible subsetting of Single-Cell data that comes from the same experiment as well as the consequent storage of these subsets back into the same object. It offers the same interface to the users as other Experiment classes but with additional subset support.
ExPheWas is a browser for gene-based pheWAS associations. The ExPheWas browser showcases the results of a phenome-wide association study (PheWAS) using an approach that models the joint effect of variants at protein coding genes.
ExpHunterSuite is an R package for the comprehensive analysis of transcriptomic data.
Expipe is a lightweight data management platform to simplify the steps from experiment to data analysis.
A Visual Analytics Framework for Interactive and Explainable Machine Learning | The framework for explainable AI and interactive machine learning. Making XAI accessible | The recent abundance of artificial intelligence and the resulting spread of black-box models in critical domains has lead to an increasing demand for explainability. The field of eXplainable Artificial Intelligence tackles this challenge by providing ways to interpret the decisions of such models. Which, in turn, resulted in a variety of different explaining techniques, all having various dependencies and providing highly diverse outputs | Besides the variety of XAI methods, there also is a variety of user-groups with different interests and requirements. They need tailored access to XAI methods that suit their needs and support them in their daily workflow | Our XAI framework structures the process of XAI
Linkage analysis of quantitative trait loci using bulk segregant analysis.
Content Prefetching for Tile-Based Immersive Video Streaming Applications.
Explore and analyze *omics data with R and GGobi.
A pipeline to explore active transposable elements from RNA-seq data.
ExploreModelMatrix is a small R package that lets the user interactively explore a design matrix as generated by the model.matrix() R function. In particular, given a table with sample information and a design formula, ExploreModelMatrix illustrates the fitted values from a general linear model (or, more generally, the value of the linear predictor of a generalized linear model) for each combination of input variables, simplifying understanding and generation of contrasts. A number of other visualizations are also included in the interactive interface, particularly simplifying the interpretation of linear models.
Reconstruction and annotation of bacterial mobile elements from draft genomes.
A tool for online learning, blockchain network, and consensus algorithm. EXpectation Propagation LOgistic REgRession on permissioned blockCHAIN (ExplorerChain): Decentralized privacy-preserving online healthcare/genomics predictive model learning.
ExpoKids is an R-based tool for characterizing aggregate chemical exposure during childhood.
Helps researchers quickly find knowledge gaps and identify what research projects have been completed before.
Export objects described in a logical matrix, label matrix or voxel list to STL and PovRay mesh2.
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.
To export ONE history data, WARNING this tool duplicate the data, remember to delete redundant data.
Export history data for SynBioWatch projet files and user.
Export stiffness and mass matrices from NASTRAN
The Exposome Maps contain geospatially resolved data on environmental exposures (Exposome Surfaces), categorized into the following Exposome dimensions: Built Environment28 exposures related to: • Green space • Blue space • Grey space Food Environment4 exposures related to: • Food landscape / healthy food index Physico-Chemical Environment99 exposures related to: • Air pollution • Biodiversity • Weather conditions • Light intensity at night • Noise • Pesticides • Electromagnetic fields Social Environment70 exposures related to: • Neighbourhood socio-economic position • Neighbourhood Demographic surfaces and population characteristics • Social capital • Security • Mental health • Proximity to facilities • Energy use • Labour market
ExposomeShiny is a standalone web application implemented in R. It is available as source files and can be installed in any server or computer avoiding problems with data confidentiality. It is executed in RStudio which opens a browser window with the web application and provides a bridge between researchers and most of the state-of-the-art exposome analysis methodologies, without the need for advanced programming skills.
Streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It can be used to resolve ambiguous mappings in other high-throughput sequencing based applications.
Unified platform for RNA-sequencing analysis in non-model species.
Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells.
Open science resource that gives users a powerful way to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others.
Web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.
It is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.
ExpressionBlast is a search engine for gene expression data. It allows you to compare your own expression results to over thousands of studies and close to a million samples currently available at GEO, and find other studies (even across species) that have similar (or opposite) expression patterns to your results.
R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.
identify and explore the binding of transcription factors to their target genes in plants using available ChIP-Seq data.
A biologist-oriented interactive web server for exploring multi-omics data.
ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
Rapidly build and deploy supervised machine learning in a high-throughput manner. It provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, as well as regression, with minimal programming experience necessary.
Customizable RNA-seq Data Analysis and Visualization Platform.
exRNADisease is a database designed for providing the landscape of different types of extracellular RNAs (mRNAs, lncRNAs, miRNAs, circRNAs, tRFRNAs and piRNAs) from body fluids in human diseases.
EXSIMO (EXecutable SImulation MOdel) is a Python package for executing simulation models of the liver.
exSTRa is an R package for the detection of repeat expansions with Illumina next-generation sequencing (NGS) data of cases and controls. exSTRa supports both whole-genome and whole-exome sequencing (WGS and WES). Only paired-end data is supported.
Latent variable modelling and variational inference for scRNA-seq differential expression analysis
eXtasy is a pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype. It takes into account the putative deleteriousness of the variant, haploinsufficiency predictions of the underlying gene and the similarity of the given gene to known genes in the given phenotype.
ExTaxsI (Exploring Taxonomy Information)I is a bioinformatic tool aimed to elaborate and visualize molecular and taxonomic informations. This open-source user friendly project, written in Python 3.7, allows the creation of interactive plots starting from NCBI search query or directly from offline taxonomic files.
The tool provides a semi-supervised metric (EAPP) for binary classification tasks that considers not only the a priori probability but also some possible bias present in the dataset, as well as other features that could provide a relatively trivial separability of the target classes. Therefore, it allows for evaluating the ease or complexity of the task or bias of the data beyond the well-established baseline for any binary classification.
EAPP - Extended a Priori Probability tool
EXTRACT identifies genes/proteins, chemical compounds, organisms, environments, tissues, diseases, phenotypes and Gene Ontology terms mentioned in a given piece of text and maps them to their corresponding ontology/taxonomy entries.
Threshold microscope images and calculate object area fractions.
Extract platelet area fraction from microscope images
A tool for decompressing an archive file (zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2) and merging all files into only one.
Script used to extract protein names from a peptide identification file.
Extract regions from a sequence alignment.
The project is based on real time multiple particle to extracted bigger particle using microscope and count particle
Extract central regions of ChIP-seq peaks.
MATLAB tool fpr extracting reaction rate from SimBiology model.
Extraction of reaction rates from SimBiology
Function for calculating the extracted drug fraction in liquid-liquid extraction
ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequence conservation.
ExtRamp Online is an interfaced version of the original ExtRamp software that extracts ramp sequences in the browser using Pyodide. All options are set to defaults for an analysis on human genes.
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm | Extract discriminatory ARGs from metagenomics samples
ExVe is the knowledge base of orthologous proteins identified in fungal extracellular vesicles.
Eye Disk Segmentation Using Luminance Channel and Active Contour. This program try to segment eye disk area using luminance channel and active contour.
Eye Disk Segmentation Using Luminance Channel and Active Contour
Exploring the potential of convolutional neural networks for identification of multiple eye diseases through retinal imagery.
An integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.
EyeDose is an open-source tool for using published Monte Carlo results to estimate the radiation dose delivered to the tumor and critical ocular structures for 125I Collaborative Ocular Melanoma Study eye plaques.
EyeLoop is a Python 3-based eye-tracker tailored specifically to dynamic, closed-loop experiments on consumer-grade hardware. This software is actively maintained: Users are encouraged to contribute to its development.
An open-source video analysis pipeline for the investigation of animal behavior. This repository contains iPython files that can be used to track the location, motion, and freezing of an animal. For the sake of clarity, these processes are described as two modules: one for the analysis of freezing; the other for tracking an animal's location.
This tool produces histograms or density plots from any tabular datasets, using ggplot2. You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable.
EzAAI is a pipeline for high throughput calculations of prokaryotic average amino acid identity. EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis.
ezAlign is an open-source software package that converts coarse-grained molecular dynamics structures to atomistic resolution for multiscale modeling of biomolecular systems. The tool aligns a template molecule, minimizes energy, and combines molecules to facilitate more detailed simulations.
EZcalcium is a flexible, user-friendly toolbox for analysis of calcium imaging data, controlled by a set of intuitive graphical user interfaces (GUI) based on MATLAB.
An open-access drug repurposing and data-collection tool to enhance target validation and optimize international research efforts against highly progressive cancers.
EZcount is an all-in-one software for microRNA expression quantification from NGS sequencing data.
ezGeno is an open source genomics data analysis package based on deep learning for auto tuning network structure and building models.
The EZImputer workflow is a modular set of scripts for genome-wide imputation. It automates many of the steps regularly needed for an imputation project.
EZmito is a bioinformatic tool for phylogenetic data preparation, nucleotide composition analysis of mitogenomes and chimerical regions detection produced during the assemly step
A Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci and GWAS.
ezSingleCell is a user-friendly, integrated platform for single-cell and spatial omics data analysis, combining publicly available methods within a unified interface. It's available as a web application or a downloadable Shiny app.
ezTree is a Perl pipeline for identifying marker genes and build phylogenetic trees for a set of genomes. This script is used to get single copy marker genes from a set of genomes, including genome bins recovered from metagenomes, and align them for phylogenetic tree reconstruction.
EzySCR is a free, semi-automated tool for scoring event-related skin conductance responses (SCRs) in the first, second, and third interval latency windows, designed to reduce processing time while maintaining high data quality comparable to manual scoring.
F-seq is a software package that generates a continuous tag sequence density estimation based on tag sequencing to identify specific sequence features such as transcription factor binding sites (ChI-seq) or regions of open chromatin (DNase-seq).
F3UTER (Finding 3' UnTranslated Expressed Regions) is a R library and web application that enables identification of unannotated 3’UTRs for synaptic genes.
GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis | Re-engineered and optimised Nanopolish call-methylation module (supports CUDA acceleration) | An optimised re-implementation of the call-methylation module in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, f5c detects the methylated cytosine bases. f5c can optionally utilise NVIDIA graphics cards for acceleration
Flexible annotation atlas (FAA) of the mouse brain is a pipeline for constructing a mouse brain atlas using Allen Institute for Brain Science (AIBS) data.
Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes.
FaaPred is a SVM-based prediction method for fungal adhesins and adhesin-like proteins
Focal Adhesion Analysis Server. Implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells.
Model-based technique for biclustering where the biclusters are found by factor analysis. It is a multiplicative model that extracts linear dependencies between samples and feature patterns capturing realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. Finally, it ranks biclusters according to their information content and separates spurious biclusters from true biclusters.
FABIAN-variant uses transcription factor flexible models (TFFMs) and position weight matrices (PWMs) to predict the effect of DNA variants on transcription factor binding.
FABRIC Cancer Portal is a comprehensive catalogue of human coding genes in cancer based on the FABRIC framework. FABRIC quantifies the selection of genes in tumor and weighs their evidence for being cancer drivers.
FACETS is an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms.
Package for fine-tuned cancer CNA association modeling. Association is measured directly at the genomic features of interest and, in the case of genes, downstream gene-set enrichment analysis can be performed thanks to novel internal processing of the data. The software opens a way to systematically scrutinize the differences in CNA distribution across tumoral phenotypes, such as those that relate to tumor type, location and progression.
Rapid and accurate classification of sequences as belonging or not belonging to a reference sequence.
antimicrobial peptide screening in genomes and metagenomes. The antimicrobial peptides prospection pipeline. Fast AMP Classification System: Predict AMPs in (meta)genomes and peptides. FACS pipeline - Fast AMP Classification System.
Profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.
Real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed, with additional features to help users to discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds.
This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
An updated catalog of transcription factor motifs and candidate regulatory motif sites.
FactorHNE is a factor graph-aggregated heterogeneous network embedding for disease-gene association prediction.
A scalable interpretable approach to context modeling for medical image segmentation.
FactorViz provides an interactive visualization and reporting environment for exploring the results of the methylome decomposition experiments carried out by MeDeCom or similar deconvolution tools.
Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. A web server for predicting of FAD Binding Sites Using Pre-training of Deep Bidirectional Transformers. During cellular respiration in general and electron transport chain in particular, flavin adenine dinucleotide (FAD) plays a vital role.
FaDA is a user-friendly data visualization and analysis tool developed in R programming with the R Shiny package. FaDA provides users of non-computational background to analyze their data for statistical analysis and quick visualization. This application is useful for common laboratory data outputs, including quantitative PCR, Flow Cytometry or ELISA.
FADB-China is a molecular-level food adulteration database in China based on molecular fingerprints and similarity algorithms prediction expansion.
FADPred is a web-server specially trained for the FAD interacting residues. The prediction is based on the basis of binary pattern of 17 window motif of amino acid sequence by using support vector machines(SVM).
A Quantification Tool for Prokaryotic Transcriptomic Analyses. Most current available quantification tools for transcriptomics analyses have been designed using human data sets, in which full-length transcript sequences are available. In most prokaryotic systems, full-length transcript sequences are unavailable, causing prokaryotic transcriptomics analyses being performed using coding sequences instead. In contrast to eukaryotes, prokaryotes contain polycistronic transcripts and when genes are quantified based on coding sequences instead of transcript sequences, this leads to an increased abundance of ambiguous multi-gene fragments, especially between genes in operons.
Feature Analysis Explorer (FAE) can help researchers develop a classification model with comparison among different methods. This project was inspired on the Radiomics, and provides a GUI to help analyze the feature matrix, including feature matrix pre-process, model development, and results visualization.
Comparing drug safety of hepatitis C therapies using post-market data. FAERS Quarterly Data Extract Files. U.S. Department of Health and Human Services. FDA Adverse Event Reporting System (FAERS) Quarterly Data Extract Files. A simple search of FAERS data cannot be performed with these files by persons who are not familiar with creation of relational databases. However, you can get a summary FAERS report for a product by sending a Freedom of Information Act (FOIA) request to FDA. You can also request individual case reports by submitting a FOIA request listing case report numbers.
Process compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.
synteny-based phylostratigraphy and finer classification of young genes | This repo contains the code needed to generate the tables and figures used in the synder paper and its supplementary files. And more | install_github("arendsee/fagin") | The CRAN packages can be installed from an R shell with as so
FAIDARE: FAIR Data-finder for Agronomic Research. The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories. It is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services. It is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
FAIMS is a native Android application that can be used for data capture when doing field work.
FAIR-Checker is a tool aimed at assessing FAIR principles and empowering data provider to enhance the quality of their digital resources. Data providers and consumers can check how FAIR are web resources. Developers can explore and inspect metadata exposed in web resources.
This is a standalone, desktop application developed by the FAIR4Health project (https://www.fair4health.eu/). The tool is used to connect the health data sources which can be in various formats (Excel files, CSV files, SQL databases) and migrate data into a HL7 FHIR Repository. The tool shows the available FHIR profiles to the user so that he/she can perform mappings appropriately. The tool can also contact a Terminology Server (which is actually another HL7 FHIR Repository) so that data fields can be annotated if coding schemes such as ICD10 or SNOMED-CT are in use.
This is a standalone, desktop application developed by the FAIR4Health project (https://www.fair4health.eu/). The tool aims to handle the privacy challenges exposed by the sensitive health data. It is designed to work on an HL7 FHIR API so that it can be used on top of any standard FHIR Repository as a data de-identification, anonymization, and related actions toolset. The tool accesses FHIR resources, presents metadata to the user, guide the user about the configuration to be applied and then output the processed FHIR resources.
A framework for FAIRification processes.
The FAIR Data Cube (FDCube) is an infrastructure component of the Netherlands X-omics initiative designed to facilitate the reuse of multi-omics data by making it FAIR and enabling integration across different data layers while ensuring data security and privacy.
FAIR Data Station for Lightweight Metadata Management & Validation of Omics Studies
FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects. This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.
Best practice database platform for genomics data, developer in the Netherlands. Has diverse implementations including MOLGENIS
FAIRSCAPE is a reusable computational framework, enabling simplified access to modern scalable cloud-based components. It fully implements the FAIR data principles and extends them to provide FAIR Evidence, including provenance of datasets, software and computations,as metadata for all computed results.
fast approximate contig coverage for metagenomic binning Fairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning. Fairy is used after metagenomic assembly and before binning. It can - Calculate coverage 100x-1000x faster than read alignment (e.g. BWA) - Give comparable bins for multi-sample binning (short read or nanopore reads) - Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more
Web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method.
A high-speed FastQC emulation for quality control of sequencing data.
Falco is a quick and flexible single-cell RNA-seq processing framework on the cloud. Falco is a software bundle that enables bioinformatic analysis of large-scale transcriptomic data by utilising public cloud infrastructure. The framework currently provide supports for single cell RNA feature quantification, alignment and transcript assembly analyses.
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. The falcon spectrum clustering tool uses advanced algorithmic techniques for highly efficient processing of millions of MS/MS spectra. First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity searching. The nearest neighbor indexes are used to efficiently compute a sparse pairwise distance matrix without having to exhaustively compare all spectra to each other. Finally, density-based clustering is performed to group similar spectra into clusters.
Toolbox for the fast contextualization of logical networks.
a highly flexible open-source software for closed-loop neuroscience. OBJECTIVE:Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. APPROACH:We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation
FalseColor-Python is a rapid intensity-leveling and digital-staining package for fluorescence-based slide-free digital pathology. It can be used for translating two-channel fluorescence images (i.e. a nuclear and cytoplasmic stain) to the traditional H&E histopathology color space.
Library for spatial exploratory data analysis of protein structures.
A focal attention module (FAM) for lesion segmentation of COVID-19 CT images. It contains a channel attention module and a spatial attention module.
Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.
FASTMAP Shim Tool towards user-friendly single-step B0 homogenization.
Fingerprint Analysis with Missing Data is an easy-to-use general-purpose program for dominant fingerprint data handling and analysis with a graphical user interface, supporting flexible data input and export to a variety of formats. Analysis capabilities include distance-based analysis, bootstrapping and consensus tree generation, allele frequency estimation, AMOVA, inter-population distances, Shannon’s index.
Famdenovo is a pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome. Famdenovo is an algorithm that calculates the probability of de novo status in deleterious germline mutations using family history data.
FAME is fast and memory efficient multiple sequences alignment tool through compatible chain of roots
FaME is a tool that can test the aberrations of the samples in one or more datasets in order to find signals of mutual exclusivity or co-occurrence between all the pairs of genes.
Mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism.
FamFetch is the general interface used to query the families databases developed using the HOBACGEN model.
A region-based association test for familial data under functional linear models
Family Rank is a graphical domain knowledge informed feature ranking algorithm. Grows families of features by selecting features that maximize a weighted score calculated from empirical feature scores and graphical knowledge. The final weighted score for a feature is determined by summing a feature's family-weighted scores across all families in which the feature appears.
It is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text.
Algorithm for large-scale multiple sequence alignments
FAN-C (Framework for the ANalysis of C-like data) provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.
FANCY is a fasttool for estimation for of privacy risk in functional genomics data.
FaNDOM (Fast Nested Distance Aligner for Optical Maps) performs alignment of Bionano Saphyr optical map molecules and contigs to a reference, using a seed-based filter.
A Feedback Attention Network for Improved Biomedical Image Segmentation.
FangNet is a tool for mining herb hidden knowledge from traditional Chinese medicine clinical effective formulas using structure network algorithm.
Machine learning approach to classify genes and genera in the family Geminiviridae.
Fast Network Motif Detection is for fast network motif detection; it relies on recently developed algorithms to improve the efficiency of network motif detection by some orders of magnitude over existing tools. This facilitates the detection of larger motifs in bigger networks than previously possible. Its additional benefits are the ability to analyze colored networks, a graphical user interface and the ability to export results to a variety of machine- and human-readable file formats.
fanta.bio is a database providing functional genome annotations, particularly focusing on cis-regulatory elements (CREs) and their impact on gene regulation, with a focus on non-coding RNA and chromatin interactions.
FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for annotating GO terms in protein sequence files using GOPredSim with the protein language model ProtT5
FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for protein annotating via GO term transference using the embedding space. FANTASIA’s latest developments include additional protein language models and provide enhanced functionalities.
"Fantastic databases and where find them" is a collection of databases for omics data.
FANTEN (Finding Anisotropy TENsor) is a new user-friendly web tool for the determination of the anisotropy tensors related to PCSs (pseudo-contact shifts) and RDCs (residual dipolar couplings).
The Functional Annotation Of the Mammalian Genome is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression, sequencing mRNA 5-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments.
Functional annotations for RIKEN full-length cDNA clones.
for inquiry to the FANTOM Administrative Office
questions or comments on Annotation or FANTOM system
FaReT (Face Research Toolkit) is a free and open-source toolkit of three-dimensional models and software to study face perception.
fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization and a novel unsupervised feature selection criterion called "I/NI-calls".
FarmTest (FarmTest: Factor-Adjusted Robust Multiple Testing) Performs robust multiple testing for means in the presence of known and unknown latent factors.
A novel deep network named feature aggregation and refinement network (FARNet) for automatically detecting anatomical landmarks.
Assessing the similarity between proteins using multi-layered feature architectures.
Fas2Nex can read a .FAS (FASTA) file and save it as .NEX (NEXUS) file (or again as a .fas file) for phylogenetic analysis with PAUP*, with the option of removing columns of characters consisting only of gaps. If necessary, the ends of short sequences in the .fas file will be padded to full length.
Graphical platform for manipulating sequences and alignments in a batch mode.
FASPR is an open-source tool for fast and accurate protein structural modeling of protein side-chain conformations and packing.
FAssign (Fuzzy Assignment) is new algorithm for the protein secondary structure assignment, using fuzzy logic based on backbone angles.
The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools (for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics modeled after the Unix textutils (such as grep, cut, head, tr, etc).
FAST: Fast Analysis of Sequences Toolbox
A fast method to compute AUC (area under the curve).
Rapid fitting of Gaussian PSF models to a list of candidate positions in an image.
Fast Gaussian Point Spread Function Fitting (MEX)
Fast-GBS is an analysis toolkit for genotyping-by-sequencing data. Genotyping-by-sequencing (GBS) is a rapid, flexible, low-cost, and robust genotyping method that simultaneously discovers variants and calls genotypes within a broad range of samples. These characteristics make GBS an excellent tool for many applications and research questions from conservation biology to functional genomics in both model and non-model species. Continued improvement of GBS relies on a more comprehensive understanding of data analysis, development of fast and efficient bioinformatics pipelines, accurate missing data imputation, and active post-release support.
Fast-HBR is duplicate reads removing tool from fastq and fasta files. Fast-HBR is fast and memory-efficient because it does not need to store reads in string form on the memory. Instead of that, it will store their hash value as integer. Moreover, it will write directly to the output file and remove duplicate reads on-the-fly.
Factored Spectrally Transformed Linear Mixed Models is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.
A faster version of perfcurve for False- and True Positive Rate.
Fast registration of 4D microscopy datasets.
Tool for ultrafast and robust cell segmentation in large-scale microscopy.
R package for robust and efficient feature selection for machine learning and genome-wide association studies.
FAST MS is an open-source software for the automated analysis of top-down mass spectra of polymeric molecules, including RNA, DNA, and proteins. It identifies, assigns, and quantifies signals, offering a toolbox for statistical analysis.
The FASTA programs find regions of local or global similarity between protein or DNA sequences, either by searching protein or DNA databases, or by identifying local duplications within a sequence. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
FASTA Canonical Sequences deletes comments from FASTA files. It can also change sequences by deleting specified characters or whitespace, introduce newlines for readibility, or change sequence case.
Fastachar is a graphical user interface that allows a simple comparison of two sets of DNA sequences. A typical working example is to have a selection of DNA sequences of different, but related species. These sequences are divided in a set A, which are thought to be a single taxon (species) and a set B, which is a collection of different taxa.
Extract/Exclude one or more sequence(s) from a multifasta file using a dataset of identifiers.
Fasta File Comparer compares protein sequences from two different Fasta files and outputs the matching proteins and sequences to a text file.
Create fasta files with DNA sequences given a BED file.
FASTAFS is toolkit for file system virtualisation of random access compressed FASTA files. Although it is uncommon, the FASTAFS format denotes the index (a typical header) after the data. The reason for this location is that most metadata can only be known after converting the entire FASTA file to FASTAFS. For instance, the number of nucleotides encoded within 2bit data, the number of N-characters or the checksum.
FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both, match/mismatch based and thermodynamic binding energy searches.
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
Parallel and Sequential Bioinformatics Libraries for High Throughput Sequences
Fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data.
FastBiCmrMLM is a fast and powerful compressed variance component mixed logistic model designed for large genomic case-control genome-wide association studies, addressing challenges in computational complexity and missing heritability.
Fast, scalable, parallel and distributed inference of very large networks by Bayesian Model Averaging.
FastBMD is an online tool for rapid benchmark dose-response analysis of transcriptomics data. FastBMD is a computationally efficient implementation of the National Toxicology Program Approach to Genomic Dose-Response Modeling. Key features include a simplified workflow, ability to download results at each step, and interactive exploration of pathway-level BMDs. In addition to model organisms, FastBMD is designed to support non-model organisms by enabling an annotation-free pipeline that includes feature sensitivity-based point-of-departure analysis. The final part of the analysis is designed to allow users to interactively explore BMDs at different levels of organization:.
FastCodeML is a collection of optimization strategies for fast detection of positive selection on phylogenetic trees.
FastContact is a free energy scoring tool for protein-protein complex structures.
A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data.
Fast Reconstruction of Compact Context-Specific Metabolic Network Models
fastDFE is a Python-based software package for fast and flexible inference of the distribution of fitness effects (DFE) from site-frequency spectrum (SFS) data. It provides efficient joint inference, introduces genomic covariates, and includes comprehensive VCF-to-SFS parsing utilities with various annotation options.
A webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation.
FastdRNA: a workflow for analysis of ONT direct RNA seq dataset.
Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes
An extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.
Fast calculation of AUC of an ROC for binary classification problems, written in C++.
FastField is an open-source toolbox for efficient approximation of deep brain stimulation electric fields.
A scalable and efficient implementation that is 2 to 3 orders of magnitude faster than the previous version. This is achieved by exploiting the sparsity of the model using the SuperLU direct solver for parameter fitting, and sparse Cholesky factorization together with the sparse inverse subset algorithm for computing standard errors.
FastGrow is a fast fragment growing approach using a shape-based algorithm. It also features pharmacophore-like constraints, geometry optimization using JAMDA, and built-in ensemble flexibility
A generalized linear mixed model association tool for biobank-scale data. fastGWA-GLMM data portal.
Fast and scalable program for constructing haplotype network for large-sample sequences.
FastHMM and FastBLAST are fast heuristics to replace HMM search, InterProScan, and all-versus-all BLAST. FastHMM uses PSI-BLAST to quickly select likely members of the family and then uses HMMer to confirm those hits. FastBLAST relies on alignments of proteins to known families from FastHMM and from rpsblast against COG. FastBLAST uses these alignments to avoid most of the work of all-versus-all BLAST. FastBLAST further reduces the work by clustering similar sequences.
FastISM is a Python package for in-silico saturation mutagenesis for convolutional neural networks.
FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.
The fastLSAsoftware package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FAST LSA allows investigators to view correlated cliques and explore previously unrecognized network relationships.
Includes FASTF, that compares an ordered peptide mixture, as would be obtained by Edman degradation of a CNBr cleavage of a protein, against a protein database; FASTM, that compares an ordered set of peptides to a protein sequence database or an ordered set of oligonucleotides to a nucleotide sequence database; and FASTS, that compares a set of short peptide fragments, as would be obtained from mass-spec. analysis of a protein, against a protein database.
Sequence similarity search with peptide fragment searches using the FASTF, FASTM or FASTS programs from the FASTA suite.
It is used for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. It exploits the discrete nature and structure of the measured single nucleotide polymorphisms. SNPs are organized into a Hamming distance-based tree. Its tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.
Distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ. It includes Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.
FastML is a webserver for computing and reconstructing ancestral sequences using maximum likelihood.
FastMLST is a multi-core tool for multilocus sequence typing of draft genome assemblies.
FastMM is an efficient toolbox for personalized constraint-based metabolic modeling. In FastMM, most of the time-cost functions of metabolic modeling are written by C. These functions including: flux variability analysis, genome-wide single gene knockout analysis, genome-wide double gene knockout analysis, genome-wide single metabolite knockout analysis, genome-wide double metabolite knockout analysis, and MCMC sampling.
FastMulRFS is a pipeline for estimating species trees from multi-copy gene trees, based on the Robinson-Foulds supertree problem for MUL-trees (MulRF).
FastOMA is a scalable software package to infer orthology relationship.
Read huge FastQ and FastA files (both normal and gzipped) an demanipulate them.
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
FastPCR is an integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching
FastPG is a tool for the fast clustering of millions of single cells.
fastPHASE is a program to estimate missing genotypes and unobserved haplotypes. It is an implementation of the model described in Scheet & Stephens (2006). This is a cluster-based model for haplotype variation, and gains its utility from implicitly modeling the genealogy of chromosomes in a random sample from a population as a tree but summarizing all haplotype variation in the "tips" of the trees.
Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).
FastProject is a software tool which analyzes a gene expression matrix and produces a dynamic output report in which two-dimensional projections of the data can be explored.
A tool to download FASTQs associated with Study, Experiment, or Run accessions.
Convert between various FASTQ quality formats for a list of inputs.
A simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.
This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.
Reports from FastQC with option for long reads.
A FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model.
Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
FASTQINS is a Python pipeline to map transponson insertions from Tn-seq data.
FASTQuick is an ultra-fast QC tool for NGS sequencing fastq files. It generates a comprehensive list of QC statistics, including ancestry and contamination estimation, at ~50x faster turnaround time than alignment-based QC tools.
Checking that FastQ files are follows standards.
The Center for Statistical Genetics at the University of Michigan School of Public Health
fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression.
FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.
Improving scalability of phylogenomic analysis. FASTRAL is a novel approach for running ASTRAL, a widely used and popular species tree reconstruction method. FASTRAL runs up to ~800 times faster than ASTRAL but with a similar (or sometimes better) accuracy.
FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool
fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.
Implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector.
Fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.
FastSK is a tool for fast sequence analysis using gapped string kernels.
fastSKAT provides a faster implementation of SKAT, which is a tool to map the effects of rare genomic variants.
Identify and prioritize SNPs that are likely to have functional effects.
FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables.
fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
FastTargetPred is a program enabling the fast prediction of putative protein targets for input chemical databases. It allows to predict putative protein target(s) for a query compound or for a collection of compounds.
FastTENET is a GPU-accelerated implementation of the TENET algorithm for reconstructing gene regulatory networks from single-cell RNA sequencing data. It offers significant performance improvements over the original TENET algorithm and is available on GitHub.
An open-source software for tracking varying numbers of deformable objects. This is the official website of FastTrack, the free tracking software. Targeting scientists, FastTrack focuses on easy and fast objects tracking from video recordings. With easy installation, intuitive interface FastTrack is the tool of choice for every scientist. FastTrack is a desktop tracking software, easy to install, easy to use, and performant. The software can be downloaded and modified to adapt to any needs. The core of the software can also be embedded easily in any C++/Qt project. Tracking objects in video recording can be tedious. Existing software are expensive, the learning curve can be steep, and the workflow can not be easily adapted when the project evolved.
Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
Fasturec is a software for the inference of an optimal species tree under duplication and duplicaion-loss cost from a set of unrooted gene trees.
Fastutils is a light toolkit for parsing, manipulating and analysis of FASTA and FASTQ files.
fastv is a computational toolset for rapid identification of SARS-CoV-2, other viruses, and microorganisms from sequencing data. This tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.).
A software to detect viral infection and integration sites for different viruses.
Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fastxtend is an extension of FASTX-Toolkit package. It provides four commands line tools for Short-Reads FASTA/FASTQ files preprocessing.
A Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites.
FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.
A computational method for the quantification and visualisation of fate bias for multi-lineage single cell transcriptome data.
A scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.
Predict the functional class, pathogenic or neutral, of small indels throughout the whole non-coding genome.
Tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, the tool finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.
fauxcurrence is an R package for simulating multi-species occurrences for null models in species distribution modelling and biogeography. The package generates sets of randomised occurrences (long & lat coordinates) for one or more species with a spatial structure (within- and between-species distances) matching that of an observed set of coordinates. These can be used to define null expectations to test hypotheses in ecology and biogeography.
FAVA (Functional Associations using Variational Autoencoders) is a software resource for inferring high-quality functional association networks from scRNA-seq and proteomics data. It addresses biases in existing methods by utilizing data unaffected by literature bias and offers a pipeline accessible via pip/PyPI and the scverse ecosystem.
FaviCov is a comprehensive resource for functionally relevant SARS-CoV genetic variants. The resource provides a searchable interface for genomic variants and corresponding variant annotations.
Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome.
Machine Learning-Assisted Identification of Factors Contributing to the Technical Variability Between Bulk and Single-Cell RNA-Seq Experiments.
A tool to validate newly developed automated segmentation algorithms.
FBA is a flexible and streamlined Python package to perform quality control, quantification, demultiplexing, multiplet detection, clustering and visualization of feature barcoding assays.
Software for family based association tests
A Filter-Bank Multi-Scale Convolutional Neural Network for EEG-Based Motor Imagery Decoding.
FBPP is an open-source, user-friendly Python application with a graphical interface for designing PCR primers and probes for detecting foodborne pathogens. It supports simulation of PCR and gel electrophoresis and checks primer specificity.
FBPP: Foodborne Pathogen Primer Probe Design
Functional connectivity analysis tool for near-infrared spectroscopy data (FC-NIRS) is a tool for analysis of near-infrared data from functional connectivity imaging.
FC-R2 is a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study.
This open source software package automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the package is a large adaptability to the various experimental setups and to different analysis methodologies.
An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).
A semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites.
FCChumon is a database providing a systematic overview of food contact chemicals (FCCs) that have been monitored and detected in human samples. It offers an interactive dashboard enabling policymakers and researchers to prioritize FCCs of concern and improve public health.
FCChumon (Database on Food Contact Chemicals Monitored in Humans)
Vibrationally-resolved spectra simulated at the edge of the harmonic approximation.
F-divergence Cutoff Index finds DEGs in the transcriptomic & proteomic data, and identifies DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. This tool provides several advantages compared to existing methods.
FcircSEC is an R package for full length circRNA sequence extraction and classification.
A tool to quantify an individual's scientific research output based on citations, RCR, and the H-index divided by the number of authors in publications. In 2021, the tool stats are calculated based on over 34 million of PMIDs with over 555 million citations coming from over 34,000 journals.
Fast and concurrent lossless quality scores compressor.
Locating Transcription Factor Binding Sites by combing Fully Convolutional Neural Network with Gated Recurrent Unit.
fcScan is a Bioconductor package aiming at clustering genomic features based on a defined window size and combination of sites. fcScan for detecting clusters of coordinates with user defined options.
The FDALabel Database is a web-based application used to perform customizable searches of over 140,000 human prescription, biological, over-the-counter (OTC), and animal drug labeling documents.
Functional Data Consistency Explorer (FDCE). Assessing Consistency Across Functional Screening Datasets in Cancer Cells.
Fast predictor of propensity for protein production, purification, and crystallization.
A multithreaded (Windows) mex implementation of the FDK conebeam CT reconstruction algorithm.
Multithreaded mex FDK conebeam CT reconstruction algorithm
A systematic and efficient method to locate binding sites. # Fragment-Dissolved-Molecular-Dynamics. An efficient method to locate binding sites : Fragment Dissolved Molecular Dynamics (fdMD).
This server FDR4 is meant for the prediction of binding affinity of peptide binders in an antigenic sequence for a MHC class II allele HLA-DRB1*0401.
This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values. It returns the fdr adjusted p-values and plots. The second is fdr.gui() which creates a simple graphic user interface to access fdr.ma.
FDR confidence interval selection and adjustment for large-scale hypothesis testing.
Fibrotic Disease-associated RNAome database, is an open and up-to-data online manually curated depository of RNAs alterations and high-throughput datasets about fibrotic diseases across various species.
FDRestimation is a user-friendly R package that directly computes and displays false discovery rates from p-values or z-scores under a variety of assumptions.
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation.
Fe(2)OG is an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences.
FEATHER ( Force Extension Analysis using a Testable Hypothesis for Event Recognition) automatically identifies the locations of unfolding/unbinding events in single-molecule force spectroscopy records and thereby deduces the corresponding rupture force and loading rate.
An Emboss tool that merges two overlapping feature tables into one single table.
Tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments.
FEATS is a Python tool for performing downstream analysis on Single-Cell RNA-seq datasets.
feature point, retinal image , image registration, blood vessel
Feature-based retinal image registration
The tool is designed to perform harmonization at the feature-level. Feature-based harmonization method aims to reduce the variability in the radiomics features due to different scanners, acquisition protocols and conditions by using empirical Bayesian methods to estimate differences in radiomics values and then expressing them in a common space (location/scale adjustment). The tool offers two methods: (1) ComBat method, which shifts the radiomics features to the overall mean and pooled variance of all centers, and (2) M-ComBat method, which shifts the radiomics features to the mean and variance of the chosen reference center with the most samples.
Feature extraction approaches for biological sequences. FeatureExtraction_BiologicalSequences. As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced.
Self-contained package for feature selection based on mutual information/interaction information.
Feature Selection Based on Interaction Information
Feature-Viewer is a JavaScript visualization tool to display the features covering your sequence of DNA, protein, or others.
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.
The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.
FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.
Comparative analysis of protein sequences derived from the same transcript by alternative splicing, genome variation data (SNPs) or protein families from one or more organisms.
Searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.
An automated fragment-ensemble-based model for building RNA 3D structures.
Fec is a error correction tool based on two-rounds overlapping and caching.
A statistical framework for calculating prospective sample sizes and classifying efficacy results for faecal egg count reduction tests in ruminants, horses and swine.
A web application gathering information about food enzyme preparations available on the European market.
Fed-BioMed is an open-source research and development initiative for translating federated learning into real-world medical applications. The community of Fed-BioMed gathers experts in medical engineering, machine learning, communication, and security. We all contribute to provide an open, user-friendly, and trusted framework for deploying the state-of-the-art of federated learning in sensitive environments, such as in hospitals and health data lakes.
FedGMMAT is a federated genetic association testing tool designed to address privacy concerns in collaborative genetic studies. It utilizes a federated statistical testing approach to correct for confounding effects while ensuring sensitive data remains local to each collaborating site.
A feature enhanced encoder-decoder LSTM network for nuclei instance segmentation for histopathological diagnosis.
feedr is an R package developed for loading, transforming, and visualizing time‐stamped, georeferenced data, such as RFID data collected from static logger stations.
A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.
Fast Estimation of Effective Migration Surfaces (feems) is a python package implementing a statistical method for inferring and visualizing gene-flow in spatial population genetic data.
An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
Extraction model for protein sequences and its applications.
Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.
This tool features secondary structure, disorder, aggragation, sequence complexity predictions along with amino acid propensity from sequence.
This package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed.
Mining biological meaning from cell level in single-cell RNA sequencing data.
FEMA is a fast and efficient mixed-effects algorithm designed for analyzing large-scale neuroimaging data. It enables whole-brain vertex-wise, voxel-wise, and connectome-wide LME analyses, addressing limitations of traditional methods due to computational requirements.
FEMfuns (Finite Element Method for useful neuroscience simulations) is a volume conduction modeling pipeline that includes resistive, capacitive or dispersive tissue and electrodes. FEMfuns allows neuroscientists to solve the forward problem in a variety of different geometrical domains, including various types of source models and electrode properties, such as resistive and capacitive materials. The original paper can be found.
These models could be run by the matlab for femlab GUI I posted earlier.
FEOpti-ACVP is a computational model for predicting novel anti-coronavirus peptide sequences based on feature engineering and optimization. A user-friendly webserver is available for prediction tasks.
A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations.
A Tool for Feature Extraction from Protein Sequence.
FermatS is a numerical representation for protein sequence comparison and DNA-binding protein identification.
FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods.
FERMO is a metabolomics dashboard designed to facilitate hypothesis-driven prioritization of molecules and samples, and integrates LC-MS metabolomics data with phenotype information, sample grouping, and genomic data. FERMO is applicable in a variety of biological sciences, including natural product drug discovery, microbiology, or agriculture.
fermo-core is the backend of the metabolomics dashboard FERMO. It can be used for large-scale processing of metabolomics data and integration of phenotypic and other orthogonal data.
FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.
A Straight Pipeline for Functional Gene Annotation and Disease Mutation Discovery
FESTIval is a versatile framework for conducting experimental evaluations of spatial indices. FESTIval also provides default spatial datasets for evaluating spatial indices. Algorithms to generate query windows for range queries and points for point queries are further provided.
Fetal dose is a calculator for calculating the radiation dose a fetus is exposed to during Computed tomography (CT) imaging.
Fetches taxonomic information for a list of GI numbers (sequences identifiers used by the National Center for Biotechnology Information).
Retrieve information from ProDom, a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
The Federated Tumor Segmentation (FeTS) platform, describes an on-going under development open-source toolkit, with a user-friendly graphical user interface (GUI)
An interactive web-based resource for evolutionary transcriptomics across fishes.
'Squeeze & excite' guided few-shot segmentation of volumetric images. PyTorch implementation of 'Squeeze and Excite' Guided Few Shot Segmentation of Volumetric Scans.
Takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.
The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.
Fast Family-Based Sequence Kernel Association Test.
FFD is a fast scale-invariant feature detector for computer vision tasks. Features include extracting matching features across a given pair of images.
Methods for computing the (NP-hard) family-free DCJ similarity, which is a large-scale rearrangement measure for comparing two given genomes.
Software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools.
Fluctuating Finite Element Analysis (FFEA)
User-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. The web server functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.
FFParam is a Standalone python package for CHARMM force field parametrization including both the additive CGenFF/CHARMM36 and Classical Drude polarizable force fields. To assist in the parametrization process, the program is provided with a graphical user interface (GUI) and it is cross-platform. FFParam shields the user from labor-intensive manual work and shifts the focus towards the improvement and the quality of parameters.
Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed Paraffin-Embedded data. It contains a function for making Concordance At the Top plots (CAT-plots).
Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.
Distilling a Powerful Student Model via Online Knowledge Distillation.
FFselect is an improved linear mixed model for genome-wide association study in populations featuring shared environments confounded by relatedness.
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis.
FFX is an open-source software package for constant-pH molecular dynamics simulations, particularly suited for simulating the behavior of proteins and crystals across diverse pH environments using the AMOEBA force field. It incorporates polarizable atomic multipoles and supports titration state changes for crystalline systems.
fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database for Fusarium graminearum. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets.
FGDB is a database of follicle stimulating hormone glycans. FGDB provides fucosylated and non-fucosylated glycans associated with Follicle Stimulating Hormones (FSH) in human.
The FGDP (functional genomics data pipeline) is a Java-based, Microarray or Genechip data analysis system. The FGDP provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed, and provides a web server and interface for presenting results
HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences.
Resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).
Genome completeness assessment tool focused on Fungi
Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.
The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.
FGviewer is an online visualization tool for functional features of human fusion genes. FGviewer is aiming for the effective visualization of the functional features of fusion genes for better prioritization of therapeutic target selection. FGviewer provides functional feature annotations at four different levels: DNA-, RNA-, protein-, and pathogenic-levels. The same breakpoint line across four tiers will classify between FG involving or non-involving zone with multiple types of functional features. Those features include fusion mRNA and amino acid sequences based on the user’s breakpoint coordinates, swapped gene expression regulatory (i.e., transcription factor or miRNA binding sites), protein functional features (i.e., protein domains, protein- protein interactions, binding sites of all molecules, secondary structure level feature, etc.), clinically relevant variants, etc.
FHIR PIT (Health Level 7 Fast Healthcare Interoperability Resources Patient data Integration Tool) is an open software application for spatiotemporal integration of clinical data and environmental exposures data. FHIR PIT (Patient data Integration Tool) uses geocodes and time stamps of varying resolution (e.g., hour, year) to integrate the clinical data with environmental exposures data from multiple sources before stripping the data of PHI (including the geocodes and time stamps) and binning feature variables to create ICEES tables. Of note, FHIR PIT is modular and extensible and can be adapted for virtually any type of data that requires geocodes and dates for integration with personally identifiable information.
Python package to query FHIR servers. This package is meant to provide a simple abstraction to query and structure FHIR resources as pandas DataFrames.
FhirSpark is a tool for implementing a mediation layer to bring Fast Healthcare Interoperability Resources (FHIR) to the cBioPortal for cancer genomics.
"FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS)."
FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR).
FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.
FiberQ is a MATLAB script for automatic quantification of dna fibers from fluorescent images
FiberSim is software for spatially-explicit modeling of half-sarcomeres. The code tracks the position and status of each myosin head, each binding site on actin, and each molecule of myosin-binding protein C.
Pulmonary fibrosis prognosis prediction using a convolutional self attention network.
A manually curated resource for multi-omics level evidence integration of fibrosis research
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. It is a Shiny-powered application for fibrosis-related data integration and mining aiming to the acceleration of pulmonary fibrosis research.
Frequency-independent biological signal identification (FIBSI) is a free program that simplifies intensive analysis of non-stationary time series data
FiCoS (Fine- and Coarse-grained Simulator) is a novel efficient deterministic simulator of biological systems based on two different integration methods belonging to the Runge-Kutta family: the Dormand–Prince (DOPRI) method [1, 2], used in the absence of stiffness, and the Radau IIA method [3, 4] exploited when the system is stiff. Specifically, FiCoS exploits the DOPRI5 and RADAU5 methods, which are explicit and implicit adaptive Runge-Kutta methods of order 5, capable of varying the integration step-size during the resolution of the Ordinary Differential Equation (ODE) systems.
Cell Type Assignments for Spatial Transcriptomics Data. FICT - FISH Iterative Cell Typing. Is a software for achieve accurate cell typing by iteratively incorporating neighbourhood information using Expectation-Maximization algorithm, for Fluorescence in situ hybridization(FISH) technique.
fIDBAC integrated an accuracy bacterial identification, automated strain typing and downstream AR/VF gene prediction analysis in a single, coherent workflow.
Fiddle (file drawer data liberation effort) is a tool to combat publication bias by getting research out of the file drawer and into the scientific community. Fiddle is a “matchmaking” tool designed to help researchers to identify the publication format that will work best for a particular dataset that may be hard to publish in traditional journals.
FIDDLE (Finding Interactions using Diagram Driven modeL Extension) is a tool to automatically assemble or extend models with the knowledge extracted from published literature.
A web server designed to facilitate the functional interpretation of differential expression analysis. It is aimed at allowing experimentalists to "play with" their RNA-Seq data in an easy and at the same time exhaustive fashion within a single tool.
Run-time filter design and execution library.
Fido-SNP: Predicting the impact of genetic variants in dog genome
A functional site- and physicochemical interaction-annotated domain profile database, from which a sequence-based method is developed for predicting both PFSs and PLIs. The method is based on the assumption that proteins that share similar structure and sequence tend to have similar functional sites located on the same positions on a protein’s surface.
Open-source platform for the assessment of target volume delineation in radiation therapy.
A comprehensive fertility-associated indicators factor database for domestic animals. To get the most out of Fifbase start with our 3 minute tour.
Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence.
A probabilistic method for filling gaps in genome assemblies.
Figeno is a tool for generating publication-quality figures for genomics, focusing on multi-region views, long reads, and epigenomic data. It provides both a command-line interface and a graphical user interface and is available as a Python package.
Used for processing, analyzing and presenting data and creating science documents of all kinds. It is powerful but easily accessible to users of all levels of experience. Turning your data into basic figure types such as line graphs, bar charts, areagrams, drop-plots or scatter diagrams is completely automatic and there are endless refinements which can be added with the simple-to-use tools. Text-only charts can be created and 3D data graphing is also included.
This tool is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
figureComposer is a web-based interactive multi-panel bio-infographic designing tool
Analysis of Curvature in Biological Image Data using B-splines. A Fiji plugin for Curvature Analysis. Kappa is A Fiji plugin for Curvature Analysis. You can fire a remote Jupyter notebook server and reproduce the analysis using Binder: https://mybinder.org/v2/gh/brouhardlab/Kappa/master?urlpath=lab/tree/Analysis/Notebooks.
The plugin Fijiyama (Yet Another Matching and Alignment tool for Fiji) is a generic tool for registration and alignment of 3D image series collected from various imaging modalities (MRI, X-rays, Microscopy, Photography, etc.).
Large-scale, harmonized FunctIonaL gEnomics Repository. GIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files. Database with the most comprehensive harmonized, extensible, indexed, searchable human functional genomics data collection. Functional genomics repository (FILER) is a database developed by NIAGADS with the most comprehensive harmonized, extensible, indexed, searchable human functional genomics data collection across >20 data sources:.
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r.
FilTar is a tool to integrate RNA-Seq data to pre-existing miRNA target prediction workflows in order to increase prediction accuracy. Its primary purpose is to provide context-specific miRNA target prediction in vertebrates. This is achieved by integrating RNA-Seq data into existing miRNA target prediction workflows, allowing users to filter target predictions on the basis of expression information and to tailor 3'UTR annotations for specific cellular contexts, increasing the specificity of target predictions.
Produce a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.
Remove spatial frequencies beyond the optical cutoff and perform physically accurate interpolation.
Filter noise and interpolate microscopy images in frequency domain
Remove short and repeat contigs/scaffolds. Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a calculated coverage. Repeated contigs are detected based on coverage.
Filter out peaks present both in ChIP and Control dataset.
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
FilterNHP is an R package and web-based application for generating search filters to query scientific bibliographic sources (PubMed, PsycINFO via EBSCOhost and Web of Science) for non-human primate related publications.
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
The Face Image Meta-Database (fIMDb) provides researchers with the tools to find the face imagesbest suited to their research, with filters to locate databases with people of a varied racial and ethnic backgrounds and ages.
FiMDPEnv is a Python package that provides realistic simulation environments that model real-world consumption Markov decision processes (consumption MDPs).
Inferring the Temporal Order of Mutations on Clonal Phylogeny under Finite-sites Models.
Drastic improvement of approximate membership query data-structures with counts.
Developed for large scale genotype imputation in livestock where hundreds of thousands of individuals are genotypes with different panels. It uses an overlapping sliding window approach to exploit relationships or haplotype similarities between target and reference individuals. The process starts with long windows to capture haplotype similarity between close relatives.
An open source tracking and locomotion analysis software for small animals
Escherichia coli Subtyping Based on fimH Alleles.
Computer-assisted Recognition and Identification of Bottlenose Dolphin Photos in R. Dolphin Recognition via Automated Cropping Tracing and... in haimeh/finFindR. ‘finFindR’, is an R package that identifies wild dolphins using photographs of the nicks and notches on their dorsal fins. finFindR offers the capacity to automatically crop and trace images for recognition work. finFindR-package: Dolphin Recognition via Automated Cropping Tracing and..
FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase) is a comprehensive cell-free DNA (cfDNA) fragmentation pattern database to host uniformly processed and quality controlled paired-end cfDNA WGS datasets.
FInCH is a Fiji plugin designed for automated and scalable whole-image analysis of protein expression and cell morphology. It enables simultaneous assessment of cellular processes and their effects at the tissue scale, recording data with positional information for longitudinal analyses.
Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development | Fly tissue-developmental stage expression predictions | FIND (Fly in silico nanodissection) is a webserver for exploring the Drosophila embryonic development tissue-developmental stage-specific gene expression predictions. The predictions can be queried by genes (Genes Query or Genes Bulk Query) or by tissue-stages (Tissues query). The Similar Genes Query tool allows finding genes with similar spatiotemporal expression patterns. The Tissue Finder Query tool allows finding relevant tissues from ranked gene lists such as differential expression
MATLAB implementation of the FindCore and FindCore2 algorithms
find-tfbs is a tool to identify functional non-coding variants associated with complex human traits using open chromatin maps and phased whole-genome sequences.
This program is to find an ungapped pattern window of certain width from a set of protein sequences
Find an ungapped pattern window from a set of protein sequences
Finds regions of interest in a specimen image and adds them to an openDS object
Find regions of interest and update opends
Records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population.
findCPcli is a command line python-tool for the computation of chokepoint reactions in genome-scale metabolic models. The main purpose of the tool is to compute chokepoints by taking into account both the topology and the dynamic information of the network. In addition to the computation of chokepoints, findCPcli can compute and remove dead-end metabolites, find essential reactions and update the flux bounds of the reactions according to the results of Flux Variability Analysis.
An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.
Findere is a simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure (AMQ).
findGSEP estimates genome size of polyploid species using k-mer frequencies, utilizing iterative curve fitting to disentangle genomic regions and infer genome size. It is available as a web server and an R package for parallel processing.
An R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.
Calculate and plot enzyme reaction data.
A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. It provides many novel approaches to doing pangenomic analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.
An R package to automatically select number of principal components in single-cell analysis.
The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries.
FindPeaks 4.0 (Vancouver Short Read Package)
Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
We developed a comprehensive pipeline for annotating predicted NLR genes from a non-masked genome fasta file input. We identify loci using NLR-annotator software (Steuernagel et al. 2020), tblastn (Altschul et al. 1990) and Hidden Markov Model (HMM) (Eddy 2010). The unmasked loci identified through these methods, and including 20 kb flanking regions, are then annotated with Braker2 software (Hoff et al. 2019) using experimentally validated resistance genes as reference (Kourelis et al. 2021). Annotated amino acid fasta files are screened for domains using Interproscan (Jones et al. 2014) and the predicted coding and amino acid sequences containing both NB-ARC and LRR domains are located back to scaffolds/chromosomes and extracted in fasta and gff3 format.
Program to search for a promoter motif and optionally, an adapter sequence from a source species on a target species.
A web server for in silico D-peptide ligand identification.
An automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.
Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics.
This stand-alone program implements the Fine-Mapping of Adaptive Variation (FineMAV) statistic for detection of positively selected variants.
FINER is a unified deep learning framework to jointly predict protein isoform functions and isoform-isoform interactions.
FineStr (pronounced as (fi-nes’tru), from Latin fenestra—window, and from fine structure]) server allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.
fineSTRUCTURE is an algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals. Full assignment uncertainty is given.
Scan a protein sequence against PRINTS to identify the closest matching PRINTS sequence motifs/fingerprints.
High quality somatic mutations using filters for next generation sequencing. FiNGS: Filters for Next Generation Sequencing. We have developed Filters for Next Generation Sequencing (FiNGS), software written specifically to address these filtering issues. FiNGS can implement the ICGC filtering standards and has filters and thresholds that are fully configurable, which substantially increases the precision of results and provides high quality variants for further analysis.
Genetic fine-mapping from summary data using a nonlocal prior improves the detection of multiple causal variants.
Find Neuropyhsiological Networks (FiNN). A Python Toolbox for the analysis of electrophysiological data.
FINSURF (Functional Identification of Non-coding Sequences Using Random Forests) is a tool designed to analyse lists of sequences variants in the human genome. It assigns a score to each variant, reflecting its functional importance and therefore its likelihood to disrupt the physiology of its carrier. FINSURF scores Single Nucleotide Variants (SNV), insertions and deletions. Among SNVs, transitions and transversions are treated separately. Insertions are characterised by a score given to each base flanking the insertion point. Deletions are characterised by a score at every deleted base. FINSURF can (optionally) use a list of known or suspected disease genes, in order to restrict results to variants overlapping cis-regulatory elements linked to these genes. For a variant of interest, users can generate a graphical representation of "feature contributions », showing the relative contributions of genomic, functional or evolutionary information to its score.
FiPhA is an open-source R Shiny application designed for fiber photometry analysis, providing interactive visualization, quality control, and batch processing functionalities for a wide range of photometry approaches.
Droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing.
A motif discovery and characterization program based on mutual information
Motif discovery and characterization program for proteins based on mutual information
Detecting frequently interacting regions from Hi-C data. The University of North Carolina at Chapel Hill. FIREcaller: an R package for detecting frequently interacting regions from Hi-C data. Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays important roles in genome function. Frequently interacting regions (FIREs) are more informative for tissue-specific chromatin interactions than the well-established Hi-C readouts, such as A/B compartments, topologically associating domains (TADs) and chromatin loops.
A curated inventory of catalytic and biologically relevant small ligand-binding sites.
Database of PDB structures and their associated ligands. It also contains the largest set of reliably annotated functionally important residues.
The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.
FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.
FireProt-ASR is a web server for an automated calculation of ancestral sequences. Fireprot-ASR allows you to perform ancestral sequence reconstruction starting from a single protein sequence. The pipeline first compiles a dataset of catalytically similar protein sequences, aligns them, construct their phylogenetic tree, and then reconstruct ancestral nodes. It also allows user to input their own data and start from a different point in the pipeline.
FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. Proteins find their use in numerous biomedical and biotechnological applications. Naturally occurring proteins usually cannot withstand harsh industrial environments since they have evolved to function under mild conditions. Increasing protein stability is one of the key determinants of protein applicability. The predictive power of the current computational tools is compromised by the limited experimental data that would allow a rigorous training and testing.
FiRES (Find Repeated Elements in Structure) is a computational method for de novo identification of proteins with repeated elements. It relies on a topology-independent structure alignment method to identify repeating elements in protein structure. FiRES can be used for the discovery of proteins containing similar structural elements with less than 20% identical residues.
Predicts functional residues from structural templates and alignment reliability. It runs HHsearch and PSI-BLAST programs to generate alignments. Profiles are generated from a local 70% non-redundant database. Alignments are generated between the target sequences and FireDB templates.
This tool predicts functional residues from structural templates and alignment reliability. It runs HHsearch and PSI-BLAST programs to generate alignments. Profiles are generated from a local 70% non-redundant database. Alignments are generated between the target sequences and FireDB templates.
Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress Response. Summary The interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of “coessential” gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress.
FIRM is an R package for accurate integration of heterogeneous scRNA-seq datasets across multiple platforms, which specifically accounts for the heterogeneity in cell type composition between SS2 and 10X datasets. The integrated datasets generated using FIRM show accurate mixing of shared cell type identities and superior preservation of original structure for each dataset.
FIRM-AVP is a tool for antiviral peptide prediction. It is used for better understanding and prediction of antiviral peptides through primary and secondary structure feature importance.
Volumetric visualization tool which runs in all modern web browsers.
First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.
Tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.
Server for the identification of remote sequence homologues on the basis of protein domains.
FISH Amyloid is a new method for finding amyloidogenic segments in proteins based on site specific co-occurrence of aminoacids.
Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.FISH Finder is a graphical software tool to automatically analyze FISH images that vary significantly.
Visualizes data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. It comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats.
Family Identification with Structure Anchored Hidden Markov Models.
This software provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.
Fisher's Exact mid-P method to test row/col independence of a 2x2 contingency table.
Database and analysis platform for gene expression and alternative splicing of fish species.
FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles.
FishPhyloMaker is an R package to generate phylogenies for ray-finned fishes. The package has two functions FishTaxaMaker and FishPhyloMaker. The first generate a data frame from fish species names provided by the user, checking the validity of these names and possible synonyms by using the information presented in Fishbase database through the package rfishbase . Species that were not found in Fishbase are printed in the command line, and the user must inform manually the Family and the Order of these species.
fishplot is an R package that accurately and intuitively displays changes in tumor clonal structure over time.
FishSizer is an open-source software developed to assist researchers in the use of estimating length and depth of fish larvae by semi-automatization of the process.
FishTEDB is a database providing comprehensive information on transposable elements in fish genomes. Version 2.0 includes 33 new fish species, a genome browser, and estimated TE insertion times.
FISHtoFigure is a software tool designed for the analysis of subcellular mRNA transcript colocalisation in smFISH data, facilitating automated spatial analysis of transcripts without requiring extensive computational expertise. It is used in conjunction with QuPath and designed to analyse mRNA abundance and co-expression.
FiSiPred: This method predict dihedral angles of amino acids of a protein using very simple technique. This server allows users to predict dihedral angles using average based prediction (ABP) and secondary structure assisted average angle based prediction (SABP) methods.
FIST (Fast Imputation of Spatially-resolved transcriptomes by graph-regularized Tensor completion) is a graph-regularized tensor completion model for imputing the missing mRNA expressions in sptRNA-seq data.
R package for genotype calling for tetraploids with multiple population and parental data support.
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Python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics.
Fitting procedure for the parameters of the Branching Process model for COVID19 (SARS-CoV-2) epidemics.
Accurate inference of single-cell developmental potential using sample-specific gene weight.
FitDock is a novel protein–ligand docking method which outperforms state-of-the-art methods in terms of accuracy and speed, if the template is available.
Tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Fit-Hi-C (FitHiC) is a Python tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Framework for fitting conformations on a fixed backbone into electron density.
Computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user.
Forest of imputation trees for recovering true signals in single-cell open chromatin profiles. Forest of Imputation Trees (FITs) is a method to impute highly sparse and noisy data-sets from single cell epigenome profiling. FITs work in two phases. It has been made so to handle very large read-count matrixes and to get better imputation. In phase-1 it builds multiple imputation trees and from every tree it extracts 1 or 2 imputed version of original read-count matrix. One can run phase-1 of FITs in parallel processing mode also, where multiple trees can be build using several processors.After phase-1, the phase-2 part of FITs is used to accumulate the most relevant imputed version for every cell.
Estimation of coronavirus COVID-19 epidemic size by the logistic model
Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model
Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model. Code receives and plots data for the US obtained over the web.
Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model. Code receives and plots most recent data from HDX.
Fivepseq is a software package for analysis of 5prime endpoints distribution in RNA sequencing datasets. This is particularly useful for techniques that capture 5prime monophosphorylated RNAs, such as 5PSeq, PARE-seq or GMUC. It may also be useful for ribosome profiling datasets and alike.
An interactive multi-tissue eQTL browser. FIVEx: Functional Interpretation and Visualization of Expression.
Over-dispersion correction technique that serves to de-duplicate counts.
Feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.
RED is a Python package for automated truncation point selection in molecular simulations, aiming to minimize errors in calculated quantities. It offers a spectrum of heuristics, including a method equivalent to Chodera's approach, and is described in a peer-reviewed publication.
Pipeline for Single Nucleotide Variants (SNVs) and Copy Number Variation (CNVs) variant calling. This tool is no longer maintained. See the new version: PARROT-FJD.
Integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing. Circular RNAs (circRNAs) are a class of functional RNA molecules with a continuous loop structure characterized by back-splice junctions (BSJs).
FL-QSAR is a federated learning based QSAR prototype for collaborative drug discovery. FL-QSAR is an horizontal federated-learning based QSAR framework that enables clients to simulate the scenario of n clients with and without HFL(horizontal federated-learning). FL-QSAR is also a demo framework designed to help users better understanding the workflow and the underline mechanism of applying HFL for QSAR modeling. Meanwhile, FL-QSAR can be easily extended to other deep learning algorithms for solving various drug-related learning tasks.
Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data.
FlaGs (Flanking Genes) web- and command-line tool that clusters neighbourhood-encoded proteins into homologous groups and outputs the identity of the groups, a graphical visualization of the gene neighbourhood and its conservation, and optionally, a phylogenetic tree annotated with flanking gene conservation.
Method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).
FLAIR2 is a computational workflow that calls isoform models from long-read sequencing data and integrates RNA variant calls with associated isoforms, used to analyze splicing changes and RNA editing. The tool augments existing FLAIR functionality and integrates with long-read sequencing technology.
Flame is an open source framework for model development, hosting, and usage in production environments. Flame is a web application, with a Python backend and a web-based graphic interface, which can be used as a desktop application or installed in a server receiving requests from multiple users. Models can be built starting from any collection of biologically annotated chemical structures, since the software supports structural normalization, molecular descriptor generation and machine learning building, using predefined workflows. The model building workflow can be customized from the graphic interface, selecting the type of normalization, molecular descriptors, and machine learning algorithm to be used from a panel of state-of-the-art methods implemented natively.
Functional enrichment analysis using multiple lists
FLAME (Coakley et al., 2012) is an open-source, generic formal framework for agent-based modelling that allows parallelisation using MPI, and developers can use it to create models and tools. Implementing a Flame simulation is done by using finite-state automata with memory (Coakley et al., 2006). This tool has been adapted to be used with distributed GPUs using the OpenCL standard (Richmond et al., 2010). Examples of uses of FLAME range from bioreactor studies (Kaul et al., 2013) to immunogenic studies (Kabiri Chimeh et al., 2019) or also epidermis modelling (Li et al., 2013).
FLAMS is a bioinformatics tool for analyzing the conservation of post-translational modifications by searching against the CPLM and dbPTM databases. It allows researchers to verify modifications, assess species translation, and systematically evaluate novelty and conservation of modification sites.
A tool for comparative genomics of gene flanking regions. Flanker is a tool for studying the homology of gene-flanking sequences. It will annotate FASTA/multi-FASTA files for specified genes, then write the flanking sequences to new FASTA files. There is also an optional step to cluster the flanks by sequence identity.
A system-compiled program for large-scale binding site alignment.
FLARE (Forecasting Lake And Reservoir Ecosystems) is a near-term iterative forecasting system successfully predicts reservoir hydrodynamics and partitions uncertainty in real time.
Fast, accurate local ancestry inference with FLARE.
FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I.
Identifies paired-end reads which overlap in the middle, converting them to single long reads
FLASHDeconv is an algorithm based on a simple transformation of mass spectra, which turns deconvolution into the search for constant patterns thus greatly accelerating the process. It is able to deconvulute MS1 and MS2 scans from top-down proteomics.
Ultra-fast spatial transcriptomics deconvolution using structure-preserving randomized sketching. FlashDeconv estimates cell type proportions from spatial transcriptomics data (Visium, Visium HD, Stereo-seq, Xenium) with O(N) time complexity, processing 1 million spots in approximately 3 minutes on CPU without requiring GPU acceleration.
Interactive visualisation for fine-mapping of multiple quantitative traits.
FLASHIda is an intelligent online data acquisition algorithm for top-down proteomics (TDP) that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast decharging algorithms in FLASHDeconv and machine learning-based quality assessment to identify optimal precursors for fragmentation. Currently the C# source code and instruction of FLASHIda is available in here under a BSD three-clause license. We are working on merging FLASHIda into OpenMS.
FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.
FLASHQuant is a fast algorithm for proteoform quantification in top-down proteomics, capable of automatically resolving and quantifying coeluting proteoforms from MS1-level label-free quantification data.
FLAVi (Fast Loci Annotation of Viruses) is a pipeline that aims to provide an annotation framework for multiple complete or partial genomes of viruses. Currently, FLAVi is designed to annotate the genomes of viruses of the family Flaviviridae only.
Joint emulation of Earth System Model temperature-precipitation realizations with internal variability and space-time and cross-variable correlation. Given a global mean temperature pathway, generate random global climate fields consistent with it and with spatial and temporal correlation derived from an ESM. fldgen 2.0: Climate variable field generator with internal variability and spatial, temporal, and inter-variable correlation. The fldgen package provides functions to learn the spatial, temporal, and inter-variable correlation of the variability in an earth system model (ESM) and generate random two-variable fields (e.g., temperature and precipitation) with equivalent properties
flDPnn is a webserver that predicts disorder using an innovative deep neural network that uses predictions of disorder functions and disordered linkers as inputs.
Combines both thermodynamic and kinetic factors for RNA secondary structure and can predict RNA secondary structures from single primary sequences. Our early work has shown the accuracy of it is higher than the accuracy of traditional methods, especially for RNAs without pseudoknots.
This toolset can be used to analyze the sequencing data generated either by Nanopore or by PacBio using the FLEP-seq method.
FLEX (Functional evaluation of experimental perturbations) is an R package and a pipeline that utilizes several functional annotation resources to establish reference standards for systematic evaluation of genome-wide CRISPR screens.
Flexible barcode and adapter removal. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided. It increases read mapping rates and improves genome as well as transcriptome assemblies. The software supports data in fasta and fastq format from multiple sequencing platforms.
Fully automated method for flexible docking with large scale motion in one of the docked molecules. The method automatically identifies hinge regions and rigid parts using HingeProt and then docks the input molecules while explicitly considering the hinges and possible protein motions.
FlexDotPlot is a universal and modular dot plot visualization tool for complex multifaceted data.
Combining metabolic flux and regulatory network analyses.
Flexgsea is a R package to do gene set enrichment analysis. Main advantages: - Allows user defined functions. So you can use you favorite package for differential expression. - Calculates significance by sample permutation. - Parallelization using the foreach package. - Can calculate normalized enrichment scores (NES) and significance based on that. - Implements the weighted KS-like statistic.
Flexible cFDR (conditional false-discovery rate) is an extension of the cFDR framework that supports continuous auxiliary data from any arbitrary distribution, extending its use beyond only GWAS. As in the existing cFDR framework, the method requires GWAS test statistics for the trait of interest and auxiliary SNP-level data to output quantities analogous to p-values (called “v-values”), meaning that the method can be applied iteratively to incorporate additional layers of auxiliary data.
flexiMAP (flexible Modeling of Alternative PolyAdenylation) is a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. It is a beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data. Importantly, flexiMAP allows the modeling of multiple known covariates that often confound the results of RNA-seq data analysis.
Flexiplex is a versatile demultiplexer and search tool designed for omics data, particularly useful for analyzing long-read single-cell RNA-Seq data by allowing imperfect matches through Levenshtein distance. It allows flexible error tolerance during barcode assignment and target sequence identification.
FLEXIQuant-LF is a tool for robust regression to quantify protein modification extent in label-free proteomics data.
FlexPortal is a web portal containing a series of tools and databases related to macromolecular structure flexibility, developed to offer an integrated approach to study flexibility. Tools such as molecular dynamics atomistic and coarse-grained simulations, proteins and nucleic acids dynamics and flexibility analyses and structures and trajectories databases/repositories are integrated in a publicly available web interface.
FlexPred is a web-server for predicting residue positions involved in conformational switches in proteins.The server accepts either a protein sequence or a PDB file to predict residue positions involved in conformational switches.
Detect the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.
Automated multi-conformer model building using electron-density map sampling.
Web portal offering a complete set of macromolecular flexibility analyses from a coarse-grained or atomistic MD trajectory
Web-based interface that extracts DEPs through combinatory analysis.
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more ).
FlexTyper is a tool which enables the creation of an FM-index of raw, next generation sequencing data to enable rapid and flexible sequence queries.
Flexynesis is a deep learning framework designed for integrating multi-omics data, focusing on usability and adaptability for applications like precision oncology. It streamlines data processing and enables rigorous model evaluation with features like unsupervised feature selection and compatibility with various data types and modeling approaches.
A comprehensive repository of full-length isoforms across human cancers and tissues.
FLIMJ is an open-source ImageJ plugin for fluorescence lifetime image data analysis.
Flimma is a federated privacy-aware version of state-of-the art differential expression analysis method limma voom.
flimview is a software framework to handle, visualize and analyze Fluorescence-Lifetime Imaging Microscopy (FLIM) images.
Discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input, and it can also discover transcripts from several samples simultaneously, increasing statistical power.
Automated analysis of dithionite scramblase assays.
Standalone client able to register Web-Services in different catalogues (e.g. BioMOBY, INB, etc.). In addition the tool is able to perform the deployment process of command line applications. The process first registers the service, then it creates the Web-Service implementation skeletons, and finally, it deploys the skeletons and the command-line application in a server.
FLIRT is a Feature generation tooLkIt for weaRable daTa such as that from your smartwatch or smart ring. With FLIRT you can easily transform wearable data into meaningful features which can then be used for example in machine learning or AI models.
Machine Learning Improves the Identification of Novel Full-length Long Noncoding RNAs from RNA Sequencing Data Without Transcriptional Initiation Profiles.
Recognizing Floor-Level Lines With Height-Attention-Guided Multi-Task Learning.
The Flora Incognita App enables you to identify the plants of Central Europe automatically quickly, easily and accurately. The identification process is intuitive: take a picture of the flower and the leaf with camera of your smartphone. The unknown plant is then identified automatically within seconds. In addition to the specific plant species name, a species profile page presents further information such as characteristics, distribution or protection status of the species. You can also save, export or share your plant observations on different social media channels.
FLORAL is an open-source computational tool for log-ratio lasso regression modeling and compositional feature selection for diverse outcomes like continuous, binary, and time-to-event data, with compatibility for longitudinal microbiome data.
Floreada is a free web-based tool for simple flow cytometry analysis. It includes all basic capabilities - manual gates, manual compensation, dot plots, histograms, overlays, and basic automatic clustering. It is available on any platform with a web browser, including Windows, Mac, Linux, as well as phones and tablets.
FlorItaly is a data portal for the flora of Italy. This portal organises nomenclatural and distributional data from the recent checklists of the Italian native and alien vascular plants (and their subsequent updatings), with links to resources from other projects.
FLOSS (flexible ordered subset analysis) software package uses input and output files from the MERLIN linkage analysis package (Abecasis et al, 2002) to perform an ordered subset analysis using either nonparametric linkage analysis z-scores or linear allele sharing model LOD scores.
Flow Cytometry Data Reader and Visualization Example
Flow Cytometry Data Reader and Visualization
Pipeline for analyzing flow cytometric diversity.
An automated model-based clustering tool for microbial cytometric data.
The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.
FlowAnd is designed to analyze and integrate largescale, multi-color flow cytometry data. It implements methods for data importing, various transformations, several clustering algorithms for automatic clustering, visualization tools as well as straightforward statistical testing.
This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.
Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.
A Python package that can be used to calibrate flow cytometry data as well as automatically gate data, calculate common statistics, and produce publication quality plots.
Set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent.
A package to analyze flow cytometric data of complex microbial communities based on histogram images.
Semantic labelling of flow cytometric cell populations.
A quality control tool for flow cytometry data based on compositional data analysis.
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Users should have GSL installed. Windows users: consult the README file available in the inst directory of the source distribution for necessary configuration instructions.
Provides S4 data structures and basic functions to deal with flow cytometry data.
flowCut is an R package for precise and accurate automated removal of outlier events and flagging of files based on time versus fluorescence analysis.
A package to analyze flow cytometric data using gate information to follow population/community dynamics.
This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.
Tool for reformatting SFF files into other formats or tab-delimited
Clustering algorithm designed for the identification of global homologs. It employs an iterative approach to clustering sequences. However, rather than using a single HMM or profile to expand the cluster, this tool identifies subfamilies using the SCI-PHY algorithm and then selects and aligns new homologs using subfamily hidden Markov models. It is shown to outperform BLAST, PSI-BLAST and the UCSC SAM-Target 2K methods.
This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.
Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.
FlowGateNIST is a Python package for automated flow cytometry data analysis designed for use with small cells like bacteria and yeast. FlowGateNIST uses a GMM approach and a comparison between measured cell samples and buffer blank samples for automated gating to discriminate between events that are most likely to be cells vs. events that are most likely to be background.
FlowGrid density-based clustering algorithm that can perform fast and accurate clustering on very large scRNA-seq data sets. It can be implemented with Scanpy for fast clustering of Scanpy Anndata.
A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.
Fast and precise identification and quality checking of cell populations in flow cytometry.
Quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The method is able to map cell populations of different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be incorporate in any flow cytometry work flow that requires accurat quantification of similarity between cell populations.
FLOWMAPR is an R package for extensible analysis of single-cell datasets including FCS files generated from mass/flow cytometry or data.frames of other single-cell data processed in R. It is a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets.
Matching cell populations and building meta-clusters and templates from a collection of FC samples.
Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. R 2.11.0 or newer is required.
Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Users should have a working copy of flowClust 2.0 installed.
A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.
Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.
Provides quality control and quality assessment tools for flow cytometry data.
Fully automated R BioConductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.
This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.
A Python Package Attributing Resource Use, Waste, Emissions, and Other Flows to Industries.
FlowScatt is a tool to transform an ensamble of flow cytometry data experiment in a scattering dependent and non-dependent part. It enables volume-independent flow cytometry data by decoupling fluorescence from scattering.
Suite of tools to help simulate sets of sequence reads. While the original target was to simulate 454 reads, the different tools can be used quite flexibly to simulate other kinds of sequence data sets.
Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.
This package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers.
Profile maximum likelihood estimation of parameters for flow cytometry data transformations.
Phenotyping Flow Cytometry Assays using multidimentional expansion of single dimentional partitions.
An interactive web-application for optimizing the use of flow cytometry as a screening tool in urinary tract infections.
Provides utilities for flow cytometry data.
Provides visualization tools for flow cytometry data.
Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
Classical federated learning approaches incur significant performance degradation in the presence of non-IID client data.
FLT3-ITD is a comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia.
Influenza virus infection induces widespread alterations of host cell splicing. These scripts allow to launch a local version of the Shiny web-interface to explore the RNA-seq data from XXX (2020).
FluConvert and IniFlu is a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk.
Code for reconstructing influenza dynamics from surveillance data using evidence synthesis techniques.
fluff is a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome.
Tool for determining lineages and genotypes of influenza A viruses.
FluMut is an open-source tool designed to search for molecular markers with potential impact on the biological characteristics of Influenza A viruses of the A(H5N1) subtype, starting from complete or partial nucleotide genome sequences.
FluoAnalysis is an open-source MATLAB toolbox designed for analyzing calcium imaging and electrophysiological data, particularly focusing on oscillatory signals in astrocytic and neuronal networks. It offers both GUI-based and command-line approaches for data processing, cell classification, spectral analysis, and report generation.
Interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples.
Fluorescence Tools is a suite of tools for automated and optimally FRET-assisted structural modeling.
FluorescenceViewer.m is a short script for viewing fluorescence spectra. It requires the folder containing fluorescent spectra to be in the same directory as the .m file.
Count the number of fluorescent cells (tagged with GFP) on noisy background fluorescence
Inexpensive robotic system for standard and fluorescent imaging of protein crystals. Code and .obj files for construction of a fluorescent robotic imager used for protein crystallography. Code and .obj files for construction of a robotic imager capable of using visible fluorescence to automatically image plates from protein crystallization experiments.
FluPhenotype is a one-stop platform to rapidly determinate the phenotypes of the influenza A viruses.
FluSPred(Flu Spread Prediction) is a machine learning based tool to predict the human associated Influenza A virus strains with the help of its protein and genome sequences,
A fast, open source framework for ultrasound blood flow simulations.
The FiLter for Understanding True Events (FLUTE) is a fast and reliable knowledge retrieval from biomedical literature. The tool uses public protein interaction databases to filter interactions that have been extracted by machines from databases such as PubMed and score them for accuracy. Confidence in the interactions allows for rapid and accurate model assembly.
FluxCapacitor s a computer program to predict splice form abundancies from reads of an RNA-seq experiment. FluxSimulator can generate simulated data for testing RNA-seq pipelines
Fluxer is a web application for the computation and interactive visualization of flux graphs from genome-scale metabolic models. Flux Balance Analysis is used to calculate the flux of the metabolic network, which can then be visualized with spanning trees, k-shortest paths, and complete graphs
Easy to use tool for the advanced visualization of simulated or measured flux data in biological networks. Flux data import is achieved via a structured template basing on intuitive reaction equations. Flux data is mapped onto any network and visualized using edge thickness. Various visualization options and interaction possibilities enable comparison and visual analysis of complex experimental setups in an interactive way.
MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models
Stationary 13C metabolic flux analysis for estimation of intracellular flux distribution.
Open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks.
Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.
FlyBrainLab is an interactive computing platform for studying the function of executable circuits constructed from fruit fly brain data. FlyBrainLab is designed with three main capabilities in mind: (i) 3D exploration and visualization of fruit fly brain data, (ii) creation of executable circuits directly from the explored and visualized fly brain data, and (iii) interactive exploration of the functional logic of the devised executable circuits. FlyBrainLab provides an environment where computational researchers can present configurable, executable neural circuits, and experimental scientists can interactively explore circuit structure and function ultimately leading to biological validation.
A database of DNA binding specificities for Drosophila transcription factors determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information for individual TFs, groups of TFs or for all TFs with characterized binding specificities.
An integrated database for Drosophila and Anopheles genomics.
Systematic assembly of data on Drosophila melanogaster eye development. It consists of data on eye development obtained from the literature, and a web interface for users to interactively display these data as a gene regulatory network.
Flype, a web-based bioinformatics platform to address these challenges by allowing us to: (a) securely accept data from a variety of sources, (b) send orders to a variety of destinations, (c) perform secondary analysis and annotation of NGS data, (d) provide a central repository for all genomic variants, (e) assist with tertiary analysis and clinical interpretation, (f) send signed out data to our EHR as both PDF and discrete data elements, (g) allow population frequency analysis and (h) update variant annotation when literature knowledge evolves.
An integrated web-based resource for cell-cell communication prediction in Drosophila.
Database of Dorsophila RNA interference (RNAi) Screening Center.
A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.
Database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.
FlyWire is a game-like platform open to all, to help crowdsource the first complete wiring diagram of a centralized brain. In a fruit fly brain sliced and imaged by electron microscopy (Zheng et al. 2018), we identified pieces of neurons by artificial intelligence. Players search for the right pieces and put together beautiful 3D neurons that advance science's understanding of brain circuits.
An optimized FM-index library for nucleotide and amino acid search. A fast, AVX2 accelerated FM-index library that utilizes windows of SIMD registers to quickly locate exact match kmers in genetic data. This FM-index is highly optimized for both nucleotide and amino sequences, but is unsuitable for general text.
A fiducial marker tracking software for studying cell mechanics in a three-dimensional environment.
FMAlign2 is a fast multiple sequence alignment algorithm designed for ultralong nucleotide sequences, leveraging suffix arrays and a vertical division strategy to improve accuracy and speed compared to its predecessor, FMAlign.
Funnel-Metadynamics Advanced Protocol (FMAP), which is a flexible and user-friendly graphical user interface (GUI)-based protocol to perform funnel metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to reveal the ligand binding mode and accurately calculate the absolute ligand–protein binding free energy. FMAP guides the user through all phases of the free-energy calculation process, from preparation of the input files, to production simulation, to analysis of the results.
FMAP (Folding of Membrane-Associated Peptides) is a webserver for thermodynamics-based molecular modeling of α-helices in membranes and micelles.
This package introduces an efficient maximum common substructure (MCS) algorithm combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The output flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities.
fmh-funprofiler is a pipeline that leverages FracMinHash (implemented in sourmash) to functionally profile metagenomic samples, offering a faster and more memory-efficient alternative to alignment-based methods. The pipeline is freely available on GitHub and allows researchers to analyze metagenomic data for functional capabilities.
A Fast Big Data-Oriented Genomic Selection Model Based on an Iterative Conditional Expectation algorithm.
From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.
The effects of multi-echo fMRI combination and rapid T2*-mapping on offline and real-time BOLD sensitivity. Magnetic resonance imaging (MRI) data of the brains of 28 healthy volunteers, for the study and development of functional MRI methods.
A consortium of fully automatic neuroimaging pipelines for fMRI analysis, which performs standard preprocessing, as well as 1st- and 2nd-level univariate and multivariate analyses.
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc.
A new tool for detection and identification of clusters of sequential motifs with varying characteristics inside genomic sequences.
Software tool to compute the MTP of a physical map based purely on restriction fingerprint data (and the contigs). It completely ignores the ordering of clones obtained by the physical map algorithm.
Find My Understudied Genes (FMUG) is a tool developed by researchers at Northwestern University to help identify understudied genes and characterize their tractability for future research. The tool allows scientists to engage with potential bias during the selection of research targets.
Software to Identify Homozygous Lesions in Deletion Mutant Populations.
Dissecting molecular regulatory mechanisms underlying noncoding susceptibility SNPs associated with 19 autoimmune diseases using multi-omics integrative analysis. fnGWAS, an integrative analysis frame designed for dissecting molecular mechanisms underlying noncoding GWAS SNPs through incorporating diverse functional cell-specific multi-omics data. Dissecting the functionality of noncoding GWAS SNPs. Just select interested autoimmune diseases (or select all without disease limitation) , select type and enter correspond SNPs/CotoBand/Target Gene. fnGWAS is an integrated analysis pipeline for dissecting molecular mechanisms :. Genome-wide association studies (GWASs) have unraveled thousands of susceptible variants associated with tens of different autoimmune diseases.
FNS is an event-driven Spiking Neural Network (SNN) framework, oriented to data-driven neural simulations.
Visualize small to moderately sized biological networks and pathways. The tool can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials
FOBI (Food-Biomarker Ontology) an ontology to represent food intake data and associate it with metabolomic data. It is composed of two interconnected sub-ontologies. One is a “Food Ontology” consisting of raw foods and prepared foods while the second is a “Biomarker Ontology” containing food intake biomarkers classified by their chemical classes.
This package provides a set of tools for interacting with FOBI (Food-Biomarker Ontology).
Rapid density based algorithm for detecting clusters in localization microscopy datasets. The algorithm is easily optimized to reduce artifacts that commonly degrade image reconstructions and minimize the detection of false or pseudo clusters.
Detection of genomic focal aberrations in high-resolution DNA copy number data.
FocAn is a tool for automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy.
FOCUS (Find Organisms by Composition Usage) is an agile profiler for metagenomic data.
Utilise advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualisation.
Focused multidimensional scaling (focusedMDS) is a tool for visualizing the multidimensional data contained within a pairwise distance matrix.
A deep learning method for fiber orientation distribution angular super resolution.
Analysis of the force-distance curves obtained in single-molecule force spectroscopy experiments, providing almost automatic processing, analysis, and classification of the obtained data.
A pipeline that can identify putative effectors in a provided set of Fusarium oxysporum genomes and show their presence/absence variation across all input genomes.
FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.
FogFrame-2.0 provides a framework to create a testbed for fog computing based on Raspberry Pi computers.
Align a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm.
Computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion.
Predict the folding rates of proteins from their amino acid sequences.
An APW+lo program for calculating the properties of solids. Unfolding of first-principle electronic band structure obtained with WIEN2k DFT-(L)APW code.
Fold2Seq, a transformer-based generative framework for designing protein sequences conditioned on a specific target fold.
Pairwise local and global structural alignment of RNA sequences.
A library and format for compressing and indexing large protein structure sets.
De novo protein fold design through sequence-independent fragment assembly simulations.
Folddisco enables rapid detection of discontinuous or segment 3D motifs in large protein databses.
FoldGO is a web tool for fold-change-specific functional enrichment analysis of transcriptome. FoldGO identifies gene ontology (GO) terms specifically enriched in sets of genes with a similar fold-changes in response to a stimulus.
Calculate angles between helices in the set of 3 α-helices from the same chain and the torsion angle (and handedness) of this set of helices.
Deep hyperspherical embeddings for protein fold recognition.
Interactive graphical interface to the Rosetta molecular modeling package.
FoldMason is a fast multiple structure aligner based on Foldseek's 3Di alphabet.
FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.
Server to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins, and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.
FoldRec-C2C is a tool for protein fold recognition by combining cluster-to-cluster model and protein similarity network.
Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster.
Foldseek-Multimer is an open-source software and webserver for rapidly aligning protein complexes, achieving 3-4 orders of magnitude speedup compared to existing methods while maintaining comparable accuracy. It is designed to handle the growing number of predicted protein complex structures.
Improving protein fold recognition using triplet network and ensemble deep learning.
FoldUnfold is a web server that detects disordered regions in a protein sequence.
FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.
A food-disease relation mining pipeline.
FoodKG is a tool to enrich knowledge graphs using machine learning techniques. FoodKG uses Specialization Tensor Model (STM) to predict the relation between newly added triples.
Analyse a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.
A pangenome database of Fusarium oxysporum.
ForageGrassBase is molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.).
The Finding Optimizing and Reporting Cas Targets (FORCAST) pipeline enables researchers to design Cas-mediated mutagenesis experiments in model organisms with ease. It is a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments.
Set of self-consistent AMBER forcefield parameters for non-canonical amino acids. It allows you to design and derivatize peptides containing NCAAs for use as drugs.
Set of self-consistent AMBER forcefield parameters for frequently occurring post-translational modifications (PTMs).
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.
Predict missing sequences and branch lengths in phylogenomic data.
ForeStatistics is a Windows-based feature-rich software program for performing statistics in forensic DNA analysis, paternity and relationship testing.
The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees.
Collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research.
Force-directed 3D graph editor for visualization of integrated genome scale data.
Functional element Overlap analysis of the Results of GWAS Experiments . Discover cell specific enrichments of GWAS associated SNPs in regulatory regions and provides tabular and graphical summaries of the enrichments.
FORGE2 uses an expanded atlas of cell type-specific regulatory element annotations, including DNase I hotspots, five histone mark categories and 15 hidden Markov model (HMM) chromatin states, to identify tissue- and cell type-specific signals.
forgeNet (forest graph-embedded deep feedforward networks) a graph deep neural network model using tree-based ensemble classifiers for feature graph construction.
Python library to analyze the tertiary structure of RNA secondary structure elements.
FORK-seq is a replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).
This tool creates infiles for several population genetic analysis programs from csv, genepop or convert* (excel) files. It only handles diploid microsatellite data for now.
Web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.
fortuna is an alignment-free method to quantify anambiguous building blocks of transcripts and to detect and annotate novel splicing events.
Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. FORUM is an open knowledge network aiming at supporting metabolomics results interpretation in biomedical sciences and automated reasoning. Containing more than 8 billion statements, it federates data from several life-science resources such as PubMed, ChEBI and PubMed. Leveraging the bridges in this linked dataset, we automatically extract associations between compound and biomedical concepts, using literature metadata enrichment. Find more about the method in our preprint here: BioXiv.
Forward-time simulation programs for the standard neutral model.
Given a minimum segment length and m sequences of length n drawn from an alphabet of size σ, create a segmentation in O(mn log σ) time and use various matching strategies to join the segment texts to generate founder sequences.
Computational method for detecting significantly recurrent identity by descent (IBD) in a set of haplotypes. This tool was designed for the discovery of founder mutations in dense SNP array data from a population sample of tumors.
The Foundational data initiative for Parkinson’s disease (FOUNDIN-PD).
R package dedicated to the analysis of (multiplexed) 4C sequencing data. It provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.
Fox Insight Collects Online, Longitudinal Patient-Reported Outcomes and Genetic Data on Parkinson's Disease | Fox DEN provides investigators with a tool to explore, download and apply statistical models on aggregated data collected for the Fox Insight online clinical study. The Fox Insight study collects patient-reported outcomes and genetic data from people with Parkinson's disease and their loved ones
Fast X-ray Scattering (FoXS) is a web server for computing the small angle x-ray scattering (SAXS) structure profile of a molecule in solution and for comparing the computed profile to the experimental profile.
Extensive library of fingerprint-based molecular activity prediction tools.
FPADMET is a compilation of molecular fingerprint-based predictive models for ADMET properties.
FPB is a new data-independent tool suitable for large scale projects as well as mapping of few clones.
An easy-to-use open source visualization tool that permits researchers to share their volumetric image data online and third parties to interact with, and explore, datasets in their entirety.
FPC is a tool to assemble contigs from a set of clones and their restriction fragments.
Data mining-based method for proteome-wide PPI prediction.
The fpemlocal package is the one-country implementation of FPEM (family planning estimation model) designed with tidyverse philosophy. The model in this package uses global model results from the package FPEMglobal to aid in the estimation of country level family planning indicators. fpemlocal comes equiped with survey data, country unit data, and country population count data, to produce one-country runs. Running FPEM is divided into three main functions.
FPfilter is a false-positive specific filter for vcf files from whole genome sequencing. It is proved to be more false-positive specific than GATK hard filter.
An FPGA-accelerated implementation of GWAS permutation testing designed primarily for AWS EC2 F1 (f1.2xlarge) instances.
The FPM app is an open-source application for simple and intuitive Fourier ptychographic reconstruction. FPM is a computational microscopy technique that allows obtaining microscopic image of a measured sample with much higher resolution than it would follow from the numerical aperture (NA) of used microscope objective.
Fast Parameter-free Multi-view Subspace Clustering with Consensus Anchor Guidance.
FPNuNet addresses these limitations through a frequency-aware prompt-guided architecture that integrates RGB and Hematoxylin-Eosin-Diaminobenzidine channels via a color fusion stem, processes features through SAM-based structural and ViT-based semantic encoders modulated by lightweight prompt adapters, and employs a progressive frequency-aware residual global fusion neck to aggregate multi-scale features. The network utilizes three collaborative decoder branches to jointly predict binary masks, horizontal-vertical vectors, and nuclear types, enabling robust performance across diverse IHC staining conditions. Experimental evaluation on the CD47-IHCNuSC dataset demonstrates that FPNuNet consistently outperforms state-of-the-art baselines in both segmentation accuracy and classification robustness.
Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).
Protein pocket hunting in a web browser.
Relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. To identify protein binding sites, we model the shape of a split pocket induced by a binding ligand. This database provides an easily accessible resource for studying functional surfaces, assessing conformational changes between bound and unbound forms and analyzing functional divergence.
FPSAC (Fast Phylogentic Scaffolding of Ancient Contigs) is a software for fast phylogenetic scaffolding of ancient contigs. The author apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome.
Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.
Mini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files.
Convert quality scoring to Sanger in FASTQ files.
Detect duplicate reads. Outputs a list of read names corresponding to reads already seen in the dataset with a better quality sum score (duplicates).
Output reads with low quality bases trimmed (at the extremities) or masked and/or with quality descreased to the minimum. Output an extra singlet dataset if paired-end data provided.
List names of sequences from FASTQ formatted files.
List names of sequence pairs from two FASTQ formatted files.
FQSqueezer is a FASTQ compressor based on k-mer statistics.
A package that provides tools for efficient FASTQ files manipulation.
Utility for filtering and trimming high-throughput next-gen reads.
FR-Match is a tool for robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test.
Full-Resolution Network and Dual-Threshold Iteration for Retinal Vessel and Coronary Angiograph Segmentation.
frac-kmc is a fast and efficient FracMinHash sketch generator program that provides accurate cosine similarity estimation. It is freely available as a command-line tool and supports fast data processing for large-scale genomic and metagenomic analyses.
Ridge regression (RR) is a regularization technique that penalizes the L2-norm of the coefficients in linear regression. One of the challenges of using RR is the need to set a hyperparameter (α) that controls the amount of regularization. Cross-validation is typically used to select the best α from a set of candidates. However, efficient and appropriate selection of α can be challenging, particularly where large amounts of data are analyzed. Because the selected α depends on the scale of the data and predictors, it is also not straightforwardly interpretable. In fracridge, we reparameterize RR in terms of the ratio γ between the L2-norms of the regularized and unregularized coefficients. This approach, called fractional RR (FRR), has several benefits: the solutions obtained for different γ are guaranteed to vary, guarding against wasted calculations, and automatically span the relevant range of regularization, avoiding the need for arduous manual exploration.
Multi-scenario genome-wide medical population genetics simulation framework.
FraGAT is a fragment-oriented multi-scale graph attention model for molecular property prediction.
Guided modeling of missing segments such as loops or hinge regions into cryo-Electron Microscopy (cryo-EM) density maps [1]. Segments of up to 3-35 residues length can be effectively modeled into maps of different resolution.
Application for finding (fragmented) genes in short reads
FragGeneScanRs is written in Rust, so first head over to their installation instructions. Afterwards, you can install the crate from crates.io with cargo install frag_gene_scan_rs The installation progress may prompt you to add a directory to your path so you can easily execute it.
Protein fragment picker that allows protein fragment databases to be created and queried. It can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. It also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput.
Assessing and visualizing fragility of clinical results with binary outcomes in R using the fragility package.
A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly.
The FragMAXapp is a web application for processing and visualisation of macromolecular crystallography data, with the focus on fragment screening campaigns.
A tool for analyzing MS/MS fragmentation data.
A resource for the comparison of fragments found in metabolites, drugs or toxic compounds. We generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. It provides a variety of search options. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments binding sites and classification of fragments.
FrAG is a tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand conformational space.
FragPipe-Analyst is a web application for performing differential expression analysis and visualizing quantitative proteomics data generated by the FragPipe computational platform. It supports various quantification workflows and offers functionalities like imputation, clustering, and pathway enrichment analysis.
It implements an efficient algorithm for detecting nucleotide pattern fragments in genomes that occur in a given order. For each pattern a tolerance can be specified separately.
FragRep is a web server for structure-based ligand design by fragment replacement. FragRep is a powerful computational tool for the rapid generation of ligand design ideas; either in scaffold hopping or bioisosteric replacing.
Web application designed to sample alternative protein backbone conformations in loop regions using the geometrical constrains of smotifs.
Database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model.
FRAGSITE is a fragment-based machine learning algorithm that scores protein-ligand binding for ligand virtual screening.
FRAGTE is a completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes.
A transcriptome assembly and mRNA annotation pipeline, which utilizies external and newly developed software components.
Program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.
Framework for DNA-based data storage design, verification, and validation.
Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.
Analyzes fluorescence recovery after photobleaching (FRAP) data using the Hankel transform method.
FRAP.zip is a MATLAB GUI for analysis of FRAP data.
FRC-QE is a robust and comparable 3D microscopy image quality metric for cleared organoids.
FRCD (Food Risk Component Database) is a comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis.
Colocalization of Fluorescence and Raman Microscopic Images for Training Data Collection
An ensemble predictor with effective feature representation for deleterious synonymous mutation in human genome.
FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.
Generate residue/base frequency table or plot.
Program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure. In this structure, each “child” sequence is considered to be derived from its “parent” sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree.
FRED is a framework for T-cell epitope detection that offers consistent, easy, and simultaneous access to well established prediction methods for MHC binding and antigen processing. FRED can handle polymorphic proteins and offers analysis tools to combine, benchmark, or compare different methods. It is implemented in Python in a modular way and can easily be extended by user defined methods.
Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms. Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective target of personalized cancer therapeutics. However, detecting AS events remains a challenging task, especially if these AS events are not pre-annotated.
Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.
FreeClimber is a Python-based, background-subtracting particle detection algorithm that performs a local linear regression to quantify the vertical velocity of points moving in a common direction.
FreeCT_wFBP is a software package capable of reconstructing helical scans acquired with arbitrary pitch-values, and sampling techniques such as flying focal spots and a quarter-detector offset.
Freecyto is a python web application providing accessible and collaborative flow cytometry analysis fx. K-means quantization.
FreeDTS is a software package for performing mesoscale simulations of biomembranes, enabling research on membrane shape, protein organization, and the effects of membrane proteins. It allows users to model various membrane conditions and integrate vertex-based inclusions to represent membrane proteins.
GUI allowing freehand annotations of DICOM prostate images
Freeia is a tool that uses robust algorithms to find optimal metabolic factories, which are systems of reactions that produce target molecules from source compounds while conserving or not depleting intermediate metabolites. It addresses limitations in existing shortest factory solvers and provides a complete characterization of the graph-theoretic structure of shortest factories.
FREEPII (Feature Representation Enhancement End-to-end Protein Interaction Inference) is a end-to-end learning method encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference.
FreeSASA is an open source library and command line tool to calculate the solvent accessible surface areas of protein molecules. The library is as fast and accurate as existing tools, with the advantage of being open source and available as both a library, a command line tool and it has Python bindings.
University Library, University of Bergen, Bergen, Norway
Freescore is a scoring system based on local alignment partition functions for the classification of conotoxin proteins
A free of charge volume renderer that enables you to explore 3D digital images from a selectable viewpoint. It is especially suitable for single or multi-channel images from microscopes or MRI.
Wrapper functions that interface with 'Freesurfer', a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.
FreeSurfer is an open source package for the analysis and visualization of structural, functional, and diffusion neuroimaging data from cross-sectional and longitudinal studies.
Fast regional association analysis of quantitative traits for family-based and population studies.
The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.
Method for precise high-throughput combinatorial quantification of allele frequencies.
General open-source framework to compress large amounts of biological sequence data.
FRETraj is a software framework that harmonizes single-molecule Förster resonance energy transfer (FRET) measurements with molecular dynamics simulations and de novo structure prediction for RNA and DNA.
FRET - IBRA is a fully parallelized toolkit to process fluorescence resonance energy transfer (FRET) intensity data to produce ratiometric images with low measurement bias.
FRETboard is a tool to supervise your FRET detection algorithm.
FRETBursts is an open source software for analysis of freely-diffusing single-molecule Förster Resonance Energy Transfer (smFRET) data.
A Python package for FRET efficiency predictions using rotamer libraries.
FRETraj is a Python module for predicting FRET efficiencies by calculating multiple accessible-contact volumes (multi-ACV) to estimate donor and acceptor dye dynamics.
For the FRET analysis of images of yeast cells labeled with YFP and CFP.
Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset
A Tool for Epistasis Analysis Based on Functional Regression Model.
Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.
Bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features.
Frites is a Python toolbox for assessing information-theorical measures on human and animal neurophysiological data (M/EEG, Intracranial). The aim of Frites is to extract task-related cognitive brain networks (i.e modulated by the task). The toolbox also includes directed and undirected connectivity metrics such as group-level statistics.
Preprocessing and analysis for single microarrays and microarray batches. Single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance.
Tools for advanced use of the frma package.
Imputation software FRMC for single-cell RNA-Seq data, which innovates a fast and accurate singular value thresholding approximation method.
Framelet-Based Multilevel Network for Pansharpening.
Systems biology tool to uncover the dynamic spectrum of RBP-ncRNA circuits (RNC) by integrating transcriptomics, interactomics and proteomics data.
FRnet-DTI is convolutional neural networks for feature manipulation and drug-target interaction prediction.
Generate very efficiently many potential predictions of how two proteins could interact. This approximation effectively address the complexity and sampling requirements of the initial 6D docking exhaustive search by combining the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations.
Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).
Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.
FrogAncestryCalc is a standalone batch likelihood computation tool for ancestry inference panels.
The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.
Taxonomic affiliation of each OTU's seed by RDPtools and BLAST.
Converts a FROGS BIOM in fully compatible BIOM.
This tool uses an iterative growth process and the use of sequence abundance values to delineate OTUs.
Split by samples the reads in function of inner barcode.
Keeps in each sample the same number of element by random sampling.
Denoising and dereplication in metagenomic analysis.
Allow to upload a TAR archive as one dataset in Galaxy.
A Library for the Study of Molecular Crystal Excited States at the Aggregate Scale | Framework for Molecular Aggregate Excitation | fromage (FRamewOrk for Molecular AGgregate Excitations) is a Python framework designed to facilitate the study of molecular aggregates in the excited state. It contains utilities for geometry manipulation going from periodic to finite models, exciton analysis and ONIOM calculations
Software for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores, their relative Activity Scores or enzyme enrichment odds ratios.
FSL is a comprehensive suite of analysis tools for FMRI, MRI, and diffusion brain imaging data. It provides a range of tools accessible through command-line and GUI interfaces and is widely used in neuroimaging research.
Promoting the meta-analysis of chicken microarray data. Promote, simplify, and ease the meta-analysis of chicken microarray data. This R package, named affyChickGenomeArrayfrmavecs, was automatically created by package frmaTools version 1.34.0.
Serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure.
FRTpred, simultaneously predicts the logarithmic protein folding rate constant, ln(kf), and folding type from the provided sequence.
An R package for calculating energetic local frustration in protein structures. Additionally to the functionalities present at the web server, frustratometeR offers the possibility to analyse frustration across molecular dynamics simulations and to assess the effect of amino acid variants.
FSA (Fast Statistical Alignment) is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequence. FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences.
Fast String-Based Clustering (FSBC) is a tool to estimate clusters by searching various lengths of over-represented strings as target binding regions. FSBC can perform fast calculation with search space reduction from a single round, typically the final round, of HT-SELEX data considering imbalanced nucleobases of the aptamer selection process.
fsbrain is a GNU R library for structural neuroimaging. It provides high-level functions to access (read and write) and visualize surface-based brain morphometry data (e.g. cortical thickness) for individual subjects and groups.
FSCAM enables users to easily select features from single-cell RNA sequencing. It can also automatically determine the cluster number and accurately identify the cell types.
Alternative framework for identifying sub-chromosomal copy number variations in a fetal genome.
Software that searches the genomic sequences or mRNA sequences for frameshifting sites. It is capable of finding -1 frameshift sites for most known genes and +1 frameshift sites for two genes: protein chain release factor (prfB ) and ornithine decarboxylase antizyme (oaz ).
An end-to-end spectroscopy analysis package for FMRI, MRI and DTI brain imaging data.
Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data. R package to perform Feature Specific Quantile Normalization.
FSTVAL is an open access web tool to manage bulk flanking sequence tags (FSTs).FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence.
Integrative solution to exploit inbreeding in dense SNP chip and exome data.
Software for inferring the function of proteins based on its indirect interaction partners. Its sensitivity and precision are superior to Neighbour Counting, Chi2, PRODISTIN, Functional Flow, and Markov Random Field approaches. It can also be used for ranking the reliability of individual protein interactions.
Fast and accurate phylogeny reconstruction using filtered spaced-word matches.
Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps.
Families and TAG Finder: a Snakemake workflow to identify gene families and detect Tandemly Arrayed Genes.
Discretises two molecules onto orthogonal grids and performs a global scan of translational and rotational space. In order to scan rotational space it is necessary to rediscretise one of the molecules (for speed the smaller) for each rotation. The scoring method is primarily a surface complementarity score between the two grids. To speed up the surface complementarity calculations, which are convolutions of two grids, Fourier Transforms are used.
Web server for locating probable protein coding region in nucleotide sequence using fourier tranform approach.
FTK is a library that scales, simplifies, and delivers feature tracking algorithms for scientific datasets. FTK can be used as ParaView plugins, Python bindings, or a command-line interface.
FTMAP is a webserver that globally samples the surface of a target protein using small organic molecules as probes to identify and predict binding hot spots. Users can also input small molecule probes.
A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures.
ftmsRanalysis is an R package for exploratory data analysis and interactive visualization of FT-MS data. This R package provides functionality for data formatting, preprocessing, filtering, exploratory data analysis and visualization of fourier transform (FT) mass spectrometry (MS) data.
Plugin for VMD designed to characterize and identify cross-structural ‘hot spots’ in proteins. The program identifies these druggable hot spots by docking a series of small molecular probes onto the protein surfaces. It combines these output structures, clusters them, and displays them visually for easy comparison.
Functional enrichment tool for bioinformatic analysis.
Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.
Program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure.
Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources were interconnected with our original database functionalities. By providing the largest unique full-length cDNA and dynamic transcriptome data, Full-Parasites is useful for understanding host-parasite interactions.
fullsibQTL is an R package for QTL mapping in biparental populations of outcrossing species. fullsibQTL performs QTL mapping in outbred (outcrossing) species, considering a full-sib cross (or F1 population) as a mapping population.
Program that reports identical fusion genes based on gene-name annotations.
Framework consisting of a client (Faerun) and server (Underdark) module, facilitating the creation of web-based, interactive 3D visualizations of large datasets, enabling record level visual inspection.
Comprehensive web server for gene set enrichment analysis of prokaryotes.
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
Fungal bioActive compound Resistant Target Seeker.
Web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. The program takes a list of genes as input and produces a ranked list of the Gene Ontology terms enriched in an input list.
Novel functional supervised algorithm for the integrative analysis of Infinium 450k DNA methylation and matched or unmatched gene expression data.
A web tool for automated hierarchical clustering and enrichment analysis of high-throughput genomics data with interactive visualizations of the results. It enables to obtain a first interactive overview of expression patterns, gene names and shared functionalities in the dataset.
FuncZymeDB is a resource that utilizes an LLM-assisted workflow to mine enzyme-substrate interactions from published manuscripts, particularly focusing on plant enzymes. It aims to improve biocuration and prediction of enzyme functions by extracting data from the literature.
Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.
It integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.
A web server for the identification of structural motifs in a set of non-homologous protein structures.
Genomic data analysis tool designed to perform a functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, functional analysis allows to detect co-regulated biological processes (i.e. represented by annotating genomic themes) through a specifically designed co-clustering procedure involving biological annotations and gene expression data.
Global networks of functional coupling in eukaryotes from comprehensive data integration.
FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for multiple species. It enables users to input gene identifiers and customize search parameters for various network expansions and provides consistent visualizations with the FunCoup website.
This tool was developed for inferring conserved functional regions in protein tertiary structures.
FuncPEP is a database of functional peptides encoded by non-coding RNAs.
FuncPhos-STR is a web server for functional prediction and structural visualization of human proteome-level phosphosites. It integrates AlphaFold protein structures, sequence evolution, and protein-protein interaction information to predict phosphorylation sites and their potential regulatory mechanisms.
Novel label propagation techniques applied to many different types of gene and protein data in order to predict protein function via Gene Ontology annotations.
FlyRNAi.org provides a suite of bioinformatics tools and resources for functional genomics studies in Drosophila and other arthropods. It supports various stages, including reagent design, analysis, data mining, and analysis, catering to biologists and biomedical experts.
Versatile and efficient web tool for non-model organism annotation.
A web-based application for analyzing and visualizing large-scale omics data, including but not limited to genomic, metagenomic, and transcriptomic data.
Protocol to infer functional networks from machine learning models. It is a general approach that uses BioHEL, a rule-based evolutionary classifier, to describe the expression samples as a set of rules and then infers interactions between genes that act together within rules to predict the samples class. It generates co-prediction networks, that capture biological knowledge complementary to that contained in popular similarity-based co-expression networks.
Web server that integrates protein-ligand binding and quality assessment protocols for the prediction of protein function from sequence via structure.
An R package for the functional random forest (FunFor) algorithm. The FunFor algorithm is able to predict curve responses for new observations and select important variables from a large set of scalar predictors.
A comprehensive nomenclatural repository and knowledge base for fungal taxonomy.
Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.
fungarium is an R package for enabling the use of fungaria collections data in comprehensive trait analyses.
A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.
A Comprehensive Platform For Exploring Fungal Gene Expression and Alternative Splicing Based On 35,821 RNA-Seq Experiments From 220 Fungi.
FungiExpresZ is a browser based user interface (developed in R-shiny) to analyse and visualize gene expression data.
Assign functional annotations to fungal genes or proteins. Based on different classification methods like FunCat (Functional Catalogue), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes), it categorizes genes and proteins for fungal species on different levels and conducts an enrichment analysis.
Database for the molecular weight and isoelectric points of the fungal proteomes.
FunHoP (Functional Homologous Proteins) is a Python method which improves pathway analysis done on KEGG networks in Cytoscape. It is a tool for enhanced visualization and analysis of functionally homologous proteins in Complex Metabolic Networks.
Funm6AViewer is a web server and R package for functional analysis of context-specific m6A RNA methylation.
The Funmap package is developed to identify quantitative trait loci (QTL) for a longitudinal, or vectorized, phenotypic trait as based on the Funmap model
Pipeline with built-in Fungal Taxonomic and Functional Databases for Human Mycobiome Profiling.
A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution.
FunPart is a computational tool that partitions heterogeneous cell populations into functionally distinct subpopulations and simultaneously identifies modules of functionally relevant set of genes for each of them.
R package designed to provide: a useful tool to analyze time series genomic data; a computational pipeline which integrates gene selection, clustering and functional annotations into a single framework to identify the main temporal patterns associated to functional groups of differentially expressed genes; an easy way to exploit different types of annotations from currently available databases; a user-friendly organization and visualization of the outcome.
Resolving tissue-specific functional cell states based on a cell–cell communication network model
Stand-alone software tool used mainly for functional enrichment and interaction network analysis of genes and proteins.
FunShift is a database that stores Pfam subfamily classification for protein domain families and analyses them for functional changes using evolutionary substitution rates and conservation shifts.
Functional similarity database and web service for ranking genes/proteins by function. It provides different semantic similarity measures for Gene Ontology terms and offers functional similarity values for proteins contained in UniProtKB and for protein families/domains in Pfam and SMART. Users can perform semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. It also supports prioritizing disease gene candidates.
A modular and extensible classifier for the prediction of functional sites in DNA.
Software that can be used to analyse differential expression data from RNAseq and can integrate these analyses with data from proteomic studies.
Web server attempts to automatically infer which functional specificities and commonalities exist among different taxa.
Department of Molecular Medicine, University of Padua
A simple and light solution to investigate protein functions in all living organisms.
The R package which provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.
Provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH.
identifying protein positions for variation driven functional tuning. Evaluating the impact of non-synonymous genetic variants is essential for uncovering disease associations and mechanisms of evolution. An in-depth understanding of sequence changes is also fundamental for synthetic protein design and stability assessments. However, the variant effect predictor performance gain observed in recent years has not kept up with the increased complexity of new methods. One likely reason for this might be that most approaches use similar sets of gene and protein features for modeling variant effects, often emphasizing sequence conservation. While high levels of conservation highlight residues essential for protein activity, much of the variation observable in vivo is arguably weaker in its impact, thus requiring evaluation at a higher level of resolution
FUpred is a contact map-based domain prediction method which utilizes a recursion strategy to detect domain boundary based on predicted contact-map and secondary structure information.
FuSe is a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts.
Markov network formulation that infers networks from a collection of nonidentically distributed datasets.
Web application for the integrative analysis of omics data providing a collection of new and established tools and visualization methods to support researchers in exploring multi-level omics data. The software focuses on data-rich high-throughout experiments from transcriptomics, proteomics and/or metabolomics, and offers convenient functionality for a) omics data manipulation, b) data analysis, c) cluster analysis, d) data visualization.
Fusion of MRI and CT images using guided image filter and image statistics
Fragment-free probabilistic graphical model for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise.
FusionAI, a deep learning pipeline predicting human fusion gene breakpoints from DNA sequence.
Graphical, event-driven tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data. Requires short, paired-end sequences.
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples).
An open-source software tool that identifies gene fusions in RNA-Seq data.
A multi-stage multi-modal learning algorithm for multi-label skin lesion classification.
Detects fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution.
Resource of fusion gene-specific neoantigens.
Identifies fusion transcripts from paired end RNA-Seq data.
FusOn-pLM is a protein language model fine-tuned on fusion oncoprotein sequences to improve representations for therapeutic design. The model is publicly available on Hugging Face and the methodology is described in a preprint.
A data fusion method for multi source (VCF4.0+) structural variation analysis.
FUSTA is a FUSE-based virtual filesystem mirroring a (multi)FASTA file as a hierarchy of individual virtual files, simplifying efficient data extraction and bulk/automated processing of FASTA files.
Based on the situation around April 28, we simulated the future spread of COVID-19 infection in New York City and Tokyo using MATLAB.
Future Trends in COVID-19 Infections in NY City and Tokyo
The FuzDB database assembles experimentally observed fuzzy protein complexes involved in a variety of cellular processes and biomolecular condensates
A tool to visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins.
Web server for the sequence-based prediction of the context-dependent binding modes of proteins.
Search for patterns in nucleotide sequences.
Search for patterns in protein sequences.
Search for patterns in protein sequences (translated).
A simple shiny app for fuzzy c-means clustering to multi-variate data. The parameters of the algorithm are calculated automatically or can be chosen from validation indices.
Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ) is an R package for fuzzy clustering of species in an ecological community as common or rare based on their abundance and occupancy. It also includes functions to compute confidence intervals of classification metrics and plot results.
FVE-novel is a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. FVE-novel deploys FastViromeExplorer to efficiently map metagenomic reads to viral reference genomes or contigs, performs de novo assembly of the mapped reads to generate scaffolds, and extends the scaffolds via iterative assembly to produce final viral scaffolds.
FVTLDA is a novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs.
FWAVina is a optimization algorithm for protein-ligand docking based on the fireworks algorithm. FWAVina is a kind of molecular docking tool, which was developed based on the framework of AutoDock Vina.
Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions.
Graph-based feature alignment method for untargeted LC-MS-based metabolomics.
GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
A Divide and Conquer Application for Grid Protein Classification.
Reads/Interprets simple G-Code commands, creates a tool path.
A web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data.
Set of Perl libraries for genome sequence analysis.
Compendium of more than 100 programs that focus on bacterial genome analysis. Included are programs for identification of binding sites, analysis of codons and prediction of expression levels, analysis of nucleotide composition bias and visualization of genomic information.
Great variety of useful genome analysis tools.
G-language Genome Analysis Environment WS
A gateway server for querying and retrieving gene annotation data
G-POT is a primer set selection tool that minimizes the number of primers needed to amplify a set of loci while ensuring that each locus is amplified by a pair of primers located within L basepairs of each other, where L is an input parameter.
Global Root Traits (GRooT) Database. Ready-to-use data by combining the expertise of root ecologist with data mobilization and curation. Global Root Trait (GRooT) Database. Our principal objective with GRooT is to contribute towards the inclusion of root traits in large-scale comparative studies and global models by offering standardized and curated data of key root traits.
G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.
Huffman coding-based sequencing-reads specific representation scheme that compresses data without altering the relative order. It allows selective access without scanning and decoding form start
Generating three-way synthetic datasets with triclustering solutions. Three-dimensional dataset generator with triclustering solutions. Runnable JAR to run the G-Tric's GUI version.
g-TRIS is an algorithm for comprehensive identification of vector genomic insertion sites.
Scans a human genomic region for genes related to an inherited disease. The server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.
G2G is a tool to predict genetic interactions that is based on mapping genes to Gene Ontology (GO) terms and using this mapping for genotype to phenotype predictions.
G2P provides an integrative environment for multi-model genomic selection analysis to improve genotype-to-phenotype prediction.
G2PSR is a Bayesian Genome-to-Phenome Sparse Regression method that utilizes sparse SNP-gene constraints and a Bayesian neural network to analyze genomics and phenomics data. It aims to improve scalability and interpretability in joint analysis of genomic and phenotypic information.
G2S is a deep learning tool for predicting stool microbiome structure from oral microbiome data.
G3Mclass is a software for Gaussian Mixture Model for Marker Classification. It has a complete set of help files that can be viewed after installation.
G4-FUNNIES is a webserver that predicts RNA-binding proteins involved in G-quadruplex interaction using a computational approach. It classifies proteins based on their ability to bind to G4 and is described in a recent publication.
A comprehensive transcriptome-wide G-quadruplex database.
A machine learning-based tool for quadruplex identification and stability prediction.
g4dbr is a package to access g4DB, a database of validated DNA G-quadruplexes structures in native mass spectrometry conditions.
G4detector is a multi-kernel convolutional neural networks aimed at claasifiyng DNA sequences for having the potential to form G-quadroplex (G4).
G4Killer is a web application to design G-quadruplex mutations. G4Killer is based on the G4Hunter algorithm. This tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps.
A database for discovering and studying G-quadruplex and i-Motif ligands.
Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks | Gene filtering, analysis, and conversion
An equivariant graph neural network for the scoring of protein-protein docking models.
The GA4GH Toolkit outlines a suite of secure standards and frameworks that will enable more meaningful research and patient data harmonization and sharing. This suite addresses a variety of challenges across the data sharing life cycle and is applicable across the world’s accessible medical and patient-centered systems, knowledgebases, and raw data sources.
A global search engine for genetic mutations.
It provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.
It provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.
A comprehensive resource and Genome Atlas for Breast Cancer. The Genomic Atlas of Breast Cancer — the non-coding theme.
Sequence-indexed collections of T-DNA insertion lines of Arabidopsis thaliana.
GABOLA is an integrated solution of Genome de novo Assembly aimed at Precision Medicine and Genome Breeding. The core concept is to fill in both intra and inter-scaffold gaps mainly based on 10x Genomics linked reads. GABOLA is a highly-flexible tool, it can also be used with TGS Sequencing long reads and other Gap-Filling techniques.
Gene Associations with Clinical. One-stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types.
Conjecture-Based Verification. GACAL verifies C programs by searching over the space of possible invariants, using traces of the input program to identify potential invariants. GACAL uses the ACL2s theorem prover to verify these potential invariants, using an interface provided by ACL2s for connecting with external tools. GACAL iteratively searches for and proves invariants of increasing complexity until the program is verified
A computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier.
A decentralized FAIR platform to facilitate data sharing in the life sciences.
Unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.
The program is designed to calculate pairwise distances between objects that can be represented as an "object-feature" matrix. The program accepts a dense matrix in CSV (Comma Separated Value) format or a sparse matrix in MEX (Market EXchange) format as input and calculates a distance matrix for one of the metrics selected by the user. The result of the program is a matrix of pairwise distances that can be used for practical tasks of bioinformatics data analysis at the level of individual cells. The program supports the use of graphic processors with CUDA architecture to accelerate calculations over large matrices.
Software for Genetic Analyses of quantitative traits Distributed with Spike on the base of large pedigrees without loops.
A graph auto-encoder model for miRNA-disease associations prediction.
GAEMR (Genome Assembly Evaluation Metrics and Reportin) is a complete genome analysis package that helps you evaluate and report on a genome assembly’s completeness, correctness, and contiguity.
Comprehensive genome assembly evaluating pipeline.
Gene Annotation Easy Viewer. It integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server and generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to.
GAFS-8 Scoring Tool: Eight-item General Alexithymia Factor Score [GAFS-8] Calculator (Based on TAS-20)
Generates an NCBI .tbl file of annotations on a genome.
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. A database for curated glycosaminoglycan. GAG BUILDER : A user friendly tool to build 3D structures of GlycosAminoGlycans.
Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).
Published method for gene set (enrichment or GSEA) or pathway analysis. It is generally applicable independent of microarray or RNA-Seq data attributes and consistently achieves superior performance over other frequently used methods. We provide functions for basic analysis, result processing and presentation. We have also built pipeline routines for of multiple analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies.
This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser.
This package allows to assess the statistical significance of chromosomal aberrations.
An integrated metagenomics suite. Metagenomics data analysis software. Metagenomics analysis tool: simplest, fastest and accurate solution for metagenomics data. The easiest, most accurate and reliable cloud software for Metagenomics Analysis. Gaia 2.0 uses the best, most up to date and reliable scientific methods and algorithms, and you don’t even need any bioinformatics knowledge to run it!. GAIA has a reliable upload system with integrated recovery and resume functions to allow you to quickly and securely upload your data. You can also upload it directly from your Google Drive. Use the Validate button to check the integrity of your Seq data.
GAIA (G-quAdruplexes In Alive creature) is a user-friendly database with a web interface that can be used to query a data set containing pG4s in diverse species from all three living kingdoms.
Pipeline incorporating several de novo RNA discovery tools for finding, filtering and scoring ncRNA in operon and genome wide prokaryotes.
Gene expression Analysis for Interval Time.
Galaxy tools for modeling metabolite changes as a function of gene expression. Modeling Metabolites as a function of gene expression. A python package gait-gm based on this project is avialable from PyPI.
GaitForeMer (Gait Forecasting and impairment estimation transforMer) predicts MDS-UPDRS gait impairment severity scores using learned motion features from the pre-training task of human motion forecasting.
gaitmap is an open-source Python package ecosystem for analyzing human gait using inertial measurement units (IMUs). It provides state-of-the-art algorithms, datasets, and benchmark challenges to facilitate gait analysis research and clinical applications.
gap-free chromosome-scale assembly with long reads. Abstract High-quality genome assembly has wide applications in genetics and medical studies. However, it is still very challenging to achieve gap-free chromosome-scale assemblies using current workflows for long-read platforms.
Software tool for protein function prediction. Extracts information from both protein sequences and structures, facilitating unified learning of protein structural representations. GALA incorporates domain discriminator conditioned on both representations and predicted probabilities, which undergoes adversarial training to ensure representation invariance across diverse environments.
Using the power of Galactic AI™, the Galactic Web App is Biorelate’s window to all the auto-curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore the results through different views that best suit your research needs.
Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.
It is a a joint ISA-CNR/UniSA project: a database in which information are collected and freely available about structural features of the enzymes involved in the galactose metabolism, i.e. galactose-1-phosphate uridylyltransferase (GALT, E.C. 2.7.7.12), galactokinase (GALK, E.C. 2.7.1.6), UDP-galactose-4'-epimerase (GALE, E.C. 5.1.3.2) and galactose mutarotase (GALM, E.C. 5.1.3.3).
galamm is an R package for estimating generalized additive latent and mixed models, providing a common ground between structural equation modeling and mixed effect models. It supports various model features and computational efficiency through sparse matrix methods and automatic differentiation.
Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Tool recommender system in Galaxy using deep learning (Gated recurrent units neural network).
Accessible, Reproducible, and Scalable Machine Learning for Biomedicine. Galaxy-ML is a web machine learning end-to-end pipeline building framework, with special support to biomedical data.
The Galaxy-SynBioCAD portal is a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations.
The Galaxy7TM server improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods.
Galaxy Australia is a hosted instance of the Galaxy web-based platform for data intensive biological research, for all Australian researchers. In addition to being accessible through a web interface, Galaxy Australia can also be accessed programmatically, through shell scripts and other programs via an API
Galaxy Ecology is mainly developed by the French Data Terra research infrastructure Biodiversity data hub (PNDB). Its dedication is to provide tools for biodiversity data management and analysis for the Galaxy platform. Tools are useable through dedicated Galaxy instances hosted by Galaxy Europe (ecology.usegalaxy.eu) and Galaxy France (ecology.usegalaxy.fr).
Galaxy is an open-source platform for FAIR data analysis that enables users to: i) use tools from various domains (that can be plugged into workflows) through its graphical web interface, ii) run code in interactive environments (RStudio, Jupyter, ...) along with other tools or workflows, iii) manage data by sharing and publishing results, workflows, and visualizations, iv) ensure reproducibility by capturing the necessary information to repeat and understand data analyses. UseGalaxy.fr is the national Galaxy instance for ELIXIR-FR.
Galaxy Helm is a Kubernetes chart for deploying production-grade Galaxy servers. It simplifies Galaxy installation and maintenance, providing a rapid and reproducible deployment method.
Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.
An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease.
Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis
Protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing.
An Ab Initio Domain-domain Docking Web Server for Multi-domain Protein Structure Prediction.
GalaxyGPCRloop models the second extracellular loop (ECL2) of G-protein-coupled receptor (GPCR) based on both template-based and ab initio approaches.
GalaxyHeteromer is a web server for protein structure prediction, refinement, and related methods.
Protein oligomer structure prediction from a monomer sequence or structure. It carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates.
GalaxyRefine is a web server for protein structure prediction, refinement, and related methods. The refinement method has been tested in CASP10 and first rebuilds side chains and performs side chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.
Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds. A web server for protein structure prediction, refinement, and related methods.
GalaxySite is a web server for ligand-binding site prediction by using molecular docking.
A distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians.
Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network.
GalaxyWater-wKGB is a webserver for prediction of water positions on protein structure using wKGB statistical potential.
GalaxyWeb is a webserver for predicting protein structure from sequence by template based modeling. It refines loop or terminus regions by ab initio modeling
GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.
A bi-objective evolutionary meta-heuristic identifies robust transcriptomic classifiers associated with patient outcome across multiple cancer types. Galgo: An evolutionary machine learning algorithm for the identification and study of prognostic gene expression signatures in cancer.
Identifies polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome
An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci. GALLO: Genomic Annotation in Livestock for positional candidate LOci
Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru.
MorphoGAM is a tool that identifies spatially variable genes by projecting spatial transcriptomics data onto morphologically relevant curves, enabling improved analysis and identification of biological insights.
GAM-NGS is able to merge two or more assemblies and it rteturns an improved assembly (more contiguous and more correct). GAM-NGS shows its full potential with multi-library Illumina-based projects.
GamaComet is a web-based buccal mucosa comet assay detection and classification tool, which purpose is to measure the amount of damage contained within the DNA.
A cross-platform GUI for sequence visualization and analysis.
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens. It uses an efficient genomic distance metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI RefSeq) to identify genome assemblies from across the Bacterial kingdom in seconds.
GPU-Accelerated Mixture Elucidator. GPU acceleration is useful in solving complex chemical information problems. Identifying unknown structures from the mass spectra of natural product mixtures has been a desirable yet unresolved issue in metabolomics.
The GameRank package is an R package that implements functions for variable and feature selection to create predictive models.
User-friendly software package and algorithm which generates complex biallelic single nucleotide polymorphism (SNP) disease models for simulation studies.
Whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.
GAMMA (Gene Allele Mutation Microbial Assessment) is a command line tool that finds gene matches in microbial genomic data using protein coding (rather than nucleotide) identity, and then translates and annotates the match by providing the type (i.e., mutant, truncation, etc.) and a translated description.
The GammaPred server predicts the gamma turn residues in the given protein sequence.
Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.
Conduct “global analysis” of DNA methylation data, particularly from the Illumina 450k Infinium platform. Instead of examining the effect of individual CpGs, the idea is to compare the overall profile or distribution of CpG measurements across individuals.
Platform for addressing high throughput analysis and management of variant data produced by Next Generation Sequencing techniques.
From Image-to-Image Translation to Disease Detection and Localization. This repository provides the official PyTorch implementation of Fixed-Point GAN. Fixed-Point GAN introduces fixed-point translation which dramatically reduces artifacts in image-to-image translation and introduces a novel method for disease detection and localization using image-level annotation only. StarGAN - Official PyTorch Implementation.
Generative Adversarial Network augmented the gut microbiome-based health index by profoundly improved discrimination power.
A software to cluster expression data by Gibbs sampling procedure.
Whole-genome based Average Nucleotide Identity (gANI) is an effort to delineate species-level diversity among prokaryotic organisms in the genomic era. Microorganisms are evolving continuously and the signature of evolution is observed across its entire genome. As such, a single gene or a select group of marker genes should not be used to infer new species as it may not be a correct representation in the evolutionary landscape. Especially with the wealth of genomic information currently available, one needs to graduate from the gene-centric 16S based classification to a holistic, genome-based method.
Precise metagenomics classification against large and up-to-date sets of reference sequences. benchmarking pipeline used to evaluate ganon as presented in https://www.biorxiv.org/content/10.1101/406017v3.
Training deep learning models to work on multiple devices by cross domain learning with no additional annotations.
Distinguish between amyloid fibril-forming and amorphous ß-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.
Gap-App is a web application that predicts pancreatic cancer survival based on RNA-Seq gene expression data and patient sex. It aims to facilitate personalized cancer care by providing predictions based on individual genomic profiles.
A reliable gap filling pipeline for SSPACE-LongRead scaffolder output | A reliable gap filling pipeline for draft genomes | .
GapFiller is an automated strategy, called to reliably close gaps within scaffolds using paired reads.
Genome Association and Prediction Integrated Tool.
A Proteogenomic tool for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.
Predicts gestational age using Illumina HumanMethylation450 CpG data.
Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks. gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. Based on genomic information and databases for pathways and reactions, gapseq can be used for:.
Method that leverages GWAS findings with regulatory or functional annotations to find features relevant to a phenotype. It performs greedy pruning of GWAS SNPs and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for MAF, distance to nearest transcription start site and number of LD proxies.
GARLI (Genetic Algorithm for Rapid Likelihood Inference) is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms.
A free molecular visualization program for protein structure, DNA structure, PDB, molecular rendering and biological macromolecule in unix, linux system.
Genomic Autozygosity Regions Likelihood-based Inference and Classification is a program for calling runs of homozygosity in genotype data.
GARM (Genome Assembler, Reconcilation and Merging) is a new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. It relies on the observation that a combination of sequencing methods will work better together to reconstruct a genome in its totality, overcoming the limitations of each technology and assembly method if they were used in isolation. The pipeline is based on perl scripts and third-party open source software like the AMOS package.
Coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.
Predict protein secondary structure using GOR method.
Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. It is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism.
The gasanalyzer R package streamlines photosynthesis data workflows by importing, preprocessing, and analyzing data from portable gas analyzers, facilitating reproducible research and sensitivity analyses.
GASIDN is a computational model for identifying sub-Golgi proteins using multi-scale feature fusion, combining protein sequence and contact map information derived from AlphaFold2. It achieves high accuracy and has been applied to other organelle protein identification.
Multiple local alignments of PPI (protein-protein interaction) networks. It is based on the homonymous greedy and stochastic algorithm. It starts with the identification of sets of similar nodes, called seeds of the alignment and then alignments are then extended in a greedy manner and finally refined.
Detecting germline and somatic structural variants from long-reads data.
Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System. Human protein phosphorylation sites prediction by GA-aided ant colony system.
This tool searches for given active site 3D templates in unknown proteins.
Identifying metal-binding sites on protein structures using genetic algorithms.
Web version of GASS (Genetic Active Site Search). Method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures.
Global Alignment Short Sequence Search Tool.
The GAST algorithm assigns taxonomy to SSU sequences by comparing them to a set of reference sequences with known taxonomy. In the simplest terms, taxonomy is assigned to each query sequence based on the consensus of the nearest references sequences. The alignment distance between the query and references is also reported as a measure of how similar the query and reference sequences really are.
Software for classification and comparison of structural variants measured via paired-end sequencing and/or array-CGH.
This tool tests for association between intervals in a genome analysis context.
An Integrated MATLAB Toolbox for Graph Theoretical Analysis of Task-Related Functional Dynamics. Graph Theoretical Analysis of Task-based Functional Dynamics Toolbox. Graph theoretical analysis of task-related functional dynamics (GAT-FD) is a systematically integrated user-friendly toolkit to characterize the functional dynamics for task-related fMRI data based on graph theoretical techniques. Researchers can use this toolkit to 1) implement slide-window approach for analyzing functional connectivity dynamics; 2) generate task condition files based on the experimental task, 3) calculate functional network topological measures and examine their dynamics, and 4) visually validate the results.
A graph attention network based learning and interpreting method for functional brain network classification.
C++ library of high level functions designed to benefit from recent advances in NGS data structures for handling huge datasets of sequencing data.
Probabilistic model to annotate the genome. This model detects similar but not necessarily synchronous epigenomic changes in different genomic segments.
A computational framework (GATECDA) based on graph attention auto-encoder to predict circRNA-drug sensitivity associations.
Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.
Fast Alignment Filter for DNA Short Read Mapping.
GateMeClass is an R tool designed for cytometry data mining and classification, offering both semi-supervised and supervised annotation based on a marker table. It overcomes limitations in current classification methods by combining flexibility and rapid execution times.
Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex.
Graph convolutional neural networks with global attention for improved materials property prediction. GATGNN: Global Attention Graph Neural Network. This software package implements our developed model GATGNN for improved inorganic materials' property prediction. This is the official Pytorch repository.
The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. Version 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk.
This method increases specificity and sensitivity of GATK results for mutation detection.
This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, reported quality score, cycle, and dinucleotide).
Processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.
Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.
This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads.
Realigner Target Creator for use in local realignment.
Reduce the BAM file using read based compression that keeps only essential information for variant calling.
Annotate variant calls with context information. Users can specify which of the available annotations to use.
Apply cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration.
Combine VCF records from different sources. The tool supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods.
General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more).
Filter variant calls using a number of user-selectable, parameterizable criteria.
Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score.
Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion.
Omics-based identification of regulated metabolic modules in atom transition networks.
gatoRs is an R package that streamlines downloading and cleaning biodiversity data from GBIF and iDigBio. It provides functions for downloading records, cleaning specimen records, and accounts for differences in download structure between GBIF and iDigBio.
Use genetic algorithms to determine the relationship between clones in heterogenous populations such as cancer sequencing samples.
Simple methods for fitting Lotka-Volterra models describing Gause’s “Struggle for Existence”. Package repository for the gauseR package.
GAUSS is an R package for analyzing summary statistics from large-scale genome-wide association studies, utilizing a multi-ethnic reference panel for ancestry-informed imputation and linkage disequilibrium calculation.
Fast 2-dimensional Gaussian kernel generator
Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
Tool for the integration of gene prediction signal and content sensor information into complete gene structures.
Eye-tracking data must be transformed into fixations and saccades before it can be analyzed. This package provides a non-parametric speed-based approach to do this on a trial basis. The method is especially useful when there are large differences in data quality, as the thresholds are adjusted accordingly.
A Package for Processing Gaze Position and Pupil Size Data. gazeR:A package to analyze gaze position and pupil size data.
Bioinformatics pipeline to process genotyping-by-sequencing (GBS) data.
A scoring function based on Gradient Boosting Trees algorithm for predicting ligand-protein binding affinity. PDBbind 2019v collection of the general and refined sets minus core set is used for training GB-Score and core set is used as an independent test set.
Classification of GBA1 variants in Parkinson’s disease; the GBA1 PD browser.
A gene-based association test for robust detection of trans-gene regulation. The observation that disease-associated genetic variants typically reside outside of exons has inspired widespread investigation into the genetic basis of transcriptional regulation.
Parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species.
RNA expression landscapes and ncRNA-mRNA interactions in gallbladder carcinoma.
Identifying differentially methylated CpG regions in the human genome via generalized beta regressions.
Predicting potential miRNA-disease associations by combining gradient boosting decision tree with logistic regression.
Web service for occurrence data (specimens, observations) from the global GBIF data portal.
Global Biodiversity Information Facility taxonomic web service from the centralised GBIF data portal.
Program to compare the genotypes of many pairs of people, and identify pairs of people who may be related to each other.
The information system of the German Genebank is a safeguard of plant biodiversity and is an important source of information for plant researchers as well as crop breeders, e.g. for identifying appropriate germplasm for breeding purposes. In addition, the access to genebank material as a sovereign task is also of high interest to the general public.
GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data.
GBMPredictor is part of the GBMatch project and can predict risk scores and transcriptional subtypes from whole slide images of glioblastoma.
R package for conducting GWAS with survival outcomes using Boosting and FDR control methods.
Combination of database and interactive web pages for manipulating and displaying annotations on genomes.
A genome browser instance dedicated to giant viruses discovered by the IGS Laboratory
Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data. GBRS is a suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and quantifying allele specific expression.
Group B Streptococcus Serotyping by Genome Sequencing.
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms.
An integrated tool for genome widely association study and genome selection based on genetic by environmental interaction.
This package performs in-silico MeOX + TMS derivatization (as described e.g. in https://doi.org/10.1021/acs.analchem.7b01010): Methoximation: ketone R(C=O)R' and aldehyde (-HC=O) carbonyl groups are substituted with -C=NOCH3 Trimethylsilylation: the acidic hydrogen in -OH, -SH, -COOH, -NH2, -NHR, =NH, the hydrogen is substituted with -Si(CH3)3 The substitution doesn't always have to happen; its probability is currently hardcoded in the package. Typically, multiple substitution attempts are run on each input molecule, and all distinct results are gathered. Known limitation is methoximation on cycles which should be broken. This is not implemented yet.
GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.
A transcriptomic study for identifying cardia- and non-cardia-specific gastric cancer prognostic factors using genetic algorithm-based methods. Gastric cancer (GC) is a heterogeneous tumour with numerous differences of epidemiologic and clinicopathologic features between cardia cancer and non-cardia cancer.
An R package for genetic connectedness analysis using pedigree and genomic data. Genetic connectedness quantifies the extent of linkage between individuals across management units. The concept of genetic connectedness can be extended to measure the connectedness level between training and testing sets in whole-genome prediction. We developed the genetic connectedness analysis R package, GCA, which utilizes pedigree or genomic data to measure the connectedness between individuals across units.
Simple peak alignment for gas-chromatography data in R.
a graph-based single cell type annotation method. gCAnno-A tool for cell type annotation of single-cell transcriptome sequencing.
Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.
Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing.
Association test for genome wide association studies that controls for population structure under a general class of trait. models.
Graph contextualized attention network for predicting synthetic lethality in human cancers. Our Software and test data have been archived at the dedicated repository of Zenodo. The archived Software version is available here. GCATSL is a deep learning model that can be used for SL prediction. As shown in the following flowchart (a), GCATSL first learns representations for nodes based on different feature graphs together with a known SL interaction graph, and then uses the learned node representations to reconstruct SL interaction matrix for SL prediction.
Identification of gastric cancer based on a milliliter of blood. Gastric cancer (GC) continues to be one of the major causes of cancer deaths worldwide. Meanwhile, liquid biopsies have received extensive attention in the screening and detection of cancer along with better understanding and clinical practice of biomarkers.
An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation.
A tool for determining a Pareto front of growth-coupled cell factory designs.
An informational platform for genome biology of grass carp. Grass carp (Ctenopharyngodon idellus) is a herbivorous, freshwater fish species of the family Cyprinidae, and the only species of the genus Ctenopharyngodon.
GCgx is a scientific web application that allows scientists to study the response of different cell types to glucocorticoids.
Genome Continuity Inspector (GCI) is a tool designed to assess genome assembly continuity at single-base resolution, providing a standard for evaluating T2T genome assemblies. It utilizes long-read mapping and curated coverage to identify and quantify assembly issues.
Gclust software was developed to make clusters of protein sequences from all predicted protein sequences in a selected set of genomes.
a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes. Gcluster is a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes.
Toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values the package performs differential expression analysis. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression.
This R package provides a graphical user interface for the gCMAP package. It uses the Rook package and can be used either on a local machine, leveraging R's internal web server, or run on a dedicated rApache web server installation. It allows users to search their own data sources and instructions to generate reference datasets from public repositories are included with the package.
The package constructs the mutually exclusively mutated gene networks from mutation associations and gene interactions with the graph clustering technique and identifies sub-networks with distinct biological functions with the canonical pathways.
GCModeller: genomics CAD(Computer Assistant Design) Modeller System
Deep graph representations embed network information for robust disease marker identification.
A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm. ||| HOMEPAGE BROKEN!
CircRNA-miRNA interaction Prediction Based on Graph Neural Network
Global Context Networks. GCNet is initially described in arxiv. Via absorbing advantages of Non-Local Networks (NLNet) and Squeeze-Excitation Networks (SENet), GCNet provides a simple, fast and effective approach for global context modeling, which generally outperforms both NLNet and SENet on major benchmarks for various recognition tasks.
A novel lightweight model with valid extractors for RNA secondary structure prediction.
Predicting human microbe-drug associations via graph convolutional network with conditional random field. GCNMDA: A novel Graph Convolution Network based framework for predicting Microbe-Drug Associations.
A tool of the g:Profiler web server. It enables to do functional annotation for several gene lists at the same time and compare their results.
Computer program for Bayesian analysis of case-control data that controls for population stratification and cryptic relatedness. The program performs these analyses using Markov chain Monte Carlo algorithms.
A tool of the g:Profiler web server. It converts mix of different types of gene, protein, microarray probe, standard name and other database IDs to a target database ID.
Efficient family-based gene-gene interaction test for trios.
Genomic resource of human pathogens for public health.
Tool for exploring pleiotropy at the gene level. NOTE: All SNPs and genes positions in the GWAS and annotation data used in the examples are based on GRCh37 (hg19) Human Genome Assembly.
gcProfileMakeR is an R package for automatic classification of constitutive and non-constitutive metabolites.
Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting.
Background adjustment using sequence information.
Haplotype-aware graph indexes | This is a reimplementation of the Generalized Compressed Suffix Array (GCSA), a BWT-based index for directed graphs | The old implementation indexed all paths in a directed acyclic graph, which had to be determinized before index construction. GCSA2 approximates the graph with a de Bruijn graph (with k = 256 or less), allowing it to index more complex graphs as well as graphs containing cycles. The order of the de Bruijn graph limits the length of the queries the index is able to answer correctly. Longer queries may result in false positives (but no false negatives)
GCSENet is a novel learning-based framework for miRNA-disease association identification via graph convolutional neural networks, convolutional neural networks, Squeeze-and-Excitation Networks(SENet).
GCsnap is a flexible Python-based tool that allows for the interactive comparison of the genomic contexts of protein-coding genes from any genome at any taxonomic level, integrating them with functional and structural information for any of the genes shown.
an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays. GCSscore is an R package that is available on GitHub that is also available in the BioConductor repository (release 3.10 and higher). GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays. For differential expression analysis of 3'IVT and WT-style microarrays from Affymetrix Thermo-Fisher.
Genome-wide Complex Trait Analysis. Estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
A high-quality type strain genome database for microbial phylogenetic and functional research. GCM Type Strain Sequencing project.
Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values.
Rapid GPU-based HIV-1 coreceptor usage prediction for next-generation sequencing.
GCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. k.
The Genomics and Drugs integrated Analysis portal (GDA) combines NCI60 uniquely large number of drug sensitivity data with CCLE and NCI60 gene mutation and expression profiles.
GDA (Genome Decomposition Analysis) is a bioinformatic pipeline to analyse genome architecture.
Predicts disulfide bonds for a user-supplied protein sequence. It also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.
R pipeline to identify the most important qualitative and quantitative predictor variables from phenotypic data.
A GPU parallel-based web server for detecting hidden batch factors. It provides a user-friendly web interface for detecting batch factors. Based on the good performance of DASC algorithm, it is able to give the most accurate results. For two steps of DASC, data-adaptive shrinkage and semi-non-negative matrix factorization, we designed parallelization strategies facing convex clustering solution and decomposition process. It runs more than 50 times faster than the original version on the representative RNA sequencing quality control dataset. With its accuracy and high speed, this server will be a useful tool for batch effects analysis.
ChEMBL-Likeness Score and Database GDBChEMBL. GDBChEMBL is a library of 10 million chemical structures that was extracted from the exhaustively generated database GDB17. It was generated by scoring input SMILES structures by circular substructures shared with the reference database of known chemical compounds, ChEMBL v.24.
Utility designed for compression of genome collections from the same species.
The GDC API drives the GDC Data and Submission Portals and provides programmatic access to GDC functionality. This includes searching for, downloading, and submitting data and metadata. The GDC API uses JSON as its communication format, and standard HTTP methods like GET, PUT, POST and DELETE.
The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.
Removal of Gadolinium contamination in mass cytometry data.
Easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer.
The GDD, a GPCR Decoy Database, with its accompanying GPCR Ligand Library (GLL) have been compiled to help in GPCR docking. The main characteristics of GLL and GDD are: Sets of ligands and decoys for 147 GPCR targets. For each ligand, 39 decoys were drawn from ZINC ensuring physical similarity of six properties (molecular weight, formal charge, hydrogen bond donors and acceptors, rotatable bonds and logP), but structural dissimilarity.
GDDfold is a tool for distance-guided protein folding based on generalized descent direction.
Computational genetic disease diagnosis based on phenotypes.
gDesigner is a Python pipeline for designing synthetic gRNAs for CRISPRi applications. The pipeline takes an input list of DNA sequences in FASTA format, and after various screening steps, returns a list of orthogonal gRNAs.
Method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
Method of hierarchical clustering for high throughput data. Nonlinear relations exist between features of high-throughput data. They reflect critical regulation patterns in the biological system. Clustering based on both linear and nonlinear relations in high throughput data is hampered by the high dimensionality and high noise level in the data.
Machine learning risk score for prediction of gestational diabetes in early pregnancy in Tianjin, China.
A open source Webserver for prediction of Mycobacterium Tuberculosis (M.Tb) inhibitors using QSAR and Docking strategies. GDoQ web server has been developed to serve scientific community working in the field of Drug Designing for designing inhibitors against N-acetylglucosamine-1-phosphate uridyltransferase (GLMU) protein, a potential drug target involved in bacterial cell wall synthesis.
GDPbio is the project focused upon providing various resources related to genome analysis particularly for the prediction of disease susceptibility of a particular individual and personalized medicines development, aiming public health improvement.
Uniform Genomic Data Analysis in the NCI Genomic Data Commons. The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. The Next Generation Cancer Knowledge Network.
Contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.
GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.
Mining pharmacogenomic interactions in cancer.
This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. It offers efficient operations designed for integers of less than 8 bits (single genetic/genomic variant fewer bits than a byte).
Software package for genome-wide association analysis.
Performs various functions on GenomeDiff formatted files.
Input a single Genome Diff, and as many reference files as you like. Using the Genome Diff, this will apply all the mutations to the reference sequences, output is to a single file that includes all the references in the requested format.
Compare control versus test mutations Input a single Genome Diff, and as many reference files as you like. Using the Genome Diff, this will apply all the mutations to the reference sequences, output is to a single file that includes all the references in the requested format.
Creates a Genome Variation Format (GVF) file of mutations present in an input Genome Diff file.
Creates a Variant Call Format (VCF) file of mutations present in an input Genome Diff file.
Creates a new Genome Diff file with mutations that are present in ALL input Genome Diff files.
Remove mutation predictions in masked regions Creates a GD file where mutations in the input GD that are located within certain regions of the reference genome are removed. These regions are defined as MASK entries in the mask GD file. Mutations that overlap only masked reference bases (and therefore do not overlap any unmasked bases) are removed.
Predicts mutations from the evidence entries in the input GD file. Any mutation entries (three-letter code lines) already present in the input GD file will be removed.
Creates a GD file of mutations that have been normalized to the input reference files.
Takes a GenomeDiff file and removes all of the entries that are NOT used as evidence by a mutation. Outputs to a new GenomeDiff file if specified. If no output is specified, verbose will still inform what evidence isn't being used.
Create a file containing random mutations.
Creates a new Genome Diff file that contains all entries that are still present in the input file after removing mutations that are in any of the subtracted Genome Diff files. All evidence and validation entries are retained in the output file.
Creates a GD file with entries that exist in any input GD file. Duplicate entries are merged into a single entry.
Validates whether the format of the input Genome Diff files is correct.
GE-Impute is an imputation method for scRNA-seq data based on graph embeddings.
Genomic evolutionary analysis in R with geaR. The package geaR is designed to aid with evolutionary and population genetic analysis across whole genome genotype data in the GDS format.
Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses.
Ultra-fast automated docking program, designed to predict how small ligands bind to pharmacologically relevant macromolecules. The program employs a novel hybrid force field and a Monte Carlo protocol for the efficient sampling of conformational space.
Java-based application developed to address multiple-testing issue with dependent Single-nucleotide polymorphisms (SNPs). Based on this new measure, several popular multiple-testing methods including Bonferroni, Holm, Simes correction was improved to evaluate significance level of SNP p-values in genome-wide association studies.
Software aimed at pairwise sequence comparison generating high quality results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences.
Software aimed at detecting and identifying blocks of large rearrangements taking into account repeats, tandem repeats and duplications, starting with the simple collection of ungapped local alignments produced by GECKO or equivalent software.
Web-based, platform-independent tool to analyse results of pairwise and multiple sequences comparison software. The implemented tool includes the traditional capabilities of this type of software, incorporating the concept of layers from image editing software to represent different comparisons. An innovative feature is the integration of the Evolutionary Events timeline. To extend the functionality, a set of post-processing services has been included.
The software allows for the systematic detection of gene cluster conservation in a large number of genomes. The enhancement over the original Gecko tool is the use of set-distance based gene cluster models that allow for the detection of gene clusters with diverse conservation patterns including gaps and missing genes in cluster occurrences. It is also tolerant of errors in gene homology assignment.
gene expression clustering optimization app for non-linear data visualization of patterns. Welcome to GECO (Gene Expression Clustering Optimization), the straightforward, user friendly Streamlit app to visualize and investigate data patterns with non-linear reduced dimensionality plots. Although developed for bulk RNA-seq data, GECO can be used to analyze any .csv data matrix with sample names (columns) and type (rows) [type = genes, protein, any other unique ID].
GeCo3 is a DNA compressor that uses a neural network to do the mixing of experts.
The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.
Genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective.
GECS (Gene Expression to Chemical Structure) is a collection of prediction methods linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances. This N-Glycan Prediction Server is based on the repertoire of glycosyltransferases for N-glycan biosynthesis.
Efficient short read mapping to a pangenome that is represented by a graph of ED strings.
Software tool for analysis of microarray gene expression data.
Software tool for solving the network alignment problem. It utilizes the evolutionary computing strategies for solving the so-called Graph Edit Distance problem.
Extension of the idea implemented in GEDEVO to multiple input networks which aims to minimize the sum of GEDs between every pair of input networks.
Applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes. GeDi: Generalised suffix array-based Direct SNV caller. Generalised suffix array-based Direct SNV caller, or GeDi, detects somatic Single Nucleotide Variants (SNVs) within paired tumour-control NGS datasets.
An R package for integration of transcriptomic data from multiple high-throughput platforms.
A database of gene-disease pathway association, along with tools to identify i) disease-disease comorbidity, ii) pathway enrichment, iii) disease enrichment, iv) disease enrichment using GO terms, v) polypharmacological target prediction and vi) Venn of genes, pathways, domains, GO terms, and custom list
The Genome Editing automated Design platform for point mutation construction in Corynebacterium glutamicum.
Application that holds Gene Feature data. It has been designed with the needs of researchers wanting to keep, share and annotate sequence and feature data. Gee Fu is a Ruby on Rails based RESTful web-service application that stores and serves sequence assembly and genome feature data on request.
Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, etc.
Calculate fractional GC content of nucleic acid sequences.
GEEES is a computational tool for inferring cell-specific gene-enhancer interactions from multi-modal single-cell data, evaluating performance against benchmark datasets and providing enhanced cell representation learning.
Database tool for genomic assembly and feature data
Detecting Sparse Microbial Association Signals Adaptively From Longitudinal Microbiome Data Based on Generalized Estimating Equations.
GeenaR is a tool for MALDI/ToF MS spectra analysis.
Gene function finding through cross-organism ensemble learning. GeFF (Gene Function Finder) is a Web-based portal providing an intuitive interface both to compute novel predicted annotations for multiple organisms (all organisms in the Entrez Gene database) and to browse a database of:. Known annotations of the genes of all organisms in the Entrez Gene database to Gene Ontology (GO) terms describing the gene biological function features,.
Scalable and flexible gene-environment interaction analysis in millions of samples. GEM (Gene-Environment interaction analysis for Millions of samples) is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference.
R package for the comparative analysis of evolutionary radiations.
An R package for gene-environment interaction analysis incorporating prior information.
GEInter is an R package for robust gene-environment interaction analysis.
Identify integrations of DNA elements on a genome-wide scale.
A free 1D gel electrophoresis image analysis software .The process of gel image analysis is straightforward and covers all the main aspects of evaluation from automatic lane detection to precise molecular weight calculations. Many tools help you to improve the accuracy of gel evaluation. You may obtain the gel image with a common digital camera, or even with your cell phone, and use it to get the results in just a few seconds.
Database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available.
GelBox is an open-source software designed to improve rigor and reproducibility in gel and immunoblot analysis. It combines image adjustments, background correction, band-fitting, and metadata association in a single application.
General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques.
Software for the analysis of DNA fingerprints (AFLP, t-RFLP, RAPD, ERIC-PCR, RFLP-PCR). It works in a fast and efficient way with trace files (FSA files) as well as with gel image files (TIFF, JPG, BMP, etc.) and handles AFLP, t-RFLP, ERIC-PCR, RFLP-PCR or RAPD data.
Platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank's repository.
Developed at Reed College which calculates DNA fragment sizes from gel electrophoresis migration data. It runs on a Macintosh computer only. The first step in using the this program is to enter data for a known marker. Both the distances traveled and the fragment sizes are entered. Then the distances migrated by up to 19 sets of DNA fragments are entered, and the program calculates the sizes of these fragments using a cubic-spline interpolation.
Tools for analyzing EWAS, methQTL and GxE genome widely.
GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data.
High-performance mapping for aligning sequenced reads against large reference genomes (e.g. human genome). In particular, it is designed to obtain best results when mapping sequences up to 1K bases long. It indexes the reference genome using a custom FM-Index design, and performs an adaptive gapped search based on the characteristics of the input and the user settings.
Scalable and flexible gene-environment interaction analysis in millions of samples.
A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
This method introduces gene set enrichment for mathematical biology (GEMB). Typically, gene-set analyses measure the association between a disease of interest and a set of genes related to a biological pathway. These analyses often incorporate gene network properties to account for differential contributions of each gene. With GEMB, we extend this concept further, defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict the effects of genetic perturbations on a particular downstream function.
GEMDeCan (Gene Expression and Methylation based Deconvolution for Cancer) is a tool for improved tumor immune microenvironment profiling through novel gene expression and DNA methylation signatures predicts immunotherapy response.
Generate error models from real data for GemReads.
Interactive interface for transformer-based Genomic Metadata Integration.
The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.
GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.
Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.
Gemma provides data, experimental design annotations, and differential expression analysis results for thousands of microarray and RNA-seq experiments. We re-analyze raw data from public sources (primarily NCBI GEO), annotate experimental conditions, conduct quality control and compute differential expression using standardized procedures. We have especially good coverage of experiments relevant to the nervous system.
Test for association in genome-wide association studies (GWAS) using a standard linear mixed model to account for population stratification and sample structure. It calculates exact Wald or likelihood ratio test statistics and p-values, and is computationally efficient for large GWAS.
GEMmaker is a Nextflow workflow for large-scale gene expression sample processing, expression-level quantification and Gene Expression Matrix (GEM) construction.
The GEM (GEnome Multi-tool) Library (GEM Mapper)
A web-based platform for the visualization and curation of genome ancestry mosaics.
Gene Model Mapper is a homology-based gene prediction program. GeMoMa uses the annotation of protein-coding genes in a reference genome to infer the annotation of protein-coding genes in a target genome. Thereby, it utilizes amino acid sequence and intron position conservation. In addition, it allows to incorporate RNA-seq evidence for splice site prediction.
GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.
Tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.
gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome.
Explorative visual analytics on interval-based genomic data and their metadata.
Germline Mutation Scoring Tool fOr Next-generation sEquencing data. Cloud-based variant prioritization with high-level customization and a comprehensive collection of bioinformatics tools and data libraries.
C API and a Python module to support and simplify usage of the GEM Mapper.
Computationally efficient tools for modeling genetic ancestry based in the SNP information. GemTools is a package of functions to help the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy.
A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.
The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes.
A converter for human genome imputation output format to VCF format. BACKGROUND:For a genome-wide association study in humans, genotype imputation is an essential analysis tool for improving association mapping power. When IMPUTE software is used for imputation analysis, an imputation output (GEN format) should be converted to variant call format (VCF) with imputed genotype dosage for association analysis.
Application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.
gen3sis is a general engine for eco-evolutionary simulations on the origins of biodiversity.
Aggregation and analysis of gene expression signatures from related studies.
a comprehensive R package for genetic barcode analysis. Analysis and Visualization Tools for Genetic Barcode Data. Index of /web/packages/genBaRcode/vignettes. Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>)
Institute of Applied Biotechnologies, a.s.
Gen Seeker is the browser of variants detected in the Czech population included in the Czech digital genome map. Although Slavs are the largest European ethnolinguistic group, Slavic and especially Czech genomes are underrepresented in international genomic databases, which limits the ability to understand and interpret specific slavic gene variations.
Ministry of Industry of the Czech Republic
Genome-wide association analysis between quantitative or binary traits and SNPs.
GenAIRR is a simulation framework for generating immunoglobulin (Ig) sequences and their ground truths to facilitate benchmarking of Ig sequence aligners. It provides realistic simulations of V(D)J recombination, somatic hypermutation, and sequence corruptions, alongside a comparative evaluation of established aligners.
Ultra-fast Next-Generation Sequencing (NGS) read alignment and variant calling solution.
Eeasy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.
Information on gene mapping and genetic diseases.
The Genatlas database provides information on the structure, expression and function of genes, gene mutations and their consequences on diseases.
A New Tool for Modelling and Analyzing Cancer Gene Regulatory Networks Using Delayed Nonlinear Variable Order Fractional System. Gene Regulatory Network Analysis by Variable Fractional Order Systems.
A comprehensive database of public nucleotide sequences for more than 300 000 organisms named, from small and large-scale sequencing projects. Data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage.
Convert a GenBank, EMBL or UniProt file into a GFF file.
Convert a Genbank/EMBL file into the .ffn (gene) file, .faa (protein fasta file) and ptt file (protein table), or sequin file.
Convert a Genbank file into the .ffn (gene) file.
GenBase is a publicly accessible nucleotide sequence database hosted by the National Genomics Data Center in China. It provides a platform for archiving, searching, and sharing nucleotide sequences and associated annotations, adhering to INSDC data standards.
GENBMAP (Genetical Bandwith Mapping) is a software for the study of the spatial genetic structure. It was developped by Alain Cercueil, O. Fran?ois and S. Manel. The method is essentially descriptive, and allows an user to analyze genotypes and geographic coordinates simultaneously through a two dimensional graphical representation. GenBMAP provides a basis for the interpretation of the genetic structure of a population.
Literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. It can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.
New genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods.
Efficient compression algorithm for DNA sequences. Data compression has became a tool to retrieve information hidden in genetic sequences.
an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. Generate consensus reads to reduce sequencing noises and remove duplications. A fast tool to remove sequencing duplications and eliminate sequencing errors by generating consensus reads. gencore is a tool for fast and powerful deduplication for paired-end next-generation sequencing (NGS) data. It is much faster and uses much less memory than Picard and other tools. It generates very informative reports in both HTML and JSON formats. It's based on an algorithm for generating consensus reads, and that's why it's named gencore
Genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. This annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome.
This tool was developed based on the GenDB genome annotation system that was originally designed for prokaryotic genomes only. The system has been adapted to facilitate the creation and functional annotation of sequence features that are specific for eukaryotic genomes, e.g. intron and exon gene structures.
Prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.
Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects.
A curated transcriptome dataset collection to investigate inborn errors of immunity. Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation
Gene Bench is a benchmark-ing framework used in analyzing methods that detect differentially expressed genes from biological samples. Besides being a benchmarking framework it also contains some commonly used Differential genes detection algorithms:
CLIC (Clustering by Inferred Co-expression)
GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression.
Returns a colormap for visualizing gene expression.
A tool to design polynucleotide probes for targeting microbial genes. probe designer for geneFISH and phageFISH.
Identifying genes with similar continuous trait fingerprints from phenome-wide association analyses.
Computational tool for pathway-based rational drug repositioning.
Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).
The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.
Structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc.
An Integrated Genetic Database for Hearing Loss.
a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.
R package to define gene families and their expression in legumes and beyond.
The Gene Array Analyzer (GAA) allow to process CEL files from GeneChip�� Gene 1.0 ST Arrays. Various processing steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.
See if you can generate and collect three types of protein, then move on to explore the factors that affect protein synthesis in a cell.
Semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.
Database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.
Visualize and compare gene expression from standard transcriptome (RNA-Seq) data, cluster samples and genes, and infer enrichment of gene function in gene-sets.
Genomic neighborhood data visualization web application.
Explore the effects of mutations within the lac operon by adding or removing genes from the DNA.
The Gene Ontology resource. Source ontology files for the Gene Ontology. The Gene Ontology (GO) project is a major bioinformatics initiative to develop a computational representation of our evolving knowledge of how genes encode biological functions at the molecular, cellular and tissue system levels.
Gene Ontology Browser (GOBrowser) is an interactive tool for mapping microarray gene expression data onto the GeneOntology directed acyclic graph.
Database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access.
Disease enrichment analysis on gene sets.
Open source tool for marker-assisted gene pyramiding.
A web tool that autocorrects and updates for Excel misidentified gene names.
Web application for the analysis and comparison of gene expression data.
Provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.
Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization.
Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.
GeneBase 1.1 is a tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank.
geneBasisR is a package that selects an optimal targeted gene panel (based on scRNA-seq data) as a function of designated number of genes, and provides evaluation of any selected gene panel on -cell type/-cell and -gene levels. It is a package for gene selection using k-NN graphs.
GeneBe is a web-based platform designed to streamline the automated application of ACMG pathogenicity criteria for genetic variants. It utilizes algorithms and integrates data from sources like ClinVar, offering a user-friendly interface with an API and offering free usage for research.
Recurrent breakpoint gene detection on copy number aberration profiles.
Variant simulation to improve the diagnosis of Mendelian rare genetic diseases. GeneBreaker - Mendelian Disease Simulator. GeneBreaker is a tool which facilitates the creation of rare genetic disease scenarios, allowing user to make novel variants of multiple classes or draw from databases of known pathogenic events.
Web service which allows users to search genes based on their locus tags.
Database of human genes, their products, and involvement in diseases. It automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.
Suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.
GENECI (GEne NEtwork Consensus Inference) is a software package whose main functionality consists of an evolutionary algorithm to determine the optimal ensemble of machine learning techniques for genetic network inference based on the confidence levels and topological characteristics of its results.
Generalized query application that allows you to specify sophisticated sets of queries and generates a table of the number of bio-related records found for each query. The table can be presented as a Web page or in a standard spreadsheet format that will allow you to view the full output of only those queries that generate an interesting number of records.
This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.
A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis.
Computer software which can be used as a tool for exploratory analysis of gene expression microarray data. The development of this software was motivated by surging interest to search for interpretable biological structure in gene expression microarray data.
GeneClust is a computational feature selection method for scRNA-seq cell clustering. GeneClust groups genes into clusters from which genes are evaluated and selected with the aim of maximizing relevance, minimizing redundancy and preserving complementarity.
GeneCodis is a web-based tool for the ontological analysis of lists of genes, proteins, and regulatory elements like miRNAs, transcription factors, and CpGs.
Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations. Noisy and redundant output data has been removed from enrichment results, and greater comparative analyses are possible.
An integrative tool of a novel union algorithm with various ranking techniques for multiple gene expression data.
A web application server for constructing cancer patient-specific gene correlation networks with prognostic gene pairs.
GeneCup automatically extracts information from PubMed and NHGRI-EBI GWAS catalog on the relationship of any gene with a custom list of keywords hierarchically organized into an ontology.
Genedata Expressionist performs efficient and quality compliant analysis of next generation sequencing (NGS) and other genomic profiling data
Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).
Provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. Thus, allowing an interactive and explorative approach to the hunt for the candidate gene.
GeneDive is a powerful but easy-to-use application that can search, sort, group, filter, highlight, and visualize interactions between drugs, genes, and diseases (DGR). GeneDive also facilitates topology discovery through the various search modes that reveal direct and indirect interactions between DGR.
an R package for Gene-based Differentially Methylated Regions analysis. Gene-based differentially methylated regions analysis. GeneDMRs is an R package to detect the differentially methylated regions based on genes (DMG), gene body (DMP, DME, DMI), CpG islands and gene body interacted with CpG island features (e.g., DMG/DMP/DME/DMI_CpG island and DMG/DMP/DME/DMI_CpG island shore).
An interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Gene Circuit Explorer (GeneEx) is a systems-biology tool to visualize and simulate gene regulatory circuits (GRCs).
Tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.
An R Package to Facilitate Data Reading from Gene Expression Omnibus (GEO).
This package implements the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. Its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.
Structural and functionnal annotation of plant gene and protein families by a network of experts.
Java based graphical user interface for prediction of gene function using multiple sources of data.
Tool that can compute all attractors in synchronous dynamic models and asynchronous dynamic models. It is helpful for biologist to deep understand the genetic regulatory networks.
Some basic functions for filtering genes.
GeneFinder is a software package for linkage analysis with a variety of extensions. GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc.
Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.
Based on the assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes. It is an interactive web-based program for designing degenerate primers.
Tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.
Updated co-expression databases and tools for human and mouse genes and transcripts. A guilt-by-association tool to find co-expressed genes and functions. GeneFriends employs a RNAseq based gene co-expression network for candidate gene prioritization, based on a seed list of genes, and for functional annotation of unknown genes in human and mouse.
Functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
R based genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias. It includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure that this package functions properly.
The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results.
GeneGenie is an optimised oligomer design web server for doing directed evolution.
Augmenting large language models with domain tools for improved access to biomedical information.
GeneGrouper is a command-line tool that finds gene clusters in a set of genomes and bins them into groups of similar gene clusters.
R package for gene haplotypic statistics and visualization.
Tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.
Allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is used in exact computation of multipoint LOD scores and in a method of non-parametric linkage analysis. The multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data.
It is a modification of the GENEHUNTER software package . It allows for a parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. Therefore, a disease model which accounts for imprinting includes four penetrances instead of only three.
Ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms.
Centre for Genomic Regulation (CRG), Parc de Recerca Biomedica (PRBB)
Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.
Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.
Interfaces for the exploration of space omics data. The NASA GeneLab Data Processing team and Analysis Working Group members have created standard pipelines for processing omics data from spaceflight and space-relevant experiments. This repository contains the processing pipelines that have been standardized to date for the assay types indicated below.
A data management system designed to facilitate genetic studies of complex traits. Genetic analyses of complex traits are challenging, and high quality data-management systems are often critical to the success of these projects. So, we have developed it, that enables genotypic data to be merged easily with pedigree and extensive phenotypic data. It was designed specifically to facilitate large-scale, genetic linkage or association studies and is a powerful tool for complex trait mapping.
A supervised GRN inference framework, GENELink, to predict potential interactions from scRNA-seq data and gene linkage topology.
Web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.
The plugin brings fast gene function prediction capabilities to the desktop. It identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.
A family of gene prediction programs: Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes; Gene Prediction in Eukaryotes; Gene Prediction in Transcripts; Gene Prediction in Viruses, Phages and Plasmids.
Eukaryotic gene prediction with self-training in the space of genes and proteins. Experiments for ProtHint and GeneMark-EP/EP+ projects.
GeneMark-HM is a pipeline for protein coding gene prediction in assembled metagenomes from human microbiome (HM). Pipeline integrates three algorithms from GeneMark gene finder family, MetaGeneMark-2, GeneMarkS-2 and Genemark.hmm-2, into a workflow with parameters optimized for analysis of human metagenomes.
A Database and User Interface for scRNA-seq Marker Genes.
Web site designed to enable connections between clinicians and researchers from around the world who share an interest in the same gene or genes.
An R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. GeneMates: an R package identifying horizontal gene co-transfer between bacteria.
A collection of meta-analysis tools for analysing high throughput experimental data.
Package for analyzing gene expression (time series) data with focus on the inference of gene networks.
Assess connectivity among a set of genes of interest (‘seed-genes’) within a biological network of their choosing.
Software to qualitatively infer dynamic gene regulatory interactions from gene expression data. From the time-series data of gene expression, the software identifies not only gene regulatory interactions but also the temporal aspects of the regulatory interactions using two types of scores, R1 and R2. As for the temporal aspect of gene regulatory relations, it identifies the order of the gene regulatory relations and the pace of the relations.
GeneNetFusion is a computatinal pipeline for the construction of fused co-expression networks and the extraction of relevant gene biomarkers.
Tests for Gaussian graphical models with shrinkage.
Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network.
A continuously updated tool for systems genetics analyses. GeneNetwork displays the additive values on the far right of many trait QTL maps, usually as red or green lines along the maps.
Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, this tool generates a regulatory network of the TF.
Bioinformatics toolbox for genomics-guided neoepitope prediction.
Test two sets of gene lists and visualize the results.
Standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.
Genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.
An easy to use web tool for generating disease- and phenotype-associated gene lists | Genepanel.iobio: generate list of genes based on suspected conditions and phenotypes
Identify and determine the fine structure of protein genes in genomic DNA sequences.
Tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.
GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis.
Eefficient machine learning approach to identify coordinated alterations of genes or proteins in biological networks using omics data, providing provably optimal results in few seconds.
Gene-based epistasis discovery using machine learning. GenEpi is a package to uncover epistasis associated with phenotypes by a machine learning approach, developed by Yu-Chuan Chang at c4Lab of National Taiwan University and Taiwan AI Labs.
This tool is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.
A web-server for gene discovery using network-based machine learning.
Simple and flexible tool for manipulating multilocus molecular data in R.
Web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).
Automated data analysis from gene expression experiments on a number of different platforms.
A quantitative geometry python toolbox for large scale bioimaging. dockerfiles with ready to use environements for GeNePy3d. GeNePy3D is an python library for quantitative geometry, in particular in the context of quantitative microscopy. It aims at providing an easy interface to perform complex data science workflow on geometric data, manipulating point cloud, surfaces, curves and trees, converting between them, and performing analysis tasks to extract information and knowledge out of raw geometrical data.
Tool for performing reductions on DNA-strands based on a strand-displacement algebra.
This function runs Viterbi algorithm given valid parameters and returns optimal path into a file. General implementation of MATLAB version of Viterbi algorithm specifically written for gene structure finding problem in mind. However, it can be modified to suit the goal of a user.
Matrix balancing/updating/estimation using the Generalized RAS approach.
Numerical implementation of an extended SEIR model with time-dependent death and recovery rates
Scripts that combining pre-training and multi-task learning to predict drug-target binding affinity for unknown drug discovery.
Processed gene and protein expression levels across cells and tissues for target discovery.
Generate all synonymous codon combinations
“generate_oriented_clusters” is a program that generates single-linkage clusters of loci (where a locus can be on a chromosome, transcript, etc.).
Generation Scotland is a longitudinal family health study in Scotland collecting genetic, lifestyle, and clinical data from volunteers. The study aims to identify genetic and environmental determinants of health and wellbeing and has been widely used in research.
This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.
A coalescent based tool for fine-scale association mapping.
genereg is a Python library that implements a method for analyzing the regulation systems of target genes in a specific genetic pathology, such as a cancer.
A package with focus on analysis of discrete regions of the genome using Affymetrix data, including additional information about the sequence of each probe and the probe set it is derived from. It includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.
Gene finding in distinct metagenomic data complexities. The GeneRFinder-Benchmark is a comprehensive benchmark data for gene prediction which is based on data of CAMI (Critical Assessment of Metagenome Interpretation) and contains labeled data from gene regions.
SimBiology implementation of a generic PBPK model. Contains model for human and rat fested and fat.
This package provides functions for exploring genomic insertion sites originating from two different sources.
Word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies.
Web service that retrieves all genes whose encoding protein has an epitope identified by the Immune Epitope Database and Analysis Resource with the confidence specified by the user.
Web service that retrieves all genes whose protein product has an isoelectric point in a range that user specify.
Web service that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify.
A web service which allows users to search genes based on an organism or a list of organisms.
Web service which allows users to search genes based on organism and other criteria such as minimum signalp sum score, minimum signalp D score and minimum signalp probability.
Web service that retrieves all genes having number of predicted transmembrane domains in a range that user specify.
Tool for high-throughput detection and annotation of rare sequence variants. Although analysis of sequence electropherograms can be done by eye, this is very laborious and error-prone, especially when analyzing large volumes of data.
Allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.
This web-tool enables the researchers to find differentially expressed genes using different machine learning algorithms.
Gene selection based on a mixture of marginal distributions.
Filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list. The stability of the findings can be considered in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods to find a synthesis.
Method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.
The Ensembl GeneTrees pipeline as a Galaxy workflow.
GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.
GeneSetCart is an interactive web-based application that enables users to fetch gene sets from various Common Fund programs data sources, augment these sets with gene-gene co-expression correlations or protein-protein interactions, perform set operations such as union, consensus, and intersection on multiple sets, visualize and analyze these gene sets in a single session.
A tool for summarizing and integrating gene-set analysis results. Gene-set analysis (GSA) tools aim to provide biological context by identifying gene-sets associated with a given trait or traits of interest. Gene-set analysis tools are frequently gene-centric, using as input results from studies using RNA-seq or microarrays data (e.g. Ingenuity or GSEA among many others), but it has also been adapted for interval-based analysis derived from data-types such as DNA methylation or ChIP/ATAC-seq.
This tool builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts.
Manually curated database of gene expression signatures. It focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. It provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene.
Influence network model uncovers relations between biological processes and mutational signatures.
GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.
Provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a PCA on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry.
Genesis 2 is an interactive tool for displaying PCA and Admixture charts
Various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.
GENESIS (GENEration of Supersequences In Silico) systematically generates pulse programs for arbitrary NOAH supersequences compatible with Bruker spectrometers.
Collates data from bioinformatics resources and provides automated gene-centric annotations.
Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies.
GENESPACE: an R package for synteny- and orthology-constrained comparative genomics
A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.
Tool to assemble genes using network matching algorithm. Given an already-assembled dataset, it is capable of assembling contigs together to form more complete genes with the help of a reference gene set. Currently the assembly software that is supported SOAPdenovo.
Mobile application that provides users with a synopsis regarding the information of human genes from various points of view. Synopsis is given as a little story, while, users may perform queries regarding a gene of interest. It is developed for Android and provides general, functional, clinical and network information for known and predicted human genes.
It can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.
Web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the interpretation of personal variants in clinical context.
Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.
A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. GeneTEFlow is a reproducible and platform-independent workflow for the comprehensive analysis of gene and locus-specific TEs expression from RNA-Seq data using Nextflow and Docker technologies.
A customizable multilayer approach to genomic variant prioritization and interpretation. GeneTerpret: a new way to interpret and visualize genomic variants data. GeneTerpret: a new way to interpret and visualize genomic variants dataGeneTerpret: a new way to interpret and visualize genomic variants dataGeneTerpret: a new way to interpret and visualize genomic variants data.
A medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons.
GENomics Report TEXt mining R package and Shiny application designed to capture real-world clinico-genomic data.
Allows searching information in GenBank and also in other NCBI databases through the interactive orchestration of NCBI Web services.
Automatically Designed Deep Networks for Retinal Vessel Segmentation Using a Genetic Algorithm.
This package contains functions useful for designing genetics studies, including power and sample-size calculations.
Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities.
This tool replaces the knowledge-based inference traditionally used in candidate disease gene prioritization, instead using experimental data from tissue-specific gene expression data sets.
An alignment-free method for gene copy number estimation directly from next-generation sequencing reads.
A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist.
GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.
GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures. GeneTrail2 allows the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results.
Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses. Reranked gene lists. Our final product is the set of top genes defined by (Def. def-genetrank), possibly accumulated over several values of the restart rate (Def. eq-topkler).
Software for the estimation of mutation, migration and growth rates, and ancestral inference such as the time to the most recent common ancestor of a sample of DNA sequences.
A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. Multilevel homolog-identification pipeline.
Mining transcriptomics and clinical data reveals ACE2 expression modulators and identifies cardiomyopathy as a risk factor for mortality in COVID-19 patients. GENEVA allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contains conditions modulating a gene or a gene signature. See the Help page fore more detail.
Tool to identify problematic gene predictions based on comparisons between gene predictions and similar sequences in public databases (e.g., SwissProt).
Identification of transcriptional programs using dense vector representations defined by mutual information.
High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drugs, tissues, cancers, cell lines or genotypes. The high diversity of curated experiments allows the tool to project your genes or your data against a broad spectrum of reference profiles and datasets.
Webserver that lets you search scientific articles using keywords and identifiers for specific biological entities. It has advanced features like: recognizing biological entities like genes and SNPs.
A native genome browser for the iPad/iPhone.The genome at your fingertips (literally): Tap, scroll and pinch your way through the chromosomes, genes and genomic data.
Curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes.
Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.
Enabling semantic queries across federated bioinformatics databases. Ontology Documentation generated by WIDOCO. Gene expression (GenEx) semantic model.
This is a computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and prokaryotic reference genomes. The workflow accepts a reference genome in FASTA-format and outputs coordinates of microbial-like (human-like) regions in BED-format. The workflow builds a Bowtie2 index of the reference genome and aligns pre-computed microbial (GTDB v.214 or NCBI RefSeq release 213) or human (hg38) pseudo-reads to the reference, then custom scripts are used for detection of the positions of covered regions and quantification of most abundant microbial species, the latter is only when screening for microbial-like sequences in eukaryotic references.
Tool to infer or validate genetic networks based on expression time series data.
This tool annotates a histone modification ChIP-seq peak input file with functionally important genomic features (e.g., genes associated with peaks) based on optimization calculations. It extends the boundaries of every gene in a genome by some distance in DNA base pairs, incorporating cis-regulatory elements (CREs), such as enhancers and promoters, as well as downstream elements that are important to the function of the gene relative to an epigenetic histone modification ChIP-seq dataset.
Highly reconfigurable gene finder written in C++. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well.
Geniac is an automatic configuration generator and Installer for nextflow pipelines. With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production has become a challenge such that the data can be processed in real-time and delivered to the end-users as fast as possible. The usage of workflow management systems along with packaging systems and containerization technologies offer an opportunity to tackle this challenge. While very powerful, they can be used and combined in multiple ways thus increasing their usage complexity
Analyze English sentences and output the base forms, part-of-speech tags, chunk tags, and named entity tags. The tagger is specifically tuned for biomedical text such as MEDLINE abstracts.
Genes prioritization for topics of interest using gene-related PubMed abstracts.
An Open Source MPEG-G Codec to compress and decompress FASTQ-files.
Algorithm for the inference of gene regulatory networks from expression data. It decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of the regression problems, the expression pattern of one of the genes (target gene) is predicted from the expression patterns of all the other genes (input genes), using tree-based ensemble methods Random Forests or Extra-Trees.
Génie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases.
An interactive real-time simulation for teaching genetic drift.
Genomic database with corresponding annotated samples based on a cloud data lake architecture.
Webserver that predicts potential functional associations between genes, based on other genomic data or high-throughput experimental data such as phylogenetic profiles and gene expression profiles.
Genin2 is a lightining-fast bioinformatic tool to predict genotypes for clade 2.3.4.4b H5Nx viruses collected in Europe since October 2020. Genin2 identifies only epidemiologically relevant European genotypes, i.e., detected in at least 3 viruses collected from at least 2 countries.
GENLIB is an R package that can be used to analyze genealogical data.
Web tool for NLP-based exploration and prediction of microbial gene function.
Microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.
Convert an AVS file into a MATLAB 3D double array ready for visualisation. AVS is a file format used by many CFD packages (e.g. Fluent). This tool will import an AVS file into a MATLAB 3D double array ready for viewing the mesh and velocities with mesh, surf, slice or the excellent Slice-O-Matic.
Web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.
Code generation framework for accelerated brain simulations.
GenNet is a command line tool that can be used to create neural networks for (mainly) genetics. GenNet gives the opportunity to let you decide what should be connected to what. Any information that groups knowledge can therefore be used to define connections in the network. For example, gene annotations can be used to group genetic variants into genes, as seen in the first layer of the image. This creates meaningful and interpretable connections. When the network is trained the network learns which connections are important for the predicted phenotype and assigns these connections a higher weight.
Software designed to generate multiple sequence alignments of DNA evolving on any phylogenetic tree.
Web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.
Web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis or further analysis. Users can also create personal accounts and thus can customize their workspace.
Whole-genome functional annotation approach based on unsupervised statistical learning.
Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations.
Method for identifying genetic relatives without compromising privacy by taking advantage of novel cryptographic techniques customized for secure and private comparison of genetic information.
Web tool for predicting gene expression levels from single nucleotide polymorphisms.
Genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences.
This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package 'mgcv'. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.
Genotype inference method that reduces the number of genotyping reactions and increases the power of genome-wide association studies.
An integrated environment for the analysis of microbial genomes.
GenoList comparative analysis of microbial genomes
Genom 2005 is a software to analyse microarrays or other experiment data. It has build in function predictions, pathway analysis, GO trees and a lot more.
geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.
A package for summary and annotation of genomic intervals. The genomic intervals represent regions with a defined chromosomic position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals.
Quickly reduce millions of variants obtained from Next Generation Sequencing to the few or even the single relevant one(s). It annotates SNPs and enables to perform trio analyses, compare case and control sets and identify somatic SNPs. The interaction with the Genomatix Pathway System enables to explore networks of affected genes and allows for an in-depth assessment of the biological background of variants under investigation.
Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. Tools for sampling viral genomes across time of isolation, location of isolation, and genome divergence.
A practical guide to sketching algorithms for processing the flood of genomic data | online notebooks for a review of genome sketching
Genome-wide evaluation under a multiple variance component model by using the maximum likelihood (ML) method and the MCMC implemented Bayesian method.
Genome2OR is a genetic annotation tool based on HMMER, MAFFT and CD-HIT.
Genome ARTIST is a pairwise gapped aligner tool which works out issues in mapping the hits of artificial transposons at nucleotide lever accuracy in insertion mutagenesis experiments.
Python/pyrex implementation of the Bayesian classifier of genomic signatures.
This is a computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes. The workflow accepts a reference genome in FASTA-format and outputs coordinates of microbial-like (human-like) regions in BED-format. The workflow builds a Bowtie2 index of the reference genome and aligns pre-computed microbial (GTDB v.214 or NCBI RefSeq release 213) or human (hg38) pseudo-reads to the reference, then custom scripts are used for detection of the positions of covered regions and quantification of most abundant microbial species, the latter is only when screening for microbial-like sequences in eukaryotic references.
GENome EXogenous (GENEX) sequence detection workflow
Open source and high-performance HTML5 web-based genome browser. It allows to browse several genomes and annotations by fetching data from CellBase high-performance REST web services. Custom data (BAMs, VCFs, ...) can also be loaded from remote servers and local disk by using OpenCGA server.
Searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.
Genome Search Toolkit is a set of scripts for managing massive local homology searches.
Discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals. It looks both across and within a set of sequenced genomes to detect variation. The methods are adaptive and support heterogeneous data sets. A minimum of 20 to 30 genomes are required to get acceptable results, but the method gains power across genomes and processing more genomes provide better results.
Tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.
Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes. The draft genomes now can be analyzed. Initiate the GTN with "gtn_CompleteOnly.pl" if your data consist of complete genomes only, or utilize "gtn_WithDraft.pl". The GTN firstly locates the synteny block in genomes if draft data exist. The Markov Cluster Algorithm is introduced to assign the gene families. The Markov Cluster (MCL) Algorithm is introduced in this version. This algorithm is also used in many clustering tool, such as orthoMCL,. Unique gene connection information will be yielded as a result file.
A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.
Visualize chromosomal abnormalities in the Human Genome using a U-shape layout.
Genome Alignment Tools are tools for improving the sensitivity and specificity of genome alignments.
A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.
GenomeChronicler. An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing. singularity container and workflow management.
Database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.
SVG based genome viewer written in javascript using D3.
Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
A platform for phenotype-guided medical genomic diagnosis. Genomic and Phenotypic filters for the Genome Diver project.
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This tool uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. Genomic information is plotted together with your data. Plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.
Genome browser specialized in next-generation sequencing data. Advantages are intuitive interface and smooth drag'n drop response.
A short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference.
Mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.
Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W).
Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint.
Tool that permits multi-level partitioning of large scale DNA constructs for synthetic biology applications. The partitioning algorithm fragments large DNA sequences into smaller, fabricable DNA blocks sharing flanking homologies for in vitro and in vivo DNA assembly. Overlapping homology regions between adjacent DNA blocks are optimized to remove hairpin, sequence repeats and any pattern that interferes with the DNA assembly process. Segments, blocks and sub-blocks that build the blueprint for hierarchical DNA assembly are listed in a GenBank output file.
The goal is to have a simple and straightforward way to download and use genomic sequences. Currently, genomepy supports UCSC, Ensembl and NCBI.
Genomer is command line glue for genome projects. It simplifies the small but tedious tasks required when finishing a genome. Genomer makes it easy to reorganise contigs in a genome, map annotations on to the genome and generate the files required to submit a genome.
Annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota.
This database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.
Download genome and assembly reports from NCBI.
Program for identifying the exon-intron structures of genes in genomic DNA sequences from a variety of organisms, with a focus on human and other vertebrates. The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits.
The genomeSidekick data analysis tool is a simple and efficient application that allows users to analyze and visualize RNA-seq and ATAC-seq data without having to learn the nitty gritty bioinformatics. This document will provide a comprehensive overview of the functions and capabilities of each tab within the application. For your convenience, the app can be used both online as a website or locally run in your RStudio. If you run into any problems while using the app in RStudio, refer to the Troubleshooting section to see some common errors and solutions that may occur.
GenomeSpy is a grammar-based visualization toolkit for genomic data, enabling users to create tailored, interactive visualizations. It utilizes a GPU-accelerated rendering engine and is open-source, facilitating analysis and embedded applications.
Visualize and analyze data generated on Illumina array platforms with GenomeStudio Software. This solution supports the genotyping analysis of microarray data. Performance-optimized tools and a graphical interface enable you to convert data into meaningful results.
Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence.
Analyse whether PCR primers have excessive number of binding sites in large genomes, how many PCR products would be amplified in the reaction and where are they located.
Software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.
Free collection of bioinformatics tools for genome informatics.
Comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.
Performs several carefully chosen spatial tests of independence on genome-wide data and determines the correlation of genome-wide data with other datasets or known biological features.
Next-generation stand-alone genome browser and editor. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.
Genomic signature using Chaos game representation of frequencies.
Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as Genome-Wide Association Studies and transcriptomics using RNA-Sequencing. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens, etc.
Genomic Annotation in Livestock for positional candidate LOci (GALLO)
Collection of datasets for genomic sequence classification.
The Genomic Transmission Graph Tool is a resource for modelling parasite transmission dynamics and population genetics, allowing for rapid simulation and analysis of coalescence times. It provides a theoretical model and tools for exploring the relationship between transmission and genomic diversity, exemplified by malaria.
The Genomic HyperBrowser is a web server for the analysis of genomic track data (e.g. using feature-specific coordinates relative to reference genome assemblies).
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
An R package that provides functions for calculating and visualizing a variety of statistics for a collection of genomic ranges.
A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and CDS of a given organism, from either the UCSC Genome Browser or a BioMart database. This information is then stored in a local database that keeps track of the relationship between transcripts, exons, CDS and genes.
This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.
R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots/statistics.
Genomic Knowledgebase (GenomicKB) is a graph database which use a knowledge graph to consolidates genomic datasets and annotations from over 30 consortia and portals.
GENOMICON-Seq is a tool for simulating mutations in amplicon and whole exome sequencing, allowing users to assess laboratory and bioinformatics parameters influencing mutation detection. It generates genomes with mutations and simulates sequencing biases and errors, aiding in the evaluation of bioinformatics tools and experimental designs.
This package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively.
Genomics 2 Proteins (G2P) is a browser-based portal that lets you paste or upload variants and instantly map them onto PDB or AlphaFold structures. The viewer overlays UniProt domains, PTMs, disorder, conservation, and public variant tracks such as ClinVar, gnomAD, and HGMD, highlights 3-D hotspots, and can export a combined TSV or PyMOL session. Everything runs in the browser with no installation required, and a REST API is available for batch use.
A virtual laboratory for genomics research and training.
Victorian Life Sciences Computation Initiative (VLSCI)
Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.
GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.
GenomicTools is a platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq.
GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges BioConductor package.
Tools for storing, accessing, analyzing and visualizing genomic data.
Parallel genome assembly system built from the ground up with scalability in mind. It can assemble large and high-coverage genomes from fastq files in a short time and produces assemblies similar to Velvet or Ray in quality.
Platform independent Java program for the analysis of genome wide association experiments. The software implements the workflow of an association experiment, including data management, single-point and haplotype analysis, “lead” definition, and data visualization.
Software package for internal tandem duplication detection from cancer genome sequencing data.
Software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design.
Web-based tool for species and drug resistance prediction for Mycobacterium genomes.
A genotype network is a graph in which vertices represent genotypes that have the same phenotype. This tool provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network; (iii) multiple interactive visualizations.
Cataloging large-scale phenotypic and next-generation sequencing data within human datasets. GenoPheno-CatalogShiny is an R Shiny App developed to provide a dynamic on-line catalog with datasets containing both, genomic sequencing and clinical data for the same patients.
Genopo (a.k.a. F5N) is a nanopore sequencing analysis toolkit for Android smartphones.
An open-source software for robust and standardized integration of proteomic and genetic data. Genoppi is an open-source software for performing quality control and analyzing quantitative proteomic data. In particular, it streamlines the integration of proteomic data with external datasets such as known protein-protein interactions in published literature, data from genetic studies, gene set annotations, or other user-defined inputs.
GenoPred is a Snakemake pipeline for polygenic scoring that implements leading methodologies within an easy-to-use, reference-standardized, and reproducible workflow. It facilitates the generation of interpretable polygenic scores and improves the transferability of results to external datasets.
Genopyc is a Python library designed for investigating the functional effects of genomic variants associated with complex diseases. It provides functions for variant annotation, pathway analysis, and visualization.
GenoREAD is a web-based, sequence verification software that can be used to compare Sanger sequencing trace files against a reference sequence. Users can either submit their sequencing results one clone at a time, or they can submit a series of clones (as a project) to run at once. Results can be viewed online or downloaded.
A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.
Several tools to perform reconstruction of gene regulatory networks from microarray data and connectivity information.
Online exploration of quantitative profiles along genomes via interactively customized graphical representations. Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations.
This tool provides an extension of the RangedSummarizedExperiment class with additional API features. This new class provides convenient and fast methods for working with segmented genomic data. Additionally, this extension provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).
Free tool to identify length variation of microsatellites from short sequence reads. Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise including PCR amplification errors, individual cell mutation, misalignment or mis-mapping caused by the repetitive nature of the microsatellites.
Takes in a gVCF or VCF and reports metrics to assess quality of calls.
Graphical genotyping on genetic and sequence-based maps. GenoTypeMapper (GTM) is a software to compare, visualize and analyze genomic data of one or two genetic or physical maps. More information about the software can be obtained by reading the corresponding article, which is a prerequisite to understand the idea and theoretical background of this software. GTM is available for download, together with a small manual and testdata.
Here, we present GENome Organisation Visual Analytics (GENOVA): a software suite to perform in-depth analyses on various levels of genome organisation, using Hi-C data. GENOVA facilitates the comparison between multiple datasets and supports the majority of mapping-pipelines. The increase in interest for Hi-C methods in the chromatin community has led to a need for more user-friendly and powerful analysis methods. The few currently available software packages for Hi-C do not allow a researcher to quickly summarize and visualize their data. An easy to use software package, which can generate a comprehensive set of publication-quality plots, would allow researchers to swiftly go from raw Hi-C data to interpretable results.
Freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results.
GenoVault is a private cloud-based central repository for storage and retrieval of genomics data generated in various research labs in various organizations. The solution is delivered in the form of a software suite called “GenoVault”, that enables quick archival and retrieval of data along with analytical support.
Open-source automated circular genome visualizer for bacteria and archaea.
A feature rich NGS assembly viewer/browser.
Post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. After prioritization, real disease-associated loci become easier to be identified.
A fast and efficient compression tool for FASTQ, BAM, VCF and other genomic files, and a set of analysis tools operating directly on compressed data.
This tool conducts genetic association studies by using statistical learning techniques such as random forests and support vector machines, as well as Bayesian inference with hierarchical models. It alleviates the multiple hypothesis problems and the need for P value corrections, which often lead to massive numbers of false negatives.
Standalone software for creating protein interaction networks from genomes. Ab initio protein interation network generator.
Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. Binding sites are defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach
genra-py is a Python package for GenRA. Genralised Read-Across (GenRA) is a computational toxicology tool to mimic a human expert’s manual reasoning based on similarity-weighted activity.
Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis.
GenRisk is a package that implements different gene-based scoring schemes to analyze and find significant genes within a phenotype in a population.
Simulate interactions among two genetic and one environmental factor and also allows for epistatic interactions. It is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered.
Program designed for specified-sequence retrieval and extraction from large-scale sequence sets in NCBI GenBank flatfile format.
Identify complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands.
A user friendly framework for re-sequencing in a diagnostics context: searching for mutations/variants, especially on well known genes.
GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence.
Generating Series for testing Structural Identifiability.
GENTANGLE is a high-performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames within a microbial genome. The tool utilizes Docker/Singularity containers and offers a GitHub repository for source code and related data.
GenTB is a user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. genTB is an analysis tool for Mycobacterium tuberculosis genomic data that offers three main features: a means for sharing, citing and crediting TB data and metadata, the prediction of resistance on genotype using a machine learning algorithm, and geographic resistance and mutation data mapping.
Software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
Open Targets python framework for post-GWAS analysis
Distinguish genuine untargeted metabolic features without quality control samples. distinguish genuine signal of untargeted metabolites from measurement artifacts without QC samples.
Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation.
A gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids.
Rapid Identification of Discriminative and Explainable Feature Pairs for Genomic Analysis. Genvisage - Rapid Identification of Discriminative Feature Pairs for Genomic Analysis.
Genomic visualization software package that is fully integrated with Lasergene and is designed to support easy generation of publication quality graphics and maps.
Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.
Tool for visualizing agroclimate to inform research and regulatory risk assessment.
A PyMOL plugin for protein structure ensembles analysis. The Geo Measures Plugin can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface.
GEO Platform Annotation Table Reader is MATLAB tool that reads and parses platform annotation table (*.annot) from GEO.
Segmentation of nucleic acid binding interface on protein surface with geometric deep learning.
Command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, it extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications.
A natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. GeoBoost2 (part of the ZoDo project) is a system for extracting the location of infected hosts (LOIH) for a given set of GenBank metadata accessions. This involves API implementations that utilize NCBI API's for accessing and parsing information and delivering it to the researcher interested in investigating a set of sequences. You can also use this tool mine Geographic Locations in scientific articles (available as abstracts on PubMed or PMC-OA) or text files.
A global database of political administrative boundaries. geoBoundaries by the William & Mary geoLab. Create dynamic maps, analyze and build location-aware and geospatial applications with your data using the power of PostGIS in the cloud.
Bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO).
A Slicer Toolbox for Targeting Brain Stimulation. 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public.
Program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. In the NCA, population structure can be separated from population history when it is assessed through rigorous and objective statistical tests using the temporal information contained in the a genealogy.
An R/Bioconductor package for gene expression analysis and visualisation.
GeomBD3 is a rigid body Brownian dynamics software package for simulating association rates and molecular recognition in biological or engineered systems.
A thin wrapper around the SQLite database along with associated documentation. Access to the metadata associated with samples, platforms, and datasets much more feasible.
Python program to compute the geodesic path between two phylogenetic trees.
This is fast implementation of bolstered error estimation algorithm for linear SVM classification.
Geometric Gaussian-Kernel Bolstered Error Estimation for Linear Classification
Geometricus Represents Protein Structures as Shape-mers Derived from Moment Invariants. Geometricus represents protein structures by shape-mers derived from 3D moment invariants - https://github.com/TurtleTools/geometricus.
Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank. ProteinsPlus structure-based modeling support server. This server is a common web portal for all tools related to structure-based modeling created by the AMD group (Prof. M. Rarey) at ZBH, Hamburg, including DoGSite Scorer, EDIA, PPI, PoseView, SIENA and ProToss.
Forward-time, individual-based, landscape genomic simulation in Python.
GeoPPI is a deep learning based framework that uses deep geometric representations of protein complexes to model the effects of mutations on the binding affinity.
The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. This tool is the bridge between GEO and BioConductor.
Analyze untargeted LC/MS data from stable isotope-labeling experiments useing unlabeled and labeled biologically equivalent samples to compare isotopic distributions in the mass spectra.
Extendable search engine for NCBI GEO (Gene Expression Omnibus). Instead of directly searching the term, it can find all the gene names contained in the search term and search all the alias of the gene names simultaneously in GEO database. It also provides other functions such as summarizing common biology keywords in the search results.
Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries.
GeoSPM allows the spatial analysis of diverse geographic point data. It draws upon differential geometry and random field theory, by leveraging the procedures used in statistical parametric mapping (SPM): a framework for making topological inferences about spatially structured effects, with well-behaved spatial dependencies.
Complete system used to store and analyze gene expression data. It has a relational database, a web interface, and an analysis suite. There is also a repository for each user’s files, and a comprehensive security system. The program is intended to be a multiuser archive for gene chip data, as well as a friendly, powerful analysis tool for end users. It includes workflow management features for the microarray center, and for the individual research labs.
Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).
GeoTox is an open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures. It facilitates source-to-outcome continuum modeling for individual and population-level risk assessment.
Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.
Collection of tools for the analysis of microarray data. It includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.
GEPAT (Genome Expression Pathway Analysis Tool) is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data.
Large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions.
Gene Expression Profiling Interactive Analysis. Interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis.
GEPREP is a data atlas compiling RNA-seq gene expression profiles of exercise responses across multiple species and tissues, providing curated metadata and user-friendly search and visualization tools.
The Gene Expression Database of Poplar under Stress.
GEPSi is a toolkit to simulate phenotypes for GWAS analysis, given input genotype data for a population.
A sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits.
The Genome Sequence Archive (GSA) is a data repository for collecting, archiving, and sharing raw sequence data. It provides metadata search and data download services and is crucial for maize Gibberella ear rot research by integrating transcriptomics and phytohormone analysis.
Interactive multi-omics database for cross-species data mining in horticultural crops.
An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.
Program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.
Germline Filter is a Python program used in the ICGC-TCGA DREAM Mutation Calling Challenge meant to contribute to the real data security measures.
High-throughput expression data relevant for germline development and fertility across species.
Gametogenesis and reproductive tissue expression
Identify constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint.
Implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.
Rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes.
Classifying nsSNPs to predict disease association.
Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.
Novel computational method for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites.
A database of global evaluation of SARS-CoV-2/hCoV-19 sequences. If you used GESS for scientific publication, we would appreciate citations to the following paper:.
Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2.
GestaltGAN generates photorealistic portraits of individuals with rare genetic disorders using a modified StyleGAN architecture, addressing privacy concerns and facilitating visualization for publications, education, and AI training.
A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST
get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences. MNVs occur when multiple Single Nucleotide Variants (SNVs) are present within the same codon, leading to the translation of a different amino acid. This tool addresses limitations in current annotation programs like ANNOVAR or SnpEff, which are primarily designed to work with individual SNVs and might overlook the actual amino acid changes resulting from MNVs.
A Method for Analysis of DNA and RNA Allele Frequency Distributions. Repository with the toolbox (and code used for analysis and to produce figures) described in: "GeTallele: a method for analysis of DNA and RNA allele frequencies distributions".
Determines the instantaneous treadmill belt velocity from reflective marker patches attached to the left and right borders of the treadmill.
Uncovering patterns of atomic interactions in static and dynamic structures of proteins. Interaction analysis for protein structures and dynamics. Interactions have been computed using the GetContacts framework and are visualized using Flareplots and the NGL Viewer. The molecular functions of proteins (e.g. ligand-binding) are governed by networks of molecular interactions such as hydrogen bonds and van der Waals interactions. We have precomputed interaction networks for a range of molecular families and made visualization and comparison of these networks available in this atlas
GETdb is a database providing genetic and evolutionary features of drug targets, integrating data from multiple databases and including an allosteric protein prediction model. It aims to facilitate drug target identification by providing a comprehensive resource for researchers.
Gets all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level).
Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.
Give the distances between every data from the first input set and the data from the second input set.
Get the distribution of the genomic coordinates on a genome.
Get the flanking regions of a set of reference.
Extraction of single nucleotide polymorphism data from HGVBASE
Get the introns of a set of transcripts.
Calculate distribution for each nucleotide per position for all short reads (S-MART).
downloads MLST datasets from pubmlst.org
Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.
Find and extract open reading frames (ORFs).
A fast and versatile toolkit for accurate de novo assembly of organelle genomes. This toolkit assemblies organelle genome from genomic skimming data.
Plot the number of identical reads and give the most represented.
getSequenceInfo tool allows to extract sequence data and specific information from GenBank (Galaxy Version 1.0.1)
Get the sizes of a set of genomic coordinates.
Landscape of 3′ UTR from RNA-seq data. It has three steps: preprocessing, smoothing and normalization.
Compute the average data for some genomic coordinates using WIG files.
Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).
Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).
A R package to evaluate variations in differential expression in multiple biological conditions.
This package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions.
Start-to-end framework for single-cell gene expression, hashing, and antibody analysis.
Gexplora – user interface that highlights and explores the density of genomic elements along a chromosomal sequence. plotting the density of genetic elements along a chromosome using GTF files (ideally from Ensembl) as input and using REST API calls to Ensembl, OMA and STRING database (to be done).
A C++ library and command line utilities for the Graphical Fragment Assembly formats | A C++ library and utilities for manipulating the Graphical Fragment Assembly format | GFAKluge is a C++ parser/writer and a set of command line utilities for manipulating GFA files. It parses GFA to a set of data structures that represent the encoded graph. You can use these components and their fields/members to build up your own graph representation. You can also convert between GFA 0.1 <-> 1.0 <-> 2.0 to glue programs that use different GFA versions together
Ultra-fast and accurate gene functional annotation software for plants.
Flexible and extensible software library for handling sequence graphs in Python.
Bayesian Group Factor Analysis with element wise prior inducing sparsity.
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.
The German Federation for Biological Data was established as a sustainable, national infrastructure to facilitate data sharing for the biological environmental sciences. It supports the complete life cycle of research data management, from planning, through acquisition, to publication. Research data are constantly increasing in both size and complexity, offering not only new analytical possibilities, but also posing new challenges to data processing, integration and safeguarding.
Cytoscape app designed to visualize and analyze the functional dissimilarity of gene networks. It can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes in it.
GFDC is a web application that automatically classifies glaucomatous visual field defects using the Hodapp-Parrish-Anderson criteria. It exhibits perfect accuracy and is freely hosted for clinicians and researchers.
An analysis and visualization tool for data on food fortification
Automated feature-based extraction of sequences from a GFF file.
Program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.
Program for visualizing annotations of genomic sequences. The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files.
A tool for filling the gap created by genomic data processing/analysis by rebasing some analysis results against the parent features which were originally analysed.
Program for comparing, annotating, merging and tracking transcripts in GFF files.
program for filtering, converting and manipulating GFF files
Python package for working with GFF and GTF files. It allows operations which would be complicated or time-consuming using a text-file-only approach.
GFFx is a Rust-based toolkit for ultra-fast and scalable genome annotation access. GFFx introduces a compact, model-aware indexing system inspired by binning strategies and leverages Rust’s strengths in execution speed, memory safety, and multithreading. It supports feature- and region-based feature extraction and coverage profiling with significant improvements in runtime and scalability over existing tools.
GFICLEE is a program for predicting the new members in biological pathway or biological complex.
Characterize the different gene classes in the list using annotations of various types from several different sources.
Baseline human gut microbiota profile in healthy people and standard reporting template | High-performance Integrated Virtual Environment | We have developed a proof-of-concept gut microbiome monitoring system using a sequencing and analysis pipeline implemented during our previous I-Corps award (see below) | We have collected from the individuals enrolled in our study the following: three separate fecal samples for metagenomic sequencing, anthropometric measurements, a diet history questionnaire, gastrointestinal symptoms questionnaires, perceived stress questionnaires, physical activity questionnaires, and sleep questionnaires | We would like to thank the following individuals for their significant work in curation and annotation of the GFKB:
Software for association analysis that searches for genetic variations influencing a group of correlated traits.
Automatic segmentation of COVID-19 lung infection regions using CT images based on boundary features.
Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived.
Web tool that can be used to Analysis the functional similarity of genes in the forms of “two genes”, “two gene groups “, and “pairwise gene groups” based on GO Annotation(GOA) and GO semantic similarity measurements.
R package for modular visualisation of anatograms and tissues based on ggplot2.
LncRNA-disease association prediction method based on graph-level graph attention network
The GGB (Gaggle Genome Browser) is an open source software tool for visualizing high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential use-cases. The genome browser is designed to gracefully handle large datasets, allow easy import of user data, and interoperate with other bioinformatics tools through the Gaggle framework.
Infrastructure for genetics of gene expression package GGtools.
The package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, those often asked of high throughput genomics data. All core BioConductor appropriate data structures are supported. The package supports detailed views of genomic regions and genome-wide overviews. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.
R package to visualize and annotate genome coverage for various NGS data.
With the dedicated fority method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. This wrapper and some customized layers also make it easy to add gates and population statistics to the plot.
Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data.
A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events.
Intuitive method to detect consistently and coherently enriched gene sets, based on prior knowledge derived from directed gene regulatory networks.
gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.
A Web Server for GPCR-GPCR Interaction Pair Prediction.
Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models. Variable Selection in Linear Mixed Models for SNP Data.
Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.
An R Package for the extraction and visualization of motifs from MEME software.
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on.
Central tool of the g:Profiler web server. It maps a user provided gene list to various sources of functional information and determines significantly enriched pathways, processes and other annotations.
R package for PICRUSt2 predicted functional profile analysis and visualization.
Plotting system for R, based on the grammar of graphics.
colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures
Google-like, ultrafast search engine for genes and transcripts. Users input gene names, IDs, gene descriptions, annotations or sequence and are returned relevant RefSeq transcripts.
An R package for pedigree and genetic groups data. Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>).
Command-line tool for the visualization of splicing events across multiple samples
R. Guigó Lab: Computational Biology of RNA processing @ CRG, Barcelona.
Find an optimal global alignment using the Needleman-Wunsch algorithm.
A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos.
Software and data for analyses in genetics of gene expression and/or DNA methylation.
An R package for the visualization and interpretation of transcript isoforms using ggplot2.
Extend the 'ggplot2' plotting system which implemented the grammar of graphics. It is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.
Compact visualization of richly annotated phylogenetic data. plotting-tree-with-data-using-ggtreeExtra.
GGVD is a goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions.
An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram.
A Shiny app for customizable visualization of differential expression datasets.
R package was designed to call haplotypes from phased marker data.
An R package for identifying adaptive polygenic traits. Quantifying Evolution and Selection on Complex Traits. Functions are provided for quantifying evolution and selection on complex traits.
Ghemical is a molecular modeling and editing package for GNOME. It integrates a molecular mechanics force field as well as integration with MOPAC and optionally the MPQC package for quantum mechanical calculations. It integrates Open Babel to import/export to a variety of external programs.
Multi-Receptive Lightweight Residual Modules for Hyperspectral Classification. Pytorch implementation for "GhoMR : Multi-Receptive Lightweight Residual Modules for Hyperspectral Classification ".
Software package for global biological network alignment. It computes alignments based on a novel spectral signature for comparing the topological similarity of nodes across networks.
An efficient signal processing and spectral analysis toolbox for large data.
GhostKOALA (KEGG Orthology And Links Annotation) is another service for annotating metagenomes and understanding ecosystems.
Homology search tool which can detect remote homologues like BLAST and is about 200 times more efficient than BLAST by using database subsequence clustering. GHOSTZ outputs search results in the format similar to BLAST-tabular format.
The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).
GIANA is for fast alignment of up to 10^7 TCR hypervariable CDR3 sequences. GIANA applies a mathematical framework to perform isometric encoding of amino acid sequences.
Open-source software for automated analysis of 3D microscopy images. Giani is a FIJI plugin for the routine analysis of 3D cell biology image data. Implemented specifically with batch-processing in mind, GIANI is designed to:. General Image Analysis of Nuclei-containing Images.
Pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.
Genomic-scale datasets for the eukaryotic pathogen Giardia.
Tools required for Galaxy Image Analysis
Finds motifs and the optimum width via Gibbs sampling.
Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).
Simultaneous alignment and clustering of peptide data. It takes as input a set of peptide sequences and clusters them into meaningful groups. It returns the optimal number of clusters it identified, together with the sequence alignment and sequence motif characterizing each cluster.
Software for Estimating Variance Components and Predicting Breeding Values for Ranking Traits Based on a Thurstonian Model. Breeding evaluation and variance component estimation of ranking traits.
Implemented by GIBI230, this tool is a Docker-based software designed for extracting radiomic features from 3D medical images in NIfTI format using the PyRadiomics library (if DICOM images, the DICOM to NIFTI converter must be run before using this tool). It streamlines the radiomics calculation process by generating a structured CSV file containing all extracted variables from medical images. The dockerized software enables users to configure parameters like filters, bin width, resampling spacing, and normalization settings can be specified. The output radiomic variables provide quantitative information for further analysis in medical imaging research and machine learning applications. Specially important the parameter selection of the band width. For robust and reproducible results, a bin width of 5 is commonly recommended, but it should be adjusted based on image resolution, modality, and noise levels.
Radiomic features extraction (EUCAIM-SW-055_T-02-01-003)
An iterative algorithm that improves the proximity matrix (PM) from a random forest (RF) and the resulting clusters as measured by the silhouette score.
Software that is used to detect genomic islands in prokaryotic genomes. It collects prokaryotic genome data from public websites based on users’ specification, analyzes genome features using multiple sources, including embedded third-party software Alien_hunter and REPuter, and predict genomic islands based on our trained models, which are decision-tree based ensemble classifiers.
Prediction of drug-target interactions based on global molecular and intermolecular interaction representation learning.
Gifi Array Analyzer is a Java application for integrated analysis of DNA microarray data and gene functional classification data.Gifi Array Analyzer implements Homals (Homogeneity Analysis by means of Alternating Least Square). Homogeneity analysis is a graphical, multivariate statistical method.
C++ package to infer the chemogenomic features from drug-target interactions.
General Image Fiber Tool (GIFT) is an ImageJ macro tool which allows the users to measure the average diameter of electrospun fibers in scanning electron microscopy (SEM) images.
R package to access the global inventory of floras and traits.
Multi-Omics and High-Spatial-Resolution Omics: Deciphering Complexity in Neurological Disorders
gigaScience-Multi-Omics and High-Spatial-Resolution Omics
A genomic interval searching strategy that provides users with the ability to conduct large-scale comparisons of their results with thousands of reference data sets and genome annotations in seconds. It enables the identification of novel and unexpected relationships among local data sets as well as the vast amount of publicly available genomics data.
A C++ program to detect Mendelian consistent genotyping errors of dense markers in pedigree data.
GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment.
Python package for designing custom indexing primers.
Gilda is a Python package and REST service that grounds (i.e., finds appropriate identifiers in namespaces for) named entities in biomedical text.
Stochastic simulation platform for visualization and estimation of transcriptional kinetics.
Simulate discrete stochastic models of chemical reaction networks.
Gillespie Stochastic Simulation Algorithm
GILoop is a deep learning model for detecting CTCF-mediated loops on Hi-C contact maps.
Host genetic and immune factors shaping human microbiota. Host Genetic & Immune Factors Shaping Human Microbita.
Open source and high-performance biomedical name recognition.
GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.
gimp-image-annotator or GIÀ, a lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using the powerful GIMP selection toolbox.
GiNA is an open-source software which is a simple tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds for horticultural phenotyping.
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases.
Integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level.
Detecting Rare Cell Types from Single-Cell Gene Expression Data with Gini Index.
Clustering algorithm for the simultaneous detection of common and rare cell types from single-cell gene expression data.
A measure for quantifying noise in single-cell Hi-C data. SUMMARY:Single-cell Hi-C (scHi-C) allows the study of cell-to-cell variability in chromatin structure and dynamics. However, the high level of noise inherent in current scHi-C protocols necessitates careful assessment of data quality before biological conclusions can be drawn.
User-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs).
Agent-based forward-time simulation to produce gene genealogies and incidence (occurrence) data for multiple populations of multiple species in a spatially-explicit and environmentally-heterogenous framework.
ginmappeR is an R package designed to translate gene and protein identifiers between various biological databases, streamlining data integration for biological workflows.
GInPipe (Genome-based Incidence Estimation Pipeline) is a tool for rapid incidence estimation from SARS-CoV-2 genomes.
Computer tool for the modeling and simulation of genetic regulatory networks.
Giotto is a toolbox for integrative analysis and visualization of spatial expression data.
An open-source computational pipeline for mapping genomic instability from protists to cancer cells.
Geant4 interface for particle physics experiments applied to Radioactive Particle Tracking.
Software which considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations.
This package deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.
A data management platform for the web, developed by Kitware.
Method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
Allows users to analyze protein structure families according to the SCOP classification scheme. Users can upload their own protein structures for pair-wise protein structure comparison, structure alignment or symmetry analysis.
GISAID is a global science initiative and data resource for influenza viruses and other emerging pathogens. It facilitates the rapid sharing of viral genome sequence data and related information to support global surveillance and research.
Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA).
It is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile.
Pplatform for scientific users to predict GIs (Genomic Islands ). This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction.
Solvation Free Energy as a Measure of Hydrophobicity. For a standard cpptraj installation, a shell script and a patch file has been supplied.
A framework for analysis and visualization of multidimensional genomic data using interactive heat-maps.
Display the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs.
Open source programming library that allows anyone without much programming experience to build custom genome browser websites or apps. With a few lines of codes, one can set up GIVE service on a local machine, manage custom data and build an interactive genome browser.
An R package for generalized joint location and scale analysis in X-inclusive genome-wide association studies.
Gk-arrays are a data structure to index the k-mers in a collection of reads.
glactools: A set of programs for the management of allele counts and genotype likelihoods
Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.
Mixed-membership classification model that simultaneously learns a sparse biomarker signature for each subtype as well as a distribution over subtypes for each sample.
Web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of novel, transgenic pathways.
Grow lineages along minimum spanning tree for b cell receptor sequencing data. This algorithm is developed to reconstruct lineage tree from subset of tree nodes. Grow Lineages along Minimum Spanning Tree for B Cell Recptor Seqeuence Data. GLaMST can be downloaded from https://github.com/xysheep/GLaMST/releases.
Whole Genome Based LAMP Primer Design for a Set of Target Genomes. This is a customizable LAMP primer sets designing system: GLAPD (whole genome based LAMP primer design for a set of target genomes).
GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes
fMRIPrep is a pipeline for preprocessing resting-state fMRI data, designed for robust and reproducible analysis. It provides a standardized workflow, incorporating steps like anatomical segmentation, motion correction, and spatial smoothing.
Open-source software for viewing and analyzing data from the Tobii Pro Glasses 2 eye tracker. This matlab utility can parse recording files from the Tobii Glasses 2 as stored on the SD card (no need for intervening Tobii software). Once parsed, it will display this data in a MATLAB GUI. Optional eye videos are also supported. In this GUI, sync events can be shown, and data can be optionally annotated (e.g. as slow and fast phase intervals) by hand or by a classifier algorithm, or such annotations can be loaded from file.
GLobal Automated sRNA Search go, combines iterative BLAST searches, pairwise identity filtering, and structure based clustering in an automated prediction pipeline to find sRNA homologs from scratch. The web server provides predefined parameter sets for a non-expert usage as well as enables a manual setup of the query parameters. The returned GLASSgo result is in FASTA format, whereby the first entry represents the input sequence.
A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma.
A deep-learning algorithm for the diagnosis of primary open-angle glaucoma from fundus photographs.
GLDADec is an open-source Python package that performs bulk gene expression deconvolution using a guided latent Dirichlet allocation (LDA) modeling approach, leveraging cell type-specific marker genes to estimate topic distributions for each sample.
GLEANER is a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. GLEANER provides a comprehensive collection of the transcriptome, DNA methylome, chromatin accessibility, and H3K4me3, H3K27me3, and H3K9me3 histone modification characteristics in human and mouse germline cycles.
Combining local methods and diffusion state embeddings to predict missing interactions in biological networks. MOTIVATION:One of the core problems in the analysis of biological networks is the link prediction problem. In particular, existing interactions networks are noisy and incomplete snapshots of the true network, with many true links missing because those interactions have not yet been experimentally observed. Methods to predict missing links have been more extensively studied for social than for biological networks; it was recently argued that there is some special structure in protein-protein interaction (PPI) network data that might mean that alternate methods may outperform the best methods for social networks. Based on a generalization of the diffusion state distance, we design a new embedding-based link prediction method called global and local integrated diffusion embedding (GLIDE)
GLIDER, a method that replaces a protein-protein interaction or association network with a new graph-based similarity network.
Generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.
System for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. It uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
A new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons.
Glimmer-MG is a system for finding genes in environmental shotgun DNA sequences. Glimmer-MG (Gene Locator and Interpolated Markov ModelER - MetaGenomics) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Licensed under Artistic License.
GLIMPSE2 is a set of tools that allow fast whole-genome imputation and phasing of low-coverage sequencing data.
User-friendly toolset for the analysis of high-throughput DNA-methylation array data.
Database for visualization of molecular profiles to improve prognosis of brain cancer.
An integrated database for knowledge exploration of diagnostic biomarkers in gliomas.
A comprehensive web-based tool to access and analyze glia secretome data. Gliome Database has the following feature regarding glia-secreted proteins.
Glittr is a web application that helps you find and compare bioinformatics training material on GitHub and GitLab.
Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data. Fit Gamma-Poisson Generalized Linear Models Reliably. The core design aims of glmGamPoi are:.
R package for variable selection and predictive modeling of structured genomic data.
GLMsingle is a toolbox for obtaining accurate single-trial estimates in fMRI time-series data. We provide both MATLAB and Python implementations.
Holistic glomerular detection, segmentation, and lesion characterization with large-scale web image mining.
It is a global entry point to information and knowledge for strengthening the capacity for PGRFA conservation, management and utilization. The site is managed by the FAO Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). It provides access to accessions of ex situ and in situ plant material available in decentralized collections through the use of DOIs assigned to plant material.
Global Information System on Plant Genetic Resources for Food and Agriculture (GLIS)
The GlobalAMFungi Database is an open-access, global repository of arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput sequencing studies. It aggregates millions of DNA sequence observations of AM fungi from thousands of geographically referenced environmental samples, together with rich metadata on sampling location and environmental context, to map the global distribution and diversity of these key plant symbionts. The resource is designed to be community-driven and FAIR (Findable, Accessible, Interoperable, Reusable), supporting research into AM fungal ecology, biogeography, and how environmental factors shape their diversity.
We give the following arguments in support this approach: After normalization, gene-expression-data appears symmetrical and outliers are no problem, least squares should be robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals can’t be expected. Application of ordinary least squares gives unbiased, no longer optimal estimates.
User interface to data from high-throughput sequencing studies of fungal communities across terrestrial biomes. Includes sequencing data, sample locations, sample metadata.
Learning Globally Optimal Dynamic Bayesian Network with the Mutual Information Test (MIT) Criterion
The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size.
Tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
A dereplicated set of species representative microbial genomes. The genomic era offers great opportunities for microbial genome analyses, and individual (meta)genome studies can generate thousands of microbial genomes. Although the International Nucleotide Sequence Database Collaboration (INSDC) databases are available to store these datasets, depositing assembled and binned metagenome assembled genomes (MAGs) to INSDC databases doesn't always happen. The GlobDB aims to integrate 14 genome resources that are currently not (yet) consolidated otherwise. The GTDB species representatives are the base of the GlobDB, and the other 13 datasets extend upon this. The GlobDB follows the annual GTDB release schedule. The GlobDB release 226 contains more than double the number of species-representative genomes (306 260) compared to the GTDB release 226 species representative set (143 614).
Identify, date and describe admixture events occurring in the ancestral history of a given target population within the last ~4,500 years.
Plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.
Allows the user to plot the tendency within the query protein for order/globularity and disorder.
Performs intrinsic protein disorder, domain and globularity prediction.
A method for using covariates to improve power in GWAS with related individuals
Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. New E-Resource for Drug Discovery. Regioselectivity prediction for phase 1 and phase 2 metabolism.
GloScope is a Bioconductor package for visualizing and summarizing single-cell RNA sequencing (scRNA-Seq) data at the population scale. It allows for the estimation of sample distributions, calculation of statistical divergence, and visualization of distance matrices using MDS plots.
Prioritization of gene diseases candidates by disease-aware evaluation of heterogeneous evidence networks
Open-Source Sensing Platform to Monitor the Dynamic Responses of Plants. Open-source release of code and PCB-design files of the Gloxinia platform. If you use this code for a scientific publication, please consider citing our paper Gloxinia—An Open-Source Sensing Platform to Monitor the Dynamic Responses of Plants.
Simple and effective approach to improve the accuracy of multiple sequence alignment.
A software package for analysing continuously measured glucose levels in epidemiology. GLU: A tool for analysing continuously measured glucose in epidemiology. GLU is described in the paper: L.A.C. Millard et al. GLU: A tool for analysing continuously measured glucose in epidemiology, bioRxiv, 2018. GLU is a tool for analysing continuous glucose monitoring (CGM) data in epidemiology.
Gluclas (GLUcose CLamp ASsistant) is a free software for suggesting glucose infusion rate adjustments during manual glucose clamp experiments.
A comprehensive, curated resource of glucokinase modulators for clinical and molecular research.
Graph-linked unified embedding for single-cell multi-omics data integration.
A database for improving the rational design of glucose-tolerant β-glucosidases. A database of mutant β-glucosidases. Glutantbase is a database, webtool and method to evaluate mutations for β-glucosidases proteins used in industrial applications. Glutantbase shows information of multiplie alignment generated with clustal-omega, structure modeled by homology, catalytic pocket location, catalytic residues, secondary structure, and extrapoled mutations for +3500 GH1 β-glucosidases sequences extracted from UniProt.
Identification of glycan branching patterns using multistage mass spectrometry with spectra tree analysis.
Identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported.
Automated Glycan Annotation and Quantification Using Glucose Unit Index.
Calculate the mass of an oligosaccharide structure.
A tool to quantify glycan shielding of glycosylated proteins.
Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.
A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases.
Glycoconjugate Ontology (GlycoCoO) is a standard ontology for glycoconjugate data (glycoprotein/glycolipid structures, publication information, biological source information, experimental data).
Tool that simulates the action of these exoglycosidases on released oligosaccharides. It assists glycobiologists in designing enzyme mixtures that can be used to guide the precise determination of glycan structures.
A GlycoEnzyme Pathway and Molecular Function Ontology..
GlycoEP is a new webserver for more accurate prediction of N-linked, O-linked and C-linked glycosites in eukaryotic glycoproteins using two larger datasets, namely, standard and advanced datasets.
Tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.
Welcome to the GlycoGlyph Introduction Tutorial. A glycan visualizing, drawing and naming application.
An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans.
A visualization tool for gene expression data onto glycan-related pathways.
A novel glycoconjugate data repository that bridges glycomics and proteomics.
Integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank. The database is a unified resource for carbohydrate structures. It retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases.
Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
Platform for gathering, monitoring, integrating and visualizing glycomics data.
GlyConnect Compozitor is a glycan composition visualising and comparative tool associated with the GlyConnect database.
A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.
Web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics (CFG).
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Loading GlycoPOST Application.
GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s), where N-glycosite is an Asn residue and O-glycosite could be a serine or threonine residue having a glycan attached covalently and enzymatically at amide or hydroxyl group respectively.
Takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.
Selectively align amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.
Integration efforts between GlyCosmos and PubChem.
Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG).
glycoworkis a Python package for glycan data science and machine learning.
Algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans.
Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.
A webserver for predicting glycosylation sites on small RNAs.
Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES.
GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.
Web interface to upload, visualize and interactively compare glycan expression profiles. The tool can process N- or O-linked glycan expression data.
An automated workflow for quantitative N- and O-linked glycoproteomic data analysis. A automated script for processing and combining Byonic and PD standard output. Pythons 3.4+ with the following packages installed. The program can be run from the location of the script using python main.py. The following parameters can be used for operating the script within the commandline.
Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.
GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBind or GlycomeDB.
The international glycan repository GlyTouCan version 3.0. GlyTouCan is the international glycan structure repository. This repository is a freely available, uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s). Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered as long as there are no inconsistencies in the structure.
GM-Pep is an integrated approach contained two parts, one is multi-class generator (CVAE model) which was responsibility for generating potential drug-like peptides, the other is multi-classifier (Deep-Multiclassifier) which predicted bioactivity probability of generated peptides by CVAE model.
Prediction of cancer driver genes based on gene-miRNA regulatory network with graph convolutional model
A parameter-space mapping strategy for force-field calibration.
Genomic Mapping and Alignment Program for mRNA and EST Sequences.
A database genome index for GMAP and GSNAP.
Create a map store for known genes or SNPs.
GSNAP and GMAP are a pair of tools to align short-read data. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.
Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrates SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features.
GMATo is a novel soft for faster and accurate microsatellite mining at any length and comprehensive statistical analysis for DNA sequences in any genome at any size, with easily customized parameters control for biologists and bio-informatician, running easily at common computers with Windows, Linux, MAC OS etc multiple platforms (platform independently) with both graphic and command interface programmed in Java and Perl computing language.
Fill and close the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
gMCSpy is a Python package designed to efficiently calculate genetic Minimal Cut Sets (gMCSs) in genome-scale metabolic models (GEMs), utilizing both commercial and open-source optimization solvers. It outperforms previous tools and offers improvements in accuracy and computation time.
Database which facilitates the search and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS).
Package for non-parametric distance measurement between two discrete frequency distributions.
Nonparametric and genetic model-free alternative to linear or logistic regression for detecting and characterizing nonlinear interactions among discrete genetic and environmental attributes. Compared with the MDR method, this method permits adjustment for discrete and quantitative covariates and is applicable to both dichotomous and continuous phenotypes in different population-based study designs. It will increase the precision accuracy and help users draw a more meaningful conclusion.
An R Package to Apply Embedding Techniques to Microbiome Data.
High-throughput Analysis of Biomolecular Data using Graph-based Multiple Hierarchical Consensus Clustering.
A shiny application for the identification of gene-targeted drugs for precision medicine. This is the offical repository of GMIEC-shiny. GMIEC is a shiny application to integrate multi-omics data. GMIEC is a new user-friendly and flexible application that allows to integrate gene-expression, copy-number variation, methylation, Chromatin Immuno-Precipitation followed by sequencing (ChIP-seq) data, and mutations at the level of single patient. More interestingly, GMIEC facilitates the identification of groups of genes, that presents genomic alterations (e.g. copy number alterations).This can be a support help the researchers, to identify the de-regulated genes in a given disease, but also to identify discover novel pharmacological target molecules.
Gaussian Mixture Model (GMM) detects copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage).
Comprehensive database of human gut microbial metabolite associations with diseases.
G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.
GMPEsi: Generalized Model for Predicting Efficacy of siRNAs
Next-generation query language for querying NGS data.
GMQN is a reference based method that removes unwanted technical variations at signal intensity level between samples for 450K and 850K DNA methylation array. It can also easily combined with Subset-quantile Within Array Normalization(SWAN) or Beta-Mixture Quantile (BMIQ) Normalisation to remove probe design bias.
Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.
Mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments.
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. GMSCA: Gene Multifunctionality in Secondary Co-expression Analysis.
GWAS-based marker selection tool for genomic prediction from genomic data. GWAS-based Marker Selection Tool for Genomic Prediction from Genomic Data (for continuous phenotype). GMStool is a tool of selecting an optimal marker-set for predicting a continuous phenotype.
The pipeline runs PRODIGAL gene predictions on all genomes, runs pan-reciprocal BLAST, and identifies ortholog sets. For a set of orthologous genes, if the positions of the PRODIGAL selected starts coincide in a multiple sequence alignment, they are accepted. If they do not coincide, a consistent start position is sought where a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes.
A user-friendly browser application for assessing health through metagenomic gut microbiome profiling.
GMWI2 is a command-line tool that predicts health status from gut microbiome taxonomic profiles using a Lasso-penalized logistic regression model. It incorporates quality control, taxonomic profiling with MetaPhlAn3, and transformation into a binary presence/absence profile, and is freely available as an open-source resource.
A New Tool to Perform End-State Free Energy Calculations with GROMACS.
An automated protein/protein-ligand complex simulation workflow bridged to MM/PBSA, based on Gromacs and Zenity-dependent GUI for beginners in MD simulation study.
A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
Computer tool for the qualitative modeling and simulation of genetic regulatory networks. It assists you in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Moreover, it allows you to simulate the qualitative behavior of the network in response to external perturbations.
Open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks.
Software package intended primarily for the processing of multicomponent high resolution NMR datasets such as those acquired in diffusion, relaxation and kinetic experiments.
Java-based software tool for analyzing gene networks coherence using direct and indirect relationships.
An R package for constructing gene regulatory networks from transcriptomic data. Gene regulatory network modeling tool (GNET2). GNET2 has been developed and used by the Bioinformatics, Data Mining and Machine Learning Laboratory (BDM) . Help from every community member is very valuable to make the package better for everyone. Checkout the Lab Page.
Global Nutrition and Health Atlas (GNHA).
GNIAP is a R package for gene co-expression network inference and assessment. Can be either GPL-3 or MIT license.
Molecular Docking with Deep Learning. gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina.
Inference of gene regulatory networks using pseudo-time series data. GNIPLR (gene networks inference based on projection and lagged regression) is a method for constructing gene regulatory network.
Disease subnetwork detection with explainable Graph Neural Networks.
A Hierarchical and Adaptive Graph Neural Network for Parameter Space Exploration of Unstructured-Mesh Ocean Simulations.
Using Graph Neural Networks for Site-of-Metabolism Prediction and its Applications to Ranking Promiscuous Enzymatic Products.
A graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits.
An efficient scRNA-seq dropout imputation method using graph attention network.
Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences by providing extensible APIs and implementing the glue required for combining feature sets and models for genome-wide prediction.
Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.
Transcript expression-aware annotation improves rare variant interpretation. The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
Interactive whole-genome analysis pipeline to prioritize disease-linked variants, genes, and pathways.
A multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Support: https://gitlab.com/gaspilleura/gnomo/.
gNOMO2 is a comprehensive and modular pipeline for integrated multi-omics analyses of microbiome
An R Shiny app supporting cancer genomics survival analysis with cBioPortal.
GnpIS is an integrative and multi-species information system dedicated to plants, including forest trees. It handles various types of data, focusing on genetic resources and phenomics. It allows researchers from the Plant community to access and cross-reference genetic data (accessions, phenotypes, polymorphisms, markers and QTLs) and genomic data (sequences, physical maps, genome annotations) for species of agronomic and forestry interest. Accessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services. GnpIS is used by the French National Research Institute for Agriculture, Food and Environment (INRAE) and its partners in major national and international projects.
Genetic and Genomic Information System (GnpIS)
GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.
Simulation and statistical inference tool for algebraic or differential equation systems. Other programs have been created to the same end, the Matlab family of graphical interactive programs being some of the more general and easy to use. Still, many available tools are not optimal for performing computer intensive and sophisticated Monte Carlo analyses.
The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.
Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread. Gene Novelty Unit-based Virus IDentification for SARS-CoV-2.
The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the domains. Gene product annotation continues to increase both in the number of total annotations and in species coverage. Tools have seen major improvements in functionality, speed and usage.
a highly controlled workflow to discover gene essentiality in loss-of-function screens. SUMMARY Genome-wide CRISPR screens are an effective discovery tool for genes that underlie diverse cellular mechanisms that can be scored through cell fitness. Loss-of-function screens are particularly challenging compared to gain-of-function because of the limited dynamic range of decreased sgRNA sequence detection. Here we describe G uide- O nly control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, T oolset for the R anked A nalysis of GO- C RISPR S creens (TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer and demonstrate superior performance to standard screening methods ||| HOMEPAGE MISSING! ||| CORRECT NAME OF TOOL COULD ALSO BE 'TRACS'
GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites.
Summary Visualisations of Gene Ontology Terms with GO-Figure!. GO-Figure! offers a simple solution for command-line plotting of informative summary visualisations of lists of GO terms, designed to support exploratory data analyses and multiple dataset comparisons.
GO2MSIG generates collections of gene sets in MSigDB format based on the Gene Ontology (GO) project hierarchy and gene association data, for use with the Gene Set Enrichment Analysis (GSEA) implementation available at the Broad Institute. This enables rapid creation of gene set collections for multiple species.
A shared hub for universal benchmarking of machine learning-based protein functional annotations.
Rapid web-based functional annotation tool for genomic and transcriptomic data.
A tool for finding significant GO terms shared among a list of genes from your organism of choice.
A tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms.
The UniProt GO annotation program aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). The assignment of GO terms to UniProt records is an integral part of UniProt biocuration. UniProt manual and electronic GO annotations are supplemented with manual annotations supplied by external collaborating GO Consortium groups, to ensure a comprehensive GO annotation dataset is supplied to users.
Sorts protein identifications under GOA slim terms.
A set of command line tools to manipulate multiple alignments.
Generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys.
A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life.
Machine learning classification models for fetal skeletal development performance prediction using maternal bone metabolic proteins in goats. Machine Learning for goat bone prediction. Classifiers for Liuyang black goats bone profiles using maternal serum bone metabolism. Datasets and results will be uploaded after the manuscript will be send to a journal
BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.
Next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines.
Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data.
An R package to compare functional enrichment analysis between two species.
Assigning Godel number to sequences, towards the definition of a new dimensional space for comparisons
Web portal for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.
High-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms. GODoc: A High-Throughput Protein Function Prediction using the Novel k-nearest-neighbor and Voting algorithms.
Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.
RNA-Seq-Based Breast Cancer Subtypes Classification Using Machine Learning Approaches. Paper: RNA-Seq-based breast cancer subtype classification using machine learning approaches.
GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool. GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim. The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output. It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.
This package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples.
New algorithm to efficiently identify all the connected gene pairs labeled by the same parent Gene Ontology (GO) terms.
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.
gofasta is a command-line utility developed to handle SARS-CoV-2 alignments, but should be useful more generally for handling consensus genomes of any microbial pathogen. It is used on datasets of millions of sequences, including by the United Kingdom's daily SARS-CoV-2 genome processing pipelines, Pangolin and Civet.
GoFCards is a database and analytic platform for gain-of-function variants in humans, integrating data from literature reviews and predicted variants with a proprietary scoring system. It aims to provide geneticists and clinicians with a convenient resource for understanding and prioritizing genetic variants associated with diseases.
Select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.
It performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages; the GO-graph is included in the package and updated regularly. GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests.
The GO-function package provides a tool to address the redundancy that result from the GO structure or multiple annotation genes and derive biologically relevant functions from the statistically significant functions based on some intuitive assumption and statistical testing.
Performs high-throughput text mining to complement annotation of genes. It supports search for genes in PubMed, EntrezGene and BLAST.
This tool has proven success in virtual screening, lead optimisation, and identifying the correct binding mode of active molecules. It enables to make confident binding mode predictions, and achieve high database enrichments. It reliably identifies the correct binding mode for a large range of test set cases.
GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.
Genomes OnLine Database (GOLD) v.8. GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.
Bioinformatic software provider and analytic service provider.
Goldilocks is a Python package providing functionality for collecting summary statistics, identifying shifts in variation, discovering outlier regions and locating and extracting interesting regions from one or more arbitrary genomes for further analysis, for a user-provided definition of interesting.
Linear time complexity de novo long read genome assembly with GoldRush.
Resource for sharing rare genetic variants detected in bleeding, thrombotic, and platelet disorders.
GOLEM is a web-based application that can be used to display the distribution of regulatory gene motifs within gene sequences in selected plants.
National Centre for Biomolecular Research, Masaryk University, Brno
Slovenian Research Agency (Grants J4-2228, P2-0103)
GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.
National Institute of Biology, Department of Biotechnology and Systems Biology
A tool for biological interpretation of microarray data.
Conduct a hypothesis driven interrogation of their functional genomics datasets.
This webtool performs automatic homology modeling and ligand docking of GPCR receptors. It uses HHsearch package 1.5.1 for performing sequence alignment. Only GPCR templates are chosen to build 3D model of given sequence by using Modeller 9.20. The obtained 3D model can be then docked with ligands uploaded by users with both Autodock VINA or HADDOCK. Binding pockets can be predicted by the FPOCKET, and structural alignment of models needed for VINA docking is performed by LOVOALIGN. This webtool is built by the Applied Bioinformatics Group at the Department of Biotechnology, University of Verona and by the Institute for Computational Biomedicine (INM-9/IAS-5) of the Forschungszentrum Jülich GmbH and RWTH Aachen University.
User-friendly, Windows-based program for estimating effective size (Ne) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age-structure in populations.
A collection of genomics software tools written in Go (golang).
GOntoSimis a method to determine the functional similarity between genes.
Third-party documentation for new users of GO.
The Good Statistical Monitoring (gsm) R package is an open-source tool designed to proactively monitor risks in clinical trials, supporting risk-based quality management. It provides a flexible framework for statistical data monitoring and facilitates the creation of standardized reports and interactive visualizations.
Good Statistical Monitoring (gsm) R package
Detection and reconstruction of muscle fibers from diceCT image data. Includes functions for tracking, smoothing, cleaning, plotting and exporting muscle fibers. Also calculates basic fiber properties (e.g., length and curvature).
Colaboratory, or “Colab” for short, is a product from Google Research. Colab allows anybody to write and execute arbitrary python code through the browser, and is especially well suited to machine learning, data analysis and education.
An R package to interact with the homonimous API.
GoPeaks is a peak caller designed for CUT&TAG/CUT&RUN sequencing data. GoPeaks by default works best with narrow peaks such as H3K4me3 and transcription factors. However, broad epigenetic marks like H3K27Ac/H3K4me1 require different the step, slide, and minwidth parameters. We encourage users to explore the parameters of GoPeaks to analyze their data.
R package for implementation of multilayered visualizations for enhanced graphical representation of functional analysis data.
Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 group.
The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.
Tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.
Interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.
Tool for identifying and visualizing enriched GO terms in ranked lists of genes.
A tool of the g:Profiler web server. It maps a list of genes of interest to homologous genes in another related target organism.
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became an important basis for many bioinformatics analysis approaches. This R package analyzes the semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.
Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis.
Goslin is the Grammar of succinct lipid nomenclature project. It defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. This allows to generate parsers based on the defined grammars, which provide immediate feedback whether a processed lipid shorthand notation string is compliant with a particular grammar, or not.
A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.
Calculating semantic similarities on the Gene Ontology.
Given a Gene Ontology (GO) and an annotation of genes, significance of the over-representation of the genes within the ontological categories is determined by a Fisher's exact test or modeling according to a hypergeometric distribution. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term.
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
Visualizes the GO enrichment results as word clouds and arranges them together with figures of experimental data. This allows us to draw informative summary plots for analyses such as differential expression or clustering, where for each gene list we display its behaviour in the experiment alongside with its GO annotations.
Graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics.
This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.
A program to remove annotation biases from protein function annotation datasets.
method to identify genome-wide off-target effects of genome editing in mouse embryos. Detect off-target variants of genome editing tools. The implement of GOTI-seq requires the following sofwares pre-installed on your systems:.
The GotohScan program is a search tool that finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, ..)by computing all semi-global alignments. Thus, the query sequence is never truncated or split into subsequences, but always mapped to the database over its complete length. The alignment is computed via the Gotoh-alignment algorithm using affine gap costs.
Wraper functions for description/comparison of oligo ID list using Gene Ontology database.
Gotree is a set of command line tools to manipulate phylogenetic trees.
Genome optimization via virtual simulation to accelerate maize hybrid breeding.
Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies
Information Management System for CryoEM Experiments. gP2S (for Genentech’s Protein to Structure) is a user-friendly web-based laboratory information management system (LIMS) that facilitates accurate record-keeping for cryo-EM labs and multi-user, multi-project facilities.
An integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting. Gram-Positive Protein Prediction Pipeline. GP4 - Gram Positive Protein Prediction Pipeline.
Rendering glycans and annotating glycopeptide mass spectra. Find information on common issues. Ask questions and find answers from other users. gpAnnotate: A program for the detailed annotation of MS/MS glycoproteomics spectra using DrawGlycan-SNFG sketches. The Glycopeptide Spectrum Annotation program ( gpAnnotate ) is designed to annotate individual glycoproteomics MS/MS spectrum for several established mass spectrometry fragmentation modes:
Statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data.
Statistical Approach for Functional-Annotation-Tree-Guided Prioritization of GWAS Results.
Efficient merging of genome profile alignments | André Hennig authored Jul 17, 2019
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR. GPAR Genetic Profile-Activity Relationship. GPAR provides drug repurposing and MOAs prediction services. Using gene expression profile data and Deep Learning, to build models, to make predictions.
Human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.
GPCards is an integrated database of genotype-phenotype correlations in human genetic diseases.
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments. GPcounts is Gaussian process regression package for counts data with negative binomial and zero-inflated negative binomial likelihoods described in the paper "Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments". It is implemented using the GPflow library.
2-layer predictor: the 1st layer prediction engine is for identifying a query protein sequence as GPCR on non-GPCR; if it is a GPCR protein, the process will be automatically continued with the 2nd-layer prediction engine to further identify its type among the following six main functional classes: (1) rhodopsin-like, (2) secretin-like, (3) metabotrophic/glutamate/pheromone, (4) fungal pheromone, (5) cAMP receptor, and (6) Frizzled/Smoothemed family
GPCR-EXP is a database that specializes in curating experimental and predicted structures of G protein-coupled receptors (GPCR). Structure-related data for experimental structures, such as resolution, publication information, and biological ligand, from the Protein Databank (PDB) are extracted and incorporated into the database. Additionally, all GPCRs from the human genome have been modelled using GPCR-I-TASSER and have been included. Easy-to-read tables have been constructed to faciliate the browsing of: 1. Experimental PDB Structures 2. Predicted GPCR Structures and Functions for Human Genome Furthermore, database statistics can be accessed to provide a glimpse into the current state of GPCR structural biology, while all PDB structures and data are freely available for download.
Experimentally-Solved and Predicted GPCR Structures (GPCR-EXP)
Centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs).
A database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors. To analyze the sequence either upload a file with the sequences in FASTA format, or copy and paste the sequence(s) inside the text area below.
The G Protein-Coupled Receptors-Sequence Analysis and Statistics (GPCR-SAS) web application provides a set of tools to perform comparative analysis of sequence positions between receptors, based on a curated structural-informed multiple sequence alignment. The analysis tools include: (i) percentage of occurrence of an amino acid or motif and entropy at a position or range of positions, (ii) covariance of two positions, (iii) correlation between two amino acids in two positions (or two sequence motifs in two ranges of positions), and (iv) snake-plot representation for a specific receptor or for the consensus sequence of a group of selected receptors. The analysis of conservation of residues and motifs across transmembrane (TM) segments may guide the design of more selective ligands or help to rationalize activation mechanisms, among others. As an example, here we analyze the amino acids of the "transmission switch", that initiates receptor activation following ligand binding.
GPCR-Sequence-Structure-Feature-Extractor (SSFE). Provides template suggestions and homology models of Class A GPCRs. Identifies key sequence and structural motifs in Class A GPCRs to guide template selection and build homology models.
dysregulation of GPCR ligand signaling systems in cancer genomics database
GPCR target/ off-target/ site effect prediction using a docking approach, included body distribution database
BLAST search of against GPCR domains stored in GPCR SARfari.
Search against small molecules stored in GPCR SARfari database.
GPCRana allows the quantitative conformational analysis of GPCR structures
Allows the user to upload a GPCR sequence, choose a ligand in a library and obtain the 3D structure of the free receptor and ligand-receptor complex.
GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs). GPCRdb curates sequence alignments, structures and receptor mutations from literature. Interactive diagrams visualise receptor residues (e.g. snakeplot and helix box plot) and relationships (e.g phylogenetic trees).
A hidden Markov model for GPCR detection.
Predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools: profile-profile alignment, multiple structural templates, and Z coordinate-based filtering of resulting models. Two distinct loop modeling techniques are employed - Modeller and Rosetta - and the BCL::Score (membrane-fitted knowledge-based energy function) is used to score the final ranking list of GPCR models.
Tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.
GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases.
Tool for predicting amine-binding receptors based on a protein sequence provided by the user.
GPCRsignal: web server for analysis of the interface between G protein-coupled receptors and their effector proteins by dynamics and mutations.
Machine learning based webtool for predicting the activity of compounds and their interactions with G protein-coupled receptors (GPCRs).
GPDBN is a deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction.
GPEdit systematically investigated the impact of genetic variants and pharmacogenomics landscape of RNA editing event across multiple cancer types.
GPUFRAGFOLD is a CUDA ACELERATED Protein Structure Prediction Tool.
GPHMM (Global Parameter Hidden Markov Model) is a novel statistical method dedicated to identify copy number alteration and loss of heterozygosity (LOH) in tumor samples using whole genome SNP arrays.
Genomic and Proteomic Knowledge Base (GPKB), based on the Genomic and Proteomic Data Warehouse (GPDW), is an integrative database of annotation data from several sources.
The app is used for PKPD Modeling and Simulation.
gPLINKis a Java program that provides a simple form interface to the more commonly-usedPLINKcommands (i.e. instead of using the command line options).gPLINKprovides menus and dialogs to create validPLINKcommands, executes them, keeps a record of all commands run in a project, keeps track of input and output files, allows annotation of result files and facilitates integration withHaploview.
Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.
Genome Puzzle Master (GPM) enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules.
This tool was primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.
GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest.
A REST API used to access mass spectrometry-based experimental proteomics data and information stored in GPMDB.
GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.
Integrated system for identifying promoter regions and annotating regulatory features in user-input sequences.
Toolkit for GPMsDB-tk to modify its database with user-provided bacterial and archaeal genomes/metagenome-assembled genomes (MAGs)
Toolkit for the genomically predicted protein mass database (GPMsDB) and for assigning taxonomic identification of bacteria and archaea from MALDI-TOF mass spectra.
Web server for comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. General Parsimony Phylogeny models from Frequencies. gppf [-h] -m {perfect,persistent,dollo,caminsokal} -f FILE [-k K] -t TIME -c CLONES [-e]. To reproduce experiments described in the paper the following are also required:. ./gppf -m dollo -f data/simulated/n10_m20/21.sim -t 300 -c 1 -k 4 -e starts a Dollo(4) model with a time limit of 300 seconds (5 minutes), with a clone limit of 100% and with a experimental-format output.
An ILP-based approach for inferring cancer progression with mutation losses from single cell data. Running the entire gpps pipeline. We provide gpps, that can be used to infer cancer progressions from single cell data. Differently from the previous tool. gpps employs a maximum likelihood search to find the best tree that explain the input, starting from single cell data.
A webserver for quantitative analysis of GPCR structures and comparison of residue-residue contact scores (RRCS) between two structures, activation pathway analysis, ligand-receptor interaction analysis and RRCS analysis between transmembrane helices.
An improved machine learning-based model for predicting internal m7G modifications using sequence properties. An improved machine-learning based prediction tool for identifying RNA m7G modifications. m7Gpredictor was implemented in python 2.7.
The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance.
GPrimer is a fast GPU-based pipeline for primerdesign for qPCR experiments.
Generative AI-empowered toolkit for promoter design.
gProfileR performs functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the 'g:Profiler' toolkit. The tool performs statistical enrichment analysis to find over-representation of information like Gene Ontology terms, biological pathways, regulatory DNA elements, human disease gene annotations, and protein-protein interaction networks. The basic input is a list of genes.
Public web server with several tools to perform functional enrichment analyses and mine additional information about gene functions. The used data is synchronized with Ensembl database in quarterly updates.
Institute of Computer Science, University of Tartu
Tool providing comprehensive information about G proteins.
Detection of distinct Galpha families, Gbeta and Ggamma subunits of heterotrimeric G-proteins using profile Hidden Markov Models (pHMMs).
GPRuler (metabolic Gene-Protein-Reaction rules automatic reconstruction) is an open-source tool to automate the reconstruction process of gene-protein-reaction (GPR) rules for any living organism, which describe with a Boolean logic relationships between the gene products (e.g., enzyme isoforms or subunits) associated with the catalysis of a given reaction.
High spatial resolution peak detection algorithm for ChIP-seq data.
A deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. A Graphic Presentation System for Palmitoylation Site Prediction. Kinase-specific Phosphorylation Site Prediction.
GPS-SUMO (small ubiquitin-like modifiers) is a tool for the prediction of sumoylation sites and SUMO-interaction motifs in proteins.
Hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites.
A Python library for building spatial data and extracting spatial measures from raw GPS data.
A comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.
Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.
Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum mycotoxinivorans. Genome-scaled Prediction of Substrate-specific Enzymes The workflow:. Before run GPSE to a genome or a dataset of sequences, users should carefully modify the GPSEcfg.py file and change every path according to the system!.
Analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons
An R Package for Comparing Genomic-binding Profile Similarity among Transcriptional Regulators using Customizable Databases.
The genetic and pharmacogenomic landscape of snoRNAs in human cancer. G enetic and p harmacogenomic landscape of sno RNAs in cancer. GPSno systematically investigated the impact of genetic variants and pharmacogenomics landscape of snoRNAs in multiple cancer types by using thousands of data from The Cancer Genome Atlas (TCGA).
GPSR 1.0: This package developed mainly for UNIX machines. It can be downloaded from webs.iiitd.edu.in/raghava/gpsr/
High-throughput profiling experiments based on for example microarrays or proteomics yield genes potentially important for a given biological process.
GPTCelltype is an R software package developed to automate cell type annotation in single-cell RNA sequencing analysis using the GPT-4 large language model. It leverages marker gene information to accurately annotate cell types and reduce manual effort.
GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads.
The GPU-based implementation of the CASSERT algorithm for protein 3D structure similarity searching. The algorithm is based on the two-phase alignment of protein structures when matching fragments of compared proteins.
GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads. This repository contains a GPU implementation of Darwin [1][2], a hardware-friendly DNA aligner. It consists of two parts: D-SOFT and GACT, which represent typical seed-and-extend methods. D-SOFT (Diagonal-band based Seed Overlapping based Filtration Technique) filters the search space by counting non-overlapping bases in matching Kmers in a band of diagonals. GACT (Genomic Alignment using Constant Tracebackmemory) can align reads of arbitrary length using constant memory for the compute-intensive step. This implementation can be used to run on CPU only, or use the GPU-accelerated version. For more choices between individual optimizations, go back to commit e472745e.
An open-source, docker-based, and GPU-enabled jupyterlab notebook has been developed that can run on any compute infrastructure for rapid prototyping and developing end-to-end AI projects. In addition, with such a notebook, long-running AI model training programs can be executed remotely. Other features include GPU support for faster training, git integration for version control, the option of creating and executing pipelines of notebooks, and the availability of multiple dashboards for monitoring compute resources.
GPU-enabled docker container with Jupyterlab for AI
A GPU accelerated I-TASSER protein structure prediction tool.
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction.
Modified version of MrBayes that enables running Metropolis coupled Markov chain Monte Carlo (MC)^3 sampling on a Graphics Processing Unit (GPU).
A GPU-accelerated CUDA implementation of the Levenberg-Marquardt algorithm. It was developed to meet the need for a high performance, general- purpose nonlinear curve fitting software library which is publicly available and open source.
GPU-accelerated ultra-fast and energy-efficient motif analysis program.
Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.
The Ghent Quantum Chemistry Package (GQCP) is an open-source electronic structure software package that aims to provide an intuitive and expressive software framework for electronic structure software development. Its high-level interfaces (accessible through C++ and Python) have been specifically designed to correspond to theoretical concepts, while retaining access to lower-level intermediates and allowing structural run-time modifications of quantum chemical solvers. GQCP focuses on providing quantum chemical method developers with the computational "building blocks" that allow them to flexibly develop proof of principle implementations for new methods and applications up to the level of two-component spinor bases.
A SimBiology-Based GUI for Standardized QSP Model Development and Application. version 1.0.2 (74.9 MB) by Iraj Hosseini. https://github.com/feigelman/gQSPsim-release. The app is used for QSP Modeling and Simulation.
Infrastructure for eQTL, mQTL and similar studies.
Computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
Automated processing of glycan quantitation data produced by MALDI-MS. gQuant performed spectra pre-processing, glycan mapping by exhaustive algorithms and quantitation ratio calculation for matched glycans in a sequence
Fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Opverlap maximization (CMO) paradigm. The algorithm is based on a Needleman-Wunch algorithm where the cost for matching two residues is their graphlet degree similarity.
The GR2D2 estimator for the precision matrices.
A Deep-Learning Model for Predicting the Hydration Structures around Proteins.
Dense granule protein prediction in Apicomplexa protozoa through graph convolutional network.
Aligns a pair of nodes originating in different networks based on a similarity measure of their local neighbourhoods.
Genome Region Assembly by Baiting. Assemble selected regions of the genome or transcriptome using reference sequences and NGS data.
Tool for predicting granzyme B and caspase cleavage sites.
GRable is a browser-based software tool for semi-automated Glyco-RIDGE analysis, designed for site-specific glycoform analysis of intact glycoproteins. It improves glycopeptide detection with features like parallel clustering and confidence evaluation using MS2 information.
GRABSEEDS is a command-line tool for extracting plant organ traits from digital images, employing computer vision and deep learning methods to accurately measure length, color, and other characteristics. The tool streamlines phenotyping workflows and supports association studies with agronomic traits and stress conditions.
Simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Utility for simplifying bulk downloading data from next-generation sequencing repositories, like NCBI SRA, MG-RAST, and iMicrobe.
Comprehensive web-based platform for integrative single-cell transcriptome analysis.
A Novel and Stable Knockoff Filter for Variable Selection Incorporating Gene Network Structures.
A tool for analysing human cytomegalovirus sequence data. GRACy is a bioinformatic tool designed for the analysis of Illumina data originated from Human cytomegalovirus samples. GRACy can be used to perform read quality filtering, genotyping, de novo assembly, variant detection, annotation and data submission to public database.
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). Analysis-of-a-photosynthetic-cyanobacterium-rich-in-internal-membrane-systems-via-Grad-seq.
Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens.
a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism.
GRADitude: a computational tool for Grad-seq data analysis Grad-seq is a high-throughput profiling approach for the organism-wide detection of RNA-RNA and RNA-protein interactions in which molecular complexes are separated in a gradient by shape and size (Smirnov et al., 2016, PNAS). Grad-seq separates native cellular lysates including complexes, according to their molecular weight and shape in a glycerol gradient, independent of charge and sequence. After this fractionation, RNA-seq and MS-analysis of each of the fractions generated allows the reconstruction of the sedimentation profiles of all detectable RNAs and protein in a single experiment. Further analysis can reveal possible interactions between the individual molecules.
Gadient descent-based tool for superimposing millions of protein structures from computational simulations.
Tool for aligning multiple global protein interaction networks; it also supports search for homology between a query module of proteins and a database of interaction networks.
GRAph-based Finding of Individual Motif Occurrences. GRAFIMO (GRAph-based Finding of Individual Motif Occurrences) is a command-line tool that extends the traditional Position Weight Matrix (PWM) scanning procedure to VGs. GRAFIMO can search the occurrences of a given PWM in many genomes in a single run, accounting for the effects that SNPs, indels and potentially any structural variation (handled by VG) have on found potential motif occurrences. As result, GRAFIMO produces a report containing the statistically significant motif candidates found, reporting their frequency within the haplotypes embedded in the scanned VG and if they contain genomic variants or belong to the reference genome sequence.
A webserver for substructure similarity searching and comparisons in the structures of proteins and RNA.
Scalable, phylogenetically informed classification of genes within metagenomes.
Alignment-free filtering for cfNA fusion fragments | AF4 is an alignment free fusion detector that can work with RNA-seq data, cfRNA data and cfDNA data. It consists of two stages. In stage one, it identifies candidate fusion fragments and the corresponding fusion pairs. In the second stage, a list of filtering criteria are applied to narrow down the fusion candidates | This directory contains scripts we used internally to run benchmarks presented in the ISMB paper. It may or may not run in your environment | Method: AF4 decomposes each fragment into kmers and identifies for each kmer the corresponding genes
GrainGenes, a database for Triticeae and Avena, is a comprehensive resource for molecular and phenotypic information for wheat, barley, rye, and other related species, including oat.
The Glycine Receptor Allosteric Ligands Library (GRALL). GRALL – [IFM] LABORATOIRE D’INGÉNIERIE DES FONCTIONS MOLÉCULAIRES.
A tool that for LncRNA-disease association identification using graph auto-encoder and learning to rank.
This database is a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. The database has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci, metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps.
Novel representation of noncoding RNA secondary structure. By encoding both the sequence and secondary structure of ncRNAs in a string, ncRNA structural alignment is converted to sequence alignment. The software package provides an ncRNA consensus secondary structure derivation tool.
GranatumX: A community engaging and flexible software environment for single-cell analysis.
A Python Module for Grand Canonical Water Sampling in OpenMM. grand : Grand Canonical Water Sampling in OpenMM. This Python module is designed to be run with OpenMM in order to simulate grand canonical Monte Carlo (GCMC) insertion and deletion moves of water molecules. This allows the particle number to vary according to a fixed chemical potential, and offers enhanced sampling of water molecules in occluded binding sites. The theory behind our work on GCMC sampling can be found in the References section below.
GRAND is a collection of gene regulatory networks derived from human tissues, cancer, cell lines, and small molecule drugs. These networks are bipartite graphs linking either transcription factors (TFs) or miRNAs to their target genes. GRAND includes an integrated webserver to test for enrichment of a list of TFs in a set of libraries as well as a tool (CLUEreg) to find compounds that reverse/exacerbate a gene or TF regulatory profile.
grandR is an R package providing a toolbox for quality control, kinetic modeling, differential gene expression analysis, and visualization of nucleotide conversion RNA-seq data, designed to correct for biases induced by 4sU labeling.
R package for reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data.
R package for assessing the biological relevance of any TF-Gene GRNs using a machine learning framework to predict cell-type specific differential expression.
Web server that allows users to explore abstracted representations of proteins. Large scale structural features are preserved while other surfaces are effectively reduced.
Graphical Abstracted Protein Explorer (GRAPE)
Database which provides several ways to access to the grape genomic data: as a blast search page, a genome browser and a direct link to download the data.
RNAseq Analysis Pipeline Environment that implements a set of workflows that allow for easy exploration of RNA-Seq data.
The Granule Protein Enrichment Server for prediction of biological condensate constituents.
GRAPES-DD is a tool for exploiting decision diagrams for index-driven search in biological graph databases.
Predicting enzymatic function of proteins from domain similarity graphs. An amendment to this paper has been published and can be accessed via the original article
A package that implements some simple graph handling capabilities.
Demonstration of graph-based segmentation of retinal layers in an optical coherence tomography image
Graph-based segmentation of retinal layers in OCT images
Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter.
Graphical model for prioritizing GWAS results and investigating pleiotropic architecture. Fit graph-GPA models, implement association mapping, and generate a phenotype graph.
Multi-instance learning of graph neural networks for aqueous pKa prediction.
A multi-modal graph-based representation learning model that can integrate heterogeneous information including multiple types of interaction networks (sequence similarity network and protein-protein interaction network) and protein features (amino acid sequence, subcellular location and protein domains) to predict protein functions on Gene Ontology
A multi-modal variational graph embedding model for predicting microbe-drug associations.
Graph2VR is a PhD project, a prototype for a VR application to visualize graphs (SPARQL) as 3D graphs in Virtual Reality. The idea is to explore, analyze, and interact with the data in the graph using gesture control. Graph2VR has been built in Unity and is able to connect to a SPARQL endpoint using dotNetRDF. We got inspired by many different tools to work with Linked data and to visualize Graphs. Virtual Reality offers the user way more space to expand the graph than a 2D computer screen.
A web application and a graph database for visualizing and analyzing medical databases.
Tool for digitizing data from images, similar to the classic Data Grabber and WebPlotDigitizer.
A novel and simple test to validly assess fluid reasoning.
An extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores.
An R package for graph theoretic association tests.
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model.
Refined binning of metagenomic contigs using assembly graphs. GraphBin is a NGS data-based metagenomic contig bin refinment tool that makes use of the contig connectivity information from the assembly graph to bin contigs. It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs which are discarded due to short length.
Protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. We collect two nucleic acid-binding protein benchmark datasets from BioLiP database(1), and split them to the training and test sets according to the release date. In addition, we compare GraphBind with state-of-the-art methods for predicting small ligand-binding residues, including Ca2+, Mn2+, Mg2+, ATP and HEME. GraphBind only predicts one protein chain once, please input 1-character chain ID (case sensitive) in the text boxes.
A shiny web app to easily perform popular visualization analysis for omics data.
Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs.
GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs.
GraphCompass is a set of omics-adapted graph analysis methods for quantitatively evaluating and comparing the spatial arrangement of cells across different conditions. It builds upon Squidpy and provides statistical approaches and visualization functions for analyzing spatial organization in biological samples.
GraphCovidNet is a graph neural network based model for detecting COVID-19 from CT scans and X-rays of chest.
Software tool for network analysis, modeling and alignment. It automates tasks of finding the best fitting model for the network data, pairwise comparisons of networks, alignment of two networks using GRAAL algorithm (a better network alignment algorithm, MI-GRAAL, is also available for download), and provides capabilities of clustering network nodes based on their topological surrounding in the network.
Graph convolutional networks for drug response prediction.
Predicting drug-target binding affinity with graph neural networks. GraphDTA post-hoc analysis scripts.
The first method to infer supports for evolutionary events based on their frequencies in the set of equally parsimonious reconciliations Given a , this program computes
A Python Library for Geometric Deep Learning and Network Analysis on Protein Structures. This package provides functionality for producing a number of types of graph-based representations of proteins. We provide compatibility with standard formats, as well as graph objects designed for ease of use with popular deep learning libraries.
Graphery is a web-based graph algorithm tutorial that is designed for biological researchers.
GraphFP:a dynamic inference software for reconstructing the cell state-transition complex energy landscape from time series single-cell transcriptomic data.
A self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression.
A graph neural network to predict the effect of pharmacotherapy on the cancer cell growth. GraphGR is a tool to predict drug (kinase inhibitors ONLY for now) response on a specific cell line given genetic information of the cell line, binding affinity of the drug to the proteins, and the disease association scores of the proteins. It utilizes heterogeneous data to construct a graph for each cell-line-drug combination (instance). The trained model can be used to predict the effect (currently a binary classification) of a drug on a given cell line.
A platform for the graph-based visualisation and analysis of complex data. Visualisation tool for the creation and analysis of graphs. Graphia is a powerful open source visual analytics application developed to aid the interpretation of large and complex datasets. Graphia can create and visualise graphs from tables of numeric data and display the structures that result. It can also be used to visualise and analyse any data that is already in the form of a graph.
Package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.
Web tool for for pathway analysis and network visualization for gene expression data from microarray and RNA-seq experiments.
A fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels (popular baselines), and (4) the Weisfeiler-Lehman graph kernel (state-of-the-art).
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
Long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation.
A graph neural network model for predicting protein subcellular localization from immunohistochemistry images.
Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
An Interactive Platform To Explore And Integrate Multi-Omics Data. GraphOmics is a dashboard to integrate and explore different types of biological -omics data. Using this tool, you can map transcriptomics, proteomics and metabolomics data onto metabolic pathways.
Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.
graphPAF is an R package designed for estimating, inferring, and displaying population attributable fractions (PAF) and impact fractions. It offers diverse functionalities including Bayesian network calculations and displays attributable fractions over multiple risk factors using fan-plots and nomograms.
GraphProt can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
Protein Model Quality Assessment using Graph Convolutional Networks.
Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.
Chromatin interaction-aware gene regulatory modeling with graph attention networks.
GraphRegNet is a tool for deep graph regularisation networks on sparse keypoints for dense registration of 3D Lung CTs.
GraphRepur is a tool for drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network.
An R package for simulating gene expression data from graph structures of biological pathways. Simulate Expression Data from 'igraph' Networks.
GraphSite is a novel framework for sequence-based protein-DNA binding site prediction using graph transformer and predicted protein structures from AlphaFold2.
Interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.
An attention-based graph embedding model for predicting TF-target gene interactions.
Public web server for graph-based analysis of biological networks that: analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; integrates multiple diverse datasets into global networks; incorporates multispecies data; filters nodes and edges; detects gene modules from networks; interprets discovered modules.
Graphs are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. This tool (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.
GRASP is a gene annotation tool for metagenomic studies. GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose.
A graph-based residue neighborhood strategy to predict binding sites. The discovery of protein-ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles. Detecting protein-ligand-binding sites experimentally is time-consuming and expensive.
A machine learning strategy to predict binding sites based on residue neighborhood graphs.
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP).
Fast protein structure comparison through effective representation learning with contrastive graph neural networks.
Grass Vein Image Quantification (GrasVIQ) is an image analysis framework for automatic quantification of veins in grass leaves. Designed specifically for parallel venation, GrasVIQ automatically segments veins from images of cleared grass leaves using thresholding and edge detection techniques. Veins are quantified and classified into orders, and spatial parameters, such as vein width and interveinal distance, are calculated automatically. For more details, please see.
Software for relative rate tests with groups supporting all models of nucleotide substitution known by PAUP*.
Grouping Augmented Views from Independent Sources for Dermatology Analysis.
GRAViTy-V2 is a command-line tool and application for viral taxonomy classification based on genomic sequence analysis. It leverages whole-genome analytical classification to assign viruses to taxonomic ranks and was validated against expert-curated classifications.
Online tool for calculating and mining dose–response data.
Novel computational program to characterize the zinc-binding sites in protein structures, by restricting the distances between zinc and its coordinating atoms.
A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species
A comprehensive enrichment analysis software for human genomic regions.
Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. It assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes.
This tool performs, in a systematic way, an automated analysis of regular arrangements in organisms having multiple chromosomes, for different transcription factors (or regulators, conditions) at the same time. It reports and allows identification of periodic regions of target genes for the different conditions, on each chromosome.
Institute of Systems and Synthetic Biology
Performs an automated and systematic analysis of periodic patterns in the position of a set of genomic features of interest along the genome. A complete analysis runs: detection of all possible periods from the positions of the genomic features, clustering of genomic features that are “in-phase” for every significant period found, and mapping of all the regions of the genome showing periodicities. Each step generates rich and interactive visualisations as well as machine-readable files.
The well known greedy algorithm for solving Set Cover problem, with a few changes
GreedyFHist - Registration of stained histology images.
Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees. GreedyRFS is a heuristic method developed for the Robinson-Foulds Supertree problem. It takes a set of binary source trees which have overlapping leaf sets as input and outputs a binary supertree on the union of leaves. This heuristic relies on an exact algorithm for the Robinson-Foulds Supertree problem on two source trees. It repeatedly chooses two trees from the source trees (according to some greedy criterion) and merges them using the exact algorithm until only one supertree remains. (A paper detailing the algorithm and experimental results is submitted to SODA and will be available in the future.).
A framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing. Genomic Regulatory Elements ENcyclopedia. This is the home of the GREEN-DB and companion tools (GREEN-VARAN). Genomic Regulatory Elements ENcyclopedia Database A collection of ~2.4M regulatory regions in the human genome, with information about controlled genes, tissues of activity and associated phenotypes. GREEN-DB is available for free for academic usage in a Zenodo repository.
Quantifying the Carbon Footprint of Computation.
A comprehensive database of plant long non-coding RNAs.
A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensive database containing 213,494 circRNA informations from over 4100 RNA-seq datasets across 69 different species. Based on these candidate circRNAs, we futher predicted them acting as miRNA decoys and their potential networks involving circRNA-miRNA-mRNA in the corresponding species. This database allows users not only to search, browse and freely download circRNAs with relative informations, such as full-length, graphical, parental gene and interaction network, but also provide some tools for analyze circRNAs. A Wiki-database of plant CircRNAs(v1.0).
A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease.
A database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families.
A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data.
GREG-studying transcriptional regulation using integrative graph databases. Scripts related to GREG (Gene Regulation Graph Database) and its papers. Use GREG at: http://www.moralab.science/GREG/. (The Gene Regulation Graph Database).
Tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features.
Modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem. GREMA (Gene networks Reconstruction using Evolutionary Modelling Algorithm) is a program for inferring a novel type of gene regulatory network (GRN) with confidence levels for every inferred regulation, which is emulated GRN (eGRN). The higher the confidence level, the more accurate the inferred regulation. GREMA gradually determines the regulations of an eGRN with confidence levels in descending order using either an S-system or a Hill function-based ordinary differential equation model. It makes use of an evolutionary modelling algorithm (EMA) that is based on evolutionary intelligence, including both crowd wisdom and an evolutionary strategy, to cope with the underdetermined problem. EMA uses an intelligent genetic algorithm to solve the large-scale parameter optimisation problem.
A Data-Driven Python Library to Infer Gene Regulatory Networks from Gene Expression Data.
grenedalf is a command-line tool written in C++ designed for performing population genetic statistics on pool sequencing data, offering significant performance improvements and usability features.
The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.
Count or select lines containing a motif of a dataset.
R package for mapping in silico genetic interaction and essentiality networks.
On the complexity of haplotyping a microbial community. An algorithm for recovering haplotypes from metagenomes. Sister to Hansel. Gretel is a Python package providing a command line tool for the recovery of haplotypes from metagenomic data sets. Gretel parses an alignment of reads into a Hansel matrix and uses the evidence of SNP pairs observed to appear on the same reads to probabilistically reconstruct the most likely haplotypes.
gretl is a Rust-based toolkit for analyzing genome graphs, designed to improve scalability and user-friendliness compared to existing tools. It provides a wide range of statistics and is demonstrated to outperform other tools in speed, especially for larger graphs.
Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. This code is the implementation of GRGMF, which is both CPU and CUDA compatible(CUDA is preferred).
Inductive Inference of Gene Regulatory Network Using Supervised and Semi-supervised Graph Neural Networks. GRGNN -- Gene Regulatory Graph Neural Network. Gene regulatory graph neural network (GRGNN): an end-to-end approach to reconstruct GRNs from scratch utilizing the gene expression data, in both a supervised and a semi-supervised framework.
These functions enable calculating functions using the grid-based modeling.
Find segment lengths for multiple rays/lines within an irregular n-dimensional grid
Grid Map was designed to display comparative genome mapping data in a grid format. It is a generic Java version of the Oxford Grid display (written for the ACEDB database software package), but can be used to display many kinds of gridded data.
Database and software for Earth system modeling at global and regional scales.
A Python Package of Image Analysis for Interactive Grain Counting and Measuring. Grain characteristics are critical component traits for grain yield, including kernel length, kernel width, and thousand kernel weight.
Open-source software tool conceived to build an image mosaic of a hemocytometer’s grid.
A tool for accurate, cross-platform phenotypic data collection and visualization.
A Web Server for the Prediction of Biomolecular Hydration Properties. The gridSolvate program predicts the distribution of hydration sites within proteins. Input data is provided as an atomistic model of a protein structure in PDB-like format.
A high-speed next-gen sequencing structural variation caller. It calls variants based on alignment-guided positional de Bruijn graph breakpoint assembly, split read, and read pair evidence.
Walter and Eliza Hall Institute, Melbourne, Australia
GRIEVOUS is a command-line tool for resolving cross-dataset genotype inconsistencies by harmonizing variant indexing and allele assignments. It identifies, formats, and aligns biallelic SNPs across datasets and can extract common SNPs.
Uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.
GRIMER automates analysis and reports an offline and interactive dashboard integrating annotation, taxonomy and metadata to analyse microbiome studies and detect contaminatio
A toolset for software development analytics.
GRiNCH (Graph-Regularized NMF and Clustering for Hi-C) is a tool for simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.
A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.
get Residue Interaction eNergies and Networks. Calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.
a generalist tool for network generation from segmented tissue images.
Update of the GRIP web service. GRIP ( GPCR-GPCR interaction interface predictor ). Input a target sequence in FASTA format.
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference. Gene Regulation Inference for Single-cell with LInear differential equations and velocity inference. Single-cell RNA sequencing (scRNA-seq) offers new possibilities to infer gene regulation networks (GRN) for biological processes involving a notion of time, such as cell differentiation or cell cycles.
GRISOTTO, uncovers motifs using prior information from a set of co-regulated DNA sequences.
Tool for transcript discovery and quantification via the integrated analysis of CAGE, RAMPAGE, RNAseq, and poly(A)-seq data
New pathogenic variants and insights into pathogenic mechanisms in GRK1-related Oguchi disease. LOVD - Leiden Open Variation Database. G protein-coupled receptor kinase 1 (GRK1).
Powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.
GRMhor is a tool that identifies higher-order repeat (HOR) structures in eukaryotic genomes, particularly in centromeric regions. It's designed to be sensitive and automated, enabling the study of chromosome integrity, gene expression, and evolutionary relationships.
Functions for calculating and visualizing growth-rate inhibition (GR) metrics.
GRMT (Generative Reconstruction of Mutation Tree from scratch) is a tool for tumor mutation tree inference from single-cell DNA sequencing data. GRMT is able to efficiently recover the chronological order of mutations and scale well to large datasets. It exploits BayesOpt to estimate error rates in mutation data based on the Bayesian optimization algorithm.
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.
Universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes.
A web server for benchmarking directed gene regulatory network inference methods.
Decoding the gene regulatory networks in diverse human and mouse conditions. Gene Regulatory Network database. Gene regulatory networks are crucial for understanding the mechanism of gene expression regulation and expression heterogeneity. GRNdb is a freely accessible and user-friendly database for conveniently exploring and visualizing the predicted regulatory networks formed by transcription factors (TFs) and downstream target genes (termed regulons) based on large-scale RNA-seq data as well as the known TF-target relationships for various human and mouse conditions.
NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research Program
Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.
Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data. Gene Regulatory Network reconstruction using Unrolled algorithms (Paper link and BibTex: TBD). Explore the notebook folder for a quick overview of the GRNUlar algorithm ran on jupyter notebook.
Package that allows fast and easy access to Gromacs output files from Matlab.
Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) is a software pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants using the long-fragment information from the 10x Genomics platform.
A pipeline for the analysis of GRO-seq data.
This tool is “Swiss Army knife” library for processing genomic interval data. It operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.
Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
These are a set of python scripts that allow a user to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files (.itp files). They are highly useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.
Massively parallel and GPU-accelerated non-orthogonal configuration interaction for large molecular systems. GronOR started in 2016 as a collaboration of the Theoretical Chemistry group of the University of Groningen in Groningen, the Netherlands and the National Center for Computational Sciences at the Oak Ridge National Laboratory in Oak Ridge, Tennessee, with the objective of developing massively parallel and accelerated computational chemistry applications.
GroopM is an automated tool for the recovery of population genomes from related metagenomes.
Indexed variation graphs for efficient and accurate resistome profiling.
A database of ligand-inducible transcription factors.
A genomic information repository for oilplants.
A gradient optimization toolbox for general purpose time‐optimal MRI gradient waveform design. A toolbox for MRI Gradient Optimization (GrOpt). OpenMP version of TE finder is better implemented. See demo in the test_TE_finder function of src/optimize_kernel.c, which will call multiple GrOpt evals simultaneously to find the shortest feasible T.
A procedure that uses target-decoy competition (or knockoffs) to reject multiple hypotheses in the presence of group structure. The procedure controls the false discovery rate (FDR) at a user-specified threshold.
Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function.
Designed to test multiple hypotheses and control either the false discovery rate or the family-wise error rate. The method facilitates the input of prior information in the form of groupings of tests, for example, one group might include SNPs in candidate genes, while another includes all other SNPS. For each group a weight is estimated from the observed test statistics within the group.
Graph-based clustering and annotation for improved de novo transcriptome analysis.
A groupwise one-shot deep learning-based 4D image registration method.
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.
This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.
Reference-based data compression for storage of resequencing data.
Analysis of perceptual independence using general recognition theory.
Interactive multiparameter optimization of molecules in a continuous vector space. gruenif.ai is a web application for interactive multi-parameter optimization of molecules in a continous vector space. A web application is best explained through a live demo. Please watch our video for a detailed explanation of the functionality: Showcase. In its current form grünifai is commposed of multiple microservices. We recommend the use of Docker to compose all microservises into one running environment.
GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.
Developed for aligning genomic sequences and uses bit-level operations. It is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements. It is suitable for aligning fairly divergent sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment.
GS-LAGE (Gene Specific Large-scale Analysis of Gene Expression) is a global analysis strategy for large-scale microarray datasets integrated from public databases such as NCBI GEO.
Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility. GS-Preprocess is a one-line, 6-argument pipeline that generates input data for the GUIDEseq Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.GUIDEseq) from raw Illumina sequencer output. For off-target profiling, Bioconductor GUIDEseq only requires a 2-line guideRNA fasta, demultiplexed BAM files of "plus"- and "minus"-strands, and Unique Molecular Index (UMI) references for each read. Expected Runtime and Resource Usage. Sample Bioconductor GUIDEseq Input.
GS3 (Genomic Selection / Gibbs Sampling / Gauss Seidel) is a program that estimates fixed and random effects, breeding values and SNP effects for genomic selection. It includes normal, mixture, or double exponential distributions for SNP effects, i.e. GBLUP, the so-called BayesCPi, and the Bayesian Lasso. It allows estimation of the variances and effects of SNPs, polygenic and environmental effects, and also the inclusion of heterogeneous variances as for the analysis of DYD’s
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex.
Perform gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.
A web platform to perform, learn, and discuss gene set analysis
Computational method that integrates gene expression analysis with genome wide association studies to determine whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to gene expression profiles and genotypes between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome.
Progress in the study of genome size evolution in Asteraceae. Genome Size in Asteraceae database.
Provides a fast implementation of permutation-based gene set analysis for two-sample problems. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.
An efficient sequence alignment tool for intra-species genomes. GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison. Developers: Dr. Hsin-Nan Lin and Dr. Wen-Lian Hsu Institute of Information Science, Academia Sinica, Taiwan. Personal genomics and comparative genomics are two fields that are more and more important in clinical practices and genome researches.
Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.
An Online Calculator for the Prediction of Survival in Glioblastoma Patients Using Classical Statistics and Machine Learning. BACKGROUND:Although survival statistics in patients with glioblastoma multiforme (GBM) are well-defined at the group level, predicting individual patient survival remains challenging because of significant variation within strata. OBJECTIVE:To compare statistical and machine learning algorithms in their ability to predict survival in GBM patients and deploy the best performing model as an online survival calculator. METHODS:Patients undergoing an operation for a histopathologically confirmed GBM were extracted from the Surveillance Epidemiology and End Results (SEER) database (2005-2015) and split into a training and hold-out test set in an 80 20 ratio
Genotype Sparse Compression (GSC) is an advanced tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 million variants, from an uncompressed VCF file of 803.70GB to approximately 1GB.
This tool takes as input several lists of activated and repressed genes. It then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. Finally, it provides both traditional R functions and an interactive, user-friendly interface.
An integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels.
Gene-set Distance Analysis (GSDA) is a R library for gene-set association analysis.
A database of 3D chromosome and genome structures reconstructed from Hi-C data. Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,. GSDB : Genome Structure Database.
Designed for the visualization of annotated features for genes, and the generation of high-quality figures for publication.
Database for storing, visualizing, and analyzing ChIP-based transcription factor binding data and gene expression data.
Computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
Gene Set Enrichment Analysis (GSEA) for 2 complementary gene sets
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
It implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia using parallel computation on standard workstations and institutional computer grids.
Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.
This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.
A comprehensive package for performing gene set enrichment analysis in Python.
Fast and flexible general search tool for whole-genome sequencing
Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles. General Notes and How to cite GSECA. GSECA is a R application with a Shiny web interface. The stand-alone version can be run from R GUI or from UNIX shell. Examples on how to use GSECA are provided below.
Python package for detecting signatures of diverse evolutionary forces on genomic regions.
GSIM (Gene Expression Simulator) is a C program which simulates gene expression microarray data. It will generate distributions for any number of genes and use those distributions to generate intensities for any number of replicates. It generates two-class data and any number of the genes can be chosen to be differentially expressed. The program is very flexible and the parameters of the differentially expressed genes can be set by the user.
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction.
The Genomic SSR Millets Database (GSMDB) is a web-based resource providing comprehensive details on over 6.7 million Simple Sequence Repeats (SSRs) mined from the genomic sequences of seven millet species. It aims to facilitate millet cultivar advancement and related research, contributing to global food security.
GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.
A tool for visualization of gene set over-representation analysis. A package for visualisation of gene set over-representation enrichment analysis.
A web tool to visualize, search and explore protein-ligand structural patterns. Graph-based Structural Patterns for PDB. GSP4PDB is a tool that lets the users design, search and analyze structural patterns inside biomacromolecules of the PDB in a graphic way. The novel feature of GSP4PDB is that a protein-ligand structural pattern is graphically represented as a graph such that the nodes represent protein’s components (amino acids and ligands) and the edges represent structural relationships (e.g. distance relationships). Such abstract representation is called a Graph-based Structural Pattern (GSP).
Gene set proximity analysis (GSPA) is a method for identifying critical gene sets in functional genetic datasets using low-dimensional gene embeddings.
GSpace is a simulator for large genomic data, based on a generation-by-generation coalescent that takes into account small population size, recombination, and isolation by distance.
A novel deep learning model for predicting phage-host interactions via multiple biological information. Emerging evidence suggests that due to the misuse of antibiotics, bacteriophage (phage) therapy has been recognized as one of the most promising strategies for treating human diseases infected by antibiotic-resistant bacteria.
Genome Structure Rearrangement Calling in Genomes with High Synteny.
A package for gene set analysis based on the variability of expressions. It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods.
This package estimates the number of differentially expressed genes in gene sets by using the concept of the gene set regulation index.
High sensitivity tool, based on proportion tests for linkage analysis using WES data.
Web-server specially trained for the Glutathione S-transferase protein.The prediction is based on the basis of amino acid composition, dipeptide composition, tripeptide composition by using support vector machines(SVM).
Constructing suffix arrays, LCP arrays and BWTs for string collections. gsufsort [1] is a fast, portable and lightweight tool for constructing the suffix array and related data structures for string collections.
Includes a range of tools to handle acquisition, processing and analysis of collections of genomic tracks, represented in a simple tabular format, GSuite. Please proceed in either basic or advanced mode.
Non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of an expression data set. It performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, etc., in a pathway-centric manner.
Ultra-rapid metagenotyping of the human gut microbiome. GT-Pro - the GenoTyper for PROkaryotes. Ultra-rapid genotyping of prokaryotes in shotgun metagenomes. To genotype a microbiome, GT-Pro takes as input one or more shotgun metagenomics sequencing libraries in FASTQ format. It returns counts of reads exactly matching each allele of each SNP in a concise table-shaped format for its output, with one row for each bi-allelic SNP site that has exactly 8 fields: species, SNP ID, contig, contig position, allele 1, allele 2 and coverage of allele 1 and coverage of allele 2. The k-mer exact match based genotyping algorithm is optimized for machine specificiations, and it can run on a personal computer.
GT-seq scripts is a bioinformatics workflow for developing SNP panels from low-coverage whole-genome sequencing data, designed to support fisheries stewardship in Northern Canada. It enables high-throughput genotyping for Arctic Char, Brook Trout, and Lake Whitefish.
Improved species-specific tRNA adaptation index using the genetic algorithm.
GTalign is a software tool for rapid and accurate protein structure alignment and search, leveraging spatial structure indexing for optimized superposition. It offers a significant speedup and improved accuracy compared to existing aligners, facilitating various biological research applications.
Prediction of Protein-Protein Interactions Based on L1-Regularized Logistic Regression and Gradient Tree Boosting. The code is the implementation of GTB-PPI method “Prediction of Protein-Protein Interactions Based on L1-Regularized Logistic Regression and Gradient Tree Boosting”. The dataset file contains the S. cerevisiae, H. pylori ,the indepedent data set and PPIs network (one-core network and crossover network).
Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.
Implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.
Graph Traversal Edit Distance and Extensions. Graph Traversal Edit Distance.
GTestimate is a scRNA-seq normalization method. In contrast to other methods it uses the Simple Good-Turing estimator for the per cell relative gene expression estimation.
Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.
Web platform for supporting ageing studies.
GTfold is a fast, scalable multicore code for predicting RNA secondary structure that is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.
A software package for analyzing various features of gene models.
Guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes.
Inference of population admixture network from local gene genealogies. Inference of population admixture network from local gene genealogies under coalescent theory. GTmix is a computer program for inferring population admixture networks from inferred local gene genealogies. If you use GTmix, please cite:. The key feature of GTmix is that it works with local gene genealogies inferred from haplotypes.
Context-aware non negative matrix factorization clustering
A toolkit to unify pipelines in genomic and proteomic research. GTO is a toolkit to unify pipelines in genomic and proteomic research. GTO is a toolkit for genomics and proteomics, namely for FASTQ, FASTA and SEQ formats, with many complementary tools. The toolkit is for Unix-based systems, built for ultra-fast computations. GTO supports pipes for easy integration with the sub-programs belonging to GTO as well as external tools. GTO works as LEGOs, since it allows the construction of multiple pipelines with many combinations.
Efficient implementation of the Generalized Topological Overlaping Measure (GTOM)
GTOM - Generalized Topological Overlaping Measure
Program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
Performing QTL and eQTL Analyses with the R-Package GenomicTools. This Package is the continuation of the genomic analysis tools part of the GeneticTools package. Website accompanying the R-package 'GenomicTools'. Today the versions 0.2.8 for GenomicTools and 0.1.4 for GenomicTools.fileHandler have been released with a couple of bugfixes and a list of new features.
Guanosine-5'-triphosphate (GTP) is a purine nucleotide. GTP is involved in energy transfer or an activator of substrates in biochemical reactions. GTP Binding proteins are regulatory proteins which becomes activated when bound to GTP and is involved in signal transduction.
R package GTQC streamlines a majority of the quality control steps and produces a detailed HTML report on a plethora of quality control metrics, thus enabling a swift and rigorous data quality inspection prior to downstream GWAS and related analyses
An integrated view of transcription regulation. ChIP-seq experiment information were collected in semi-automated way from literature, GEO and ENCODE. Raw ChIP-seq data in the form of fastq and SRA files were fetched from ENCODE and SRA databases. Clusters for the same TF revealed by different peak calling methods were joined into metaclusters. Metaclusters represent non-redundant set of transcription factor binding sites. The clustering algorithm used in GTRD is described in the main GTRD paper [6].
An Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population. Global Tree Reconstruction System (GTree) software is a open source software for neuron tracing. GTree is written in C++, and freely available for academic research using. GTree is used to reconstruct neurons in single images and reconstruct neuronal population from brain-wide image stacks.
Visualize genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.
Genotyping-in-thousands by sequencing (GT-seq) of non-invasive fecal and degraded samples. Genetic monitoring using non-invasive samples provides a complement or alternative to traditional population monitoring methods. However, Next Generation Sequencing approaches to monitoring typically require high quality DNA and the use of non-invasive samples (e.g. scat) is often challenged by poor DNA quality and contamination by non-target species. One promising solution is a highly multiplexed sequencing approach called Genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on non-invasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from non-invasively collected fecal samples
GTXplorer provides an interactive platform for users to access, navigate, download and visualize the evolutionary information from primary protein sequences of the GT-A fold families.
A fast compression and cloud transmission tool optimized for FASTQ files.
Tool designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.
Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.
GUESS is a computationally optimised C++ implementation of a fully Bayesian variable selection approach that can analyse, in a genome-wide context, single and multiple responses in an integrated way.
FLEXR GUI is a plugin for Coot that provides a graphical user interface for multi-conformer modeling of proteins, automating the separation of conformational signal from noise. It allows seamless integration of FLEXR models into the crystallographic modeling and validation pipeline within Coot.
Build Detection and Diagnosis Tools of Covid-19 on Chest Radiographs. Everything is in GUI.
GUI-fying to build DL Model (Classification)
The GUI is easy to access and reduces the load of ophthalmologists in analyzing the retinal profile.
Graphical User Interface for Retinal Blood Vessel Extraction from Fundus Images
A GUI for solving a set of delay differential equations (DDEs) and local search for best solutions
Graphical User Interface for Solving Delay Differential Equations and doing Local Search
Assess alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences, output is a graphic visualization of the alignment with confidence scores at each residue.
Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
Guide (Genome Informatics Data Explorer) is a desktop application designed for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules. It also integrates useful data from multiple sources, such as gene annotation and orthologue data, and enables editing of R commands to customise the analyses for advanced users.
An R package for the joint analysis of clinical microarray profiles and additional per gene measurements.
A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes. Pan-bacterial, genome-wide guide designer.
Software to design CRISPR-Cas guide RNA pools in non-model genomes.
A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. GuidePro:A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. GuidePro is a two-layer ensemble predictor that enables the integration of multiple predictive methods and feature sets to predict sgRNA efficiency for the CRISPR Cas9 protein knockouts.
Graphical User Interface for DNA Editing Screens (GUIDES) is a web application that designs CRISPR knockout libraries to target custom subsets of genes in the human or mouse genome
A generalized CRISPR guideRNA design tool.
The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.
GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats) is the integrated metadatabase in conjunction with neural network methods.
International Union of Basic and Clinical Pharmacology (IUPHAR)
An expert-curated pharmacological database of drug targets and their ligands.
revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization. GuidingNet is a method to reveal transcriptional cofactor and predict binding for DNA methyltransferase by network regularization.
GUIdock allows for the facile distribution of a systems biology application along with its graphics environment.
Using a graphical desktop sharing system to provide a browser-based interface for containerized software.
Framework built for the prioritization of disease candidate genes using a priori gene-disease associations and protein interactions. It consists of implementations of 8 algorithms: NetScore, NetZcore, NetShort, NetCombo, fFlow, NetRank, NetWalk and NetProp.
Uses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. These gene products are fed to a species-specific interaction network as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm.
A machine learning method for the identification and characterization of novel COVID-19 drug targets.
a R package for dose escalation strategies in phase I cancer clinical trials. Graphical User Interfaces for Phase I Designs.
The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.
Detection of Chimerism and Contamination in Prokaryotic Genomes. Python package for detection of chimerism and contamination in prokaryotic genomes.
Software which implements a generalized UniFrac distance for analysis of microbiome data.
Program to visualize sequence annotation data of the genetic sequence data with graphical layout. This highly interactive program allows scrolling and zooming from the genomic landscape to discrete nucleic acid sequences. Its main function is quick rendering of data on a standalone personal computer to save the layout as a parsonal file. With optional link to the internet resources, and printing support, this program tries to make more greater use of computational media in research actitiviy.
Python toolbox for the analysis of fiber photometry data.
A platform for gene function analysis in G. uralensis
Somatic selection distinguishes oncogenes and tumor suppressor genes. GUST - Genes Under Selection in Tumors. GUST predicts oncogenes (OGs), tumor suppressor gens (TSGs) and passenger genes (PGs) using somatic SNVs detected in a collection of tumors. It can classify single genes from targetted sequencing or multiple genes from whole-exome sequencing.
a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. gutMDisorder (http: bio-annotation.cn gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in disorders and interventions. Alterations in the composition of the gut microbial community play crucial roles in the development of chronic disorders. And the beneficial effects of drugs, foods and other intervention measures on disorders could be microbially mediated. The current version of gutMDisorder documents 2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse
The Gut Analysis Toolbox (GAT) is an image analysis tool developed in Fiji for characterizing enteric neurons and their neurochemical coding. It streamlines image analysis tasks in ENS research, enabling rapid, unbiased analysis of larger tissue areas and neuronal markers.
A server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. The compositionality of the microbiome data is well-known but often neglected. The compositional transformation pertains to the supervised learning of microbiome data and is a critical step that decides the performance and reliability of the disease classifiers. We value the excellent performance of the distal discriminative balance analysis (DBA) method, which selects distal balances of pairs and trios of bacteria, in addressing the classification of high-dimensional microbiome data. By applying this method to the species-level abundances of all the disease phenotypes in the GMrepo database, we build a balance-based model repository for the classification of human gut microbiome-related diseases. The model repository supports the prediction of disease risks for new sample(s)
Tool for prediction of human gut bacteria-mediated biotransformation of biotic and xenobiotic molecules using machine learning.
a database of the human gut MEtaGenome Atlas. Recently numerous studies have identified that the perturbations in the gut microbiome were associated with human health, including diseases and cancers, even mental health. The recent development of high-throughput sequencing based metagenomics technologies such as 16S ribosomal RNA gene amplicon-based and genome-centric approaches have burst the profiling of the landscape for gut microbiome and the identification of human health related microbes. Here, we presented the gutMEGA database, which hosted the results of metagenomics studies.
A comprehensive database for target genes of gut microbes and microbial metabolites.
An interactive platform for gut microbiome interaction exploration.
gutSMASH web server is an automated identification of primary metabolic gene clusters from the gut microbiota. It is an approach to functionally profile the human microbiome for specialized primary metabolic gene clusters.
GutUDB is a multiomics database designed for researchers studying intestinal diseases. It provides a platform for managing, analyzing, and visualizing knowledge related to these diseases, integrating data from various omics layers to explore genotype-phenotype characteristics.
RNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.
GVAF is a command-line software tool designed for generalized and flexible filtering of annotated variant files, eliminating the need for specialized programming skills or software.
Efficient random access compression for gene sequence variations.
A novel implementation that incorporates most features of the VISTA family—fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers.
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This package uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
GVViZ: A tool for visualizing genes with disease causing variants.
A Statistical Package to Conduct Genome-Wide Structural Equation Modeling.
Genome-Wide Association Meta Analysis software performs meta-analysis of the results of GWA studies of binary or quantitative phenotypes. Fixed- and random-effect meta-analyses are performed for both directly genotyped and imputed SNPs using estimates of the allelic odds ratio and 95% confidence interval for binary traits, and estimates of the allelic effect size and standard error for quantitative phenotypes.
GWAPP enables reseachers working with Arabidopsis thaliana to do Genome Wide Association Mapping (GWAS) on their phenotypes.
Robust Analysis and Meta-Analysis of Genome-Wide Association Studies.
an R shiny web application for visualizing genome-wide association studies data. an R shiny web application for visualizing genome-wide association studies (GWAS) data using the following plots:. The application is hosted at gwaRs.
The Parkinson’s Disease GWAS Locus Browser. The NHGRI-EBI GWAS Catalog: a curated collection of all human genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. Summary Statistics from Other GWASes:.
A curated resource of genome-wide variant-trait associations in plants and animals | a curated resource of genome-wide variant-trait associations | e.g. plant; plant height; Zm00001d021954; chr1:14702150-37601000 | GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2019. [PMID=31566222]
The variant call format provides efficient and robust storage of GWAS summary statistics. VCF vs plain text GWAS storage formats.
GWAS3D web server computes the probability of genetics variants affecting regulatory pathways and underlying disease/trait associations by integrating chromatin state, functional genomics, sequence motif, and conservation information when given GWAS data or variant list. GWAS3D also provides comprehensive annotations and visualizations to help users interpreting the results.
Systematically evaluates GWAS signals and identifies context-specific regulatory variants. The updated web server includes six major features: (i) updates the regulatory variant prioritization method with our new algorithm; (ii) incorporates 127 tissue/cell type-specific epigenomes data; (iii) integrates motifs of 1480 transcriptional regulators from 13 public resources; (iv) uniformly processes Hi-C data and generates significant interactions at 5 kb resolution across 60 tissues/cell types; (v) adds comprehensive non-coding variant functional annotations; (vi) equips a highly interactive visualization function for SNP-target interaction.
A catalogue that provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5.
Represent and model data in the EMBL-EBI GWAS catalog.
Database for human genetic variants (GV) identified by genome-wide association studies. Contains twenty times more data than the NHGRI GWAS Catalog, manually curated from literature. Also has annotations for each GV.
An R script to filter genome-wide association study
User-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware. GWASpi aims to be a start-to-finish GWAS management application, from raw data to results, containing the most common analysis tools.
Genome Wide Association Study pipeline (GWASpi)
Package to query, download and wrangle GWAS Catalog data.
GWASTool is a web pipeline designed for detecting SNP-phenotype associations, offering a unified framework that simplifies GWAS analysis by encapsulating the heterogeneity of various algorithms and providing tools for simulation, detection, visualization, and comparison.
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
R package for genome-wide survival analysis.
GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).
Gene Co-expression Networks Analysis and Extended Modules Characterization in a Single Bioconductor Package. Pipeline for augmented co-expression analysis.
Allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search
Integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions.
A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level. GWideCodeML is a Python package that provides support for testing evolutionary hypothesis using codeml (from the PAML package) in a genome-wide framework.
Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM
Specialized ribosome profiling (ribo-seq) browser providing free access to the genomic alignments of ribo-seq reads in conjunction with mRNA-seq controls along with relevant annotation tracks. Based on the UCSC Genome Browser, the tool’s ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes while the separate tracks for each ribo-seq study enables cross-study comparisons.
School of Biochemistry & Cell Biology, University College Cork
Use greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal.
A grey wolf optimization approach to rigid and flexible receptor docking. Computational Biology and Bioinformatics Lab (CBBio). Department of Computer and Information Science. GWOVina - Fast Protein-Ligand Docking Tool based on GWO and AutoDock Vina.
GWRM is an R package for fitting, describing and validating the generalized Waring regression model.
A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.
An added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data.
Semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.
Community resource of mouse developmental expression information. It integrates different types of expression data at the transcript and protein level and captures expression information from many different mouse strains and mutants.
Detects GxE Interactions in a Genome-wide Association Study
Performs the two-step GxG test to detect GxG interactions in a genome-wide association study
GXNA is an innovative method for analyzing gene expression data using gene interaction networks.
Gypsy Database of Mobile Genetic Elements is a database of viruses and transposable elements based on their phylogenetic classification. It includes long terminal repeats retroelements and relatives, Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants.
Fast protein sequence alignment toolkit on heterogeneous computers with GPUs .
Web-based JavaScript application that allows the calculation and visualization of Shannon information content or relative entropy (Kullback-Leibler ‘distance’) within sequence alignment blocks. The application was designed for use in both teaching and research. Amino acid, nucleic acid sequences, or any other type of aligned chemical structures may serve as the input.
Simple clustering method that can be used to rapidly identify a set of tag SNP’s based upon genotype data.
H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags have been generated from RNAs extracted from cytoplasmic, nuclear and polysome fractions. A comparative genomics viewer allows users can empirically understand the evolutionary turnover of AS.
This tool provides curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, and molecular evolutionary features, protein-protein interactions and gene families/groups.
Web application for prediction of residue status to be protected or unprotected from hydrogen-deuterium exchange in a protein chain.
A handy tool to rank anti-cancer synergistic drugs. H-RACS is designed to predict synergistic drug combinations based on drug features and basal expression profiling of cancer context. The advantages of H-RACS lie in 1) excellent performance with minimum data input compared to peers; 2) abundant cancer context built-in covering 928 cell lines of 24 cancers; 3) unique and outstanding extendibility to new drug combinations and new cell lines.
Hierarchical Nonlinear Dimensionality Reduction.
Novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.
Hybrid deep learning model for predicting 2'-O-methylation sites in human RNA.
A database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. Start your journey with H2V ...
Workflow for Genome Wide Association Study (QC, association study and miscellaneous functions)
Open source package for the accurate structure prediction of antibodies H3 loop ( third hypervariable loop ). The method is based on random forest automatic learning and a knowledge-based potential derived from known antibody structures.
Novel computational approach for the identification of Runs of Homozygosity by using whole-exome sequencig data generated by second generation sequencig technologies.
quick and robust calculation of codon usage from ribosome profiling data. CONCUR (Codon counts from Ribo-seq) is a tool for calculating codon usage from Ribo-seq data. These instructions will allow you to run CONCUR on your computer. CONCUR is a command line tool developed for Linux and macOS. You will need Perl and bedtools to be installed in your system.
3D structural visualization of COVID-19 genomic divergence. 3D visualization and analysis of the SARS-CoV-2 (COVID-19) protein structures with respect to the mutational patterns.
a HiChIP peak calling algorithm. This package can be used to find enriched peak regions from HiChIP datasets that can then be used as an input to available loop calling tools or to do differential peak analysis.
A Python library to facilitate programmatic analysis of data from high-throughput sequencing (HTS) experiments.
This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.
Cell-Type-Specific Analysis of G-Protein Coupled Receptor Signaling Pathways. The extended human GPCR network.
A comprehensive database for regulations of human transcription factors and their targets. Transcription factors (TFs) as key regulators could modulate the expression of target genes by binding to specific DNA sequences of their promoter(s) or enhancer(s)
HaarSeg is a segmentation algorithm for tiling microarrays.HaarSeg identifies statistically significant breakpoints in the data, using the maxima of the Haar wavelet transform, and segments accordingly.
Tool developed for fast clustering of heterogeneous interaction networks.
A hybrid attention-based convolutional neural network for highly accurate protein-ligand binding affinity prediction.
A unified and tidy R framework to easily compute gene expression signature scores.
High Ambiguity Driven biomolecular DOCKing: an information-driven flexible docking approach for the modeling of biomolecular complexes. It distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. It can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.
HADES is a set of open source R packages for large scale analytics, including population characterization, population-level causal effect estimation, and patient-level prediction.
An R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. Tools for processing, analysis and visualization of HDX-MS experiments.
The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage.
A clinically validated and scalable copy number variation detection tool for next-generation sequencing data. Hadoop-CNV-RF: A Scalable Copy Number Variation Detection Tool for Next-Generation Sequencing Data.
Java implementation of MapReduce-based copy number variation caller for next-generation whole-genome sequencing data.
Identification of haploinsufficient genes from epigenomic data using deep forest. This tool is using HaForest algorithm to identify haploinsufficient genes.
A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits. HAHmiR DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally validated to be associated with HA-stress; their level of expression in different altitudes, fold change, experiment duration, biomarker association, disease and drug association, tissue-specific expression level, Gene Ontology (GO) and Kyoto Encyclopaedia of Gene and Genomes (KEGG) pathway associations.
Generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot
An interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data.
A flexible platform for hybrid modeling with real-time visualization. Hybrid Automata Library (HAL) is a Java library that facilitates hybrid modeling: spatial models with interacting agent-based and partial-differential equation components. HAL’s components can be broadly classified into: agent containers (on and off-lattice), finite difference diffusion fields, graphical user interface (GUI) components, and additional tools or utilities for computation and data manipulation. These components have a standardized interface that expedites the construction, analysis, and visualization of complex models.
Package for performing clustering for high-dimensional data. This packages uses heavily scikit-learn and FFT accelerated t-SNE.
An implementation of DAG-based algorithm for reconstruction of synteny blocks from genome alignments
An Accurate Basecaller Exploiting An Encoder-Decoder Model With Monotonic Attention. Halcyon incorporates neural-network techniques frequently used in the field of machine translation, and employs monotonic-attention mechanisms to learn semantic correspondences between nucleotides and signal levels without any pre-segmentation against input signals.
Human aging and longevity knowledge graph for precision gerontology and geroscience analyses.
HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data, including preprocessing, single-subject, and group analysis. It provides state-of-the-art preprocessing using fmriprep, but removes the necessity to convert data to the BIDS format. Common resting-state and task-based fMRI features can then be calculated on the fly using FSL and nipype for statistics.
Package of multi-platform Java software tools, which aimed at large scale multiple similar DNA/RNA sequence alignment. It employs center star multiple sequence alignment strategy.
High-sensitivity pattern discovery in large, paired multi-omic datasets.
A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon.
HaloDom is a database of halophilic organisms across all life domains. It provides taxonomy info, halotolerance classification, salinity metadata, genomic/proteomic links and publication info.
A mapreduce implementation of the best practice DNA-seq pipeline by Broad Institute.
Halvade implements germline and somatic variant calling pipelines based on the best-practices pipelines from the Broad Institute using the Spark framework. Halvade will produce a VCF output file which contains the single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by the used tools. This program requires Spark on either a local cluster with one or more nodes, an Amazon EMR cluster or the Docker image to run.
An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
A system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.
Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.
Portable annotation pipeline for genomes and proteomes. HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of expert-curated protein family signatures and rules that specify annotations that apply to family members. HAMAP was originally developed by the Swiss-Prot group to help curators annotate UniProtKB/Swiss-Prot records and was subsequently made available to external users via the HAMAP-Scan web service. HAMAP signatures are also integrated into InterPro and the HAMAP rules into UniRule, the core part of the UniProt automatic annotation pipeline.
Database of human autophagy modulators with specific pathway and disease information.
A Bayesian regression model that integrates information to detect HLA-associated mutations.
A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization. Hamming distance calculation from multiple sequence data for heatmap visualization.
Fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration.
Tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs.
Benchmarking software to predict antibiotic resistance phenotypes in shotgun metagenomes using simulated data.
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
Tool for depicting experiments in a microarray data set as a set of minimum spanning trees.
Haplotype analyzer for the Czech population.
University of West Bohemia, Czech Republic
A dedicated quality of life resource following the diagnosis and treatment of head and neck cancer. A unique online database of papers published on quality of life in head and neck cancer. HANDLE-ON-QOL is a unique online searchable database of all papers published from 1982 to present on quality of life in head and neck cancer that have used questionnaires. This website uses cookies. By continuing to browse the site you are agreeing to our use of cookies. Accept More info.
HandyCNV is an R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH.
Tool to predict the deleterious effects of a mutation by using 10 Neutral- Disease Mis-Sense Mutation Discriminatory (NDMSMD) features.
HantaReg is a registry for epidemiological studies, outbreaks and clinical studies on hantavirus disease. Frequent outbreaks around the globe and endemic appearance in different parts of the world emphasize the substantial risk of hantavirus diseases. Increasing incidence rates, trends of changing distribution of hantavirus species and new insights into clinical courses of hantavirus diseases call for multinational surveillance. Furthermore, evidence-based guidelines for the management of hantavirus diseases and scoring systems, which allow stratification of patients into risk categories, are lacking.
A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data. The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.
Reconstructing accurate and long polyploid haplotypes using linked reads. We are providing ful support for this package. Feel free to ask your questions through email (sina.majidian@gmail.com) or Github's issue.
software for combining haplotype estimates and SNP array data for identifying somatic segmental copy number and copy-neutral mutations.
R code for mapping HAPlotype-haplotype interactions with Adaptive Lasso.
An approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model.
R package implementing methods described in Burkett et al. (2004) for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm.
This method leverages the long-range information of sequencing reads that allows to obtain assembled haplotypes fragmented in a lower number of unphased haplotype blocks. At the same time, this method is also able to deal with higher coverages to better correct the errors in the original reads and to obtain more accurate haplotypes as a result.
A software package for association mapping.
A fast and memory-efficient method for haplotype assembly from long gapless reads, like those produced by SMRT sequencing technologies (PacBio RS II) and Oxford Nanopore flow cell technologies (MinION).
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies. The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md
A package containing algorithms, exKING-robust and KIMGENS, to estimate kinship in haploid-diploid mixed populations.
Tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.
HapEvolution is a cooperative coevolutionary algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes.
Package to identify very short IBD segments in large sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
Software for the detection of selection signatures based on multiple population genotyping data.
Python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify.
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics
Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families.
HAPI-UR is a program for inferring phased haplotypes from unphased genotypes
HapKled is a software tool for haplotype-aware structural variant calling from Oxford Nanopore sequencing data. It utilizes haplotype information to improve detection performance and has been shown to outperform state-of-the-art tools.
Graphical user interface for the haplotype frequency estimation software Hapl-o-Mat.
Tool for assembling robust haplotype regions given alignments (from de-novo assembly or mapping to a reference) of genetically diverse sequence data. It compares each sequence to every other, and groups sequences together into sets that don’t have any conflicts (minimum coloring of the sequence ‘conflict graph’).
Whole-Genome Sequence Typing shows extensive diversity of Listeria monocytogenes in the outdoor environment and poultry processing plants. Haploid Sequence-Typer (Haplo-ST). Haplo-ST is a pipeline for performing standardized whole-genome multi-locus sequence typing (wgMLST) of Listeria monocytogenes (Lm) isolates from whole-genome sequencing (WGS) data. Along with wgMLST profiles, this pipeline also generates assembled allele sequences and identifies paralogous genes for each Lm isolate.
HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.
Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies. Haplocheck detects contamination in mtDNA AND WGS sequencing studies by analyzing only the mitchondrial DNA. You can use our cloud web service or install it locally.
Computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.
Program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD.
Program that can be used to implement tests of neutrality based on the frequency distribution of haplotypes in a sample of DNA sequences (the “haplotype configuration”) and the number of segregating sites. The neutrality tests can be performed conditional on the standard neutral coalescent model with or without recombination, exponential population growth, or island migration.
Unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2.
Viral Haplotype reconstruction from long reads via Deep Matrix Factorization.
The HaploDX library provides a collection of functions to generate simulated population-specific genomic data in VCF format. The library includes parameters and functions to control mutation rates, linkage disequilibrium strength and block lengths, and number of individuals. To generate genomic data, the HaploDX framework offers a pipeline of functions that can be used to simulate: (1) the allele frequency spectra of different populations; (2) the Hardy-Weinberg principle for genotypes and haplotypes; (3) linkage disequilibrium across different populations.
Web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree).
Interactive haplogroup classification and analysis platform.
Identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample.
Haploi is a haplotype inference program for multi-population data. Underlying Haploi is a new haplotype distribution model based on a nonparametric Bayesian model known as the hierarchical Dirichlet process, which represents a tractable surrogate to the coalescent process. It offers a well-founded statistical framework for posterior inference of individual haplotypes, and the size and configuration of haplotype ancestor pools given genotype data.
haploMAGIC is a pipeline for detecting crossovers in multiparental populations using SNP data, leveraging pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. It filters for genotyping errors, improving accuracy in complex plant genome analysis.
Haplotype assembly of diploid genomes using paired-end or PacBio reads
A tool for drawing pedigrees with special features for easy visualization of complex haplotype information.
Query web based genome annotation tools HaploReg and RegulomeDB. It gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.
Statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. It is especially suitable for data sets with a large number of subjects and a large number of possibly sparsely located markers.
Software package that uses Whole Genome Next Generation Sequencing data from a nuclear family to phase the genomic data into haplotypes spanning entire chromosomes.
Tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets.
Collection of R codes, including HAPLOSIM and HAPVISUAL, for the purpose of clustering haplotypes and haplotype visualization
Tools for haplotype-wise reconstruction of pseudomolecules
A web application for simple and accurate mitochondrial haplogrouping using short DNA fragments. Using fragment variant profiles. Haplotracker is a mtDNA haplogroup (HG) tracking application specifically designed for fragmented DNA samples, such as degraded DNA, commonly found in forensic specimens or human remains and difficult to obtain large DNA sequences. For primer/probe design for mtDNA.
An infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic. HaplotypeExplorer is an interactive haplotype network viewer for spatiotemporal dissection of multimodal epidemic spectra.
This pipeline prepares the population genotypes ped/map files, runs them on SHAPEIT, optionally uses the results as input for IMPUTE2 using the 1000G phase III reference panel, and finally converts them to Chromopainter_v2 formats in order to perform with fineSTRUCTURE fs 2.0.7 two clusterings of donors and recipients respectively, and with Chromopainter_v2 a painting of the resulting recipient clusters out of the donor clusters.
Genotype Transposer is an excel macro that will format data from an Excel spreadsheet to a format ready to be used by the program “Arlequin“. After which, other macros will extract the haplotype information, calculate linkage disequilibrium between markers, and prepare an input sheet for the “GOLD” program. Then, a last macro can reconstruct the haplotypes of each individual in the population,using a maximum likelihood method and the haplotypes present in the population as proposed by Arlequin.
A toolkit for accurately identifying recombination and recombinant genotypes.
Designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently supports the following functionalities: LD and haplotype analysis, estimation of haplotype frequencies, single SNP and haplotype tests, permutation teststing and visualization and plotting of PLINK whole genome association results.
Comparative haplotype browser for personal genome and metagenome.
Somatic mutation caller, which can utilize the information of heterozygous germline variants near candidate mutations.
Large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes.
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.
A Standardized Processing Pipeline for Event-Related Potential Analyses.
Holistic Analysis with Pre and Post Integration GWAS. HAPPI GWAS is a genome-wide association study (GWAS) tool written in R.
The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data
Estimates haplotype-specific odds ratios from genotype data on unrelated cases and controls using unconditional logistic regression. It can adjust for the main effects of relevant covariates and estimate stratum-specific haplotype effects.
A ILP program for infering haplotypes with shot reads, which finds the most likely haplotypes by approximating local genealogical history as a perfect phylogeny.
HApredictor is an HA-specific prediction tool which showed disease prediction accuracy comparable to other publicly available prediction software.
Program for generating case-control multi-locus genotype data under a specified disease model.
An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. HapSolo is compatible with Python 2.7 and requires the PANDAS package be installed. There is support for Python 3, but Python 2.7 runs faster.
Hapsolutely is a tool for haplotype phasing, network construction, and haploweb calculation, designed for integrative taxonomy workflows. It integrates data input, phasing, network reconstruction, and visualization of haplowebs, facilitating species delimitation.
Software for finding tag SNPs. It is compared with existing methods as well as the official tagging tool (called Haploview) of the International HapMap project using a variety of real data sets.
Haptendb is a database of haptens which provide comprehensive information about the Hapten molecule, ways to raise antibodies against particular group of haptens, specificity and cross reactivity of raised antibody with related haptens, use of antibodies in constructing cost effective and simple detection kits.
Haptools is a collection of tools for simulating and analyzing genotypes and phenotypes while taking into account haplotype and ancestry information.
Polyploid haplotype assembly tool based on a statistical framework.
Lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.
A Flexible Highlighting Annotator for Ranking and Exploration. HARE: Highlighting Annotator for Ranking and Exploration. This open-source software package implements two components of a pipeline for identifying information relevant to a specific topic in text documents:.
A curated database of RNA-small molecules structures to aid rational drug design.
PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.
A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity. This is the Github page for the code used in manuscript S. Jiang et al 2019. HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity (https://www.frontiersin.org/articles/10.3389/fgene.2020.00445/full).
Harmonization of diffusion MRI datasets with adaptive dictionary learning. Harmonization of diffusion MRI datasets across scanners.
Harmonizome is a resource integrating knowledge about genes and proteins from diverse multi-omics resources, providing researchers with a unified platform to explore and integrate biological data.
Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.
Fast, sensitive and accurate integration of single-cell data with Harmony. Scalable integration of single cell RNAseq data for batch correction and meta analysis. Check out the latest preprint of Harmony on bioRxiv. Harmony has been tested on R versions >= 3.4. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms.
A database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. Last updated on September 22, 2020. HARP - A Web Resource for Predicted Structural Impacts of Anti-microbial Resistance Mutations in Leprosy. HARP (a database of Hansen's Disease Antimicrobial Resistance Profiles) is an integrated web-resource with predicted structural implications of systematic mis-sense mutations in known drug targets of Mycobacterium leprae.
HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.
The package is used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.
HARU is a heterogenous compute solution for Oxford Nanopore Technologies' adaptive sampling (also known as selective sequencing and Read Until). Read Until allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to a genomic region of 'interest'. HARU takes advantage of heterogenous edge compute platforms and provides hardware acceleration using reconfigurable hardware on a Multiprocessor system on a chip (MPSoC).
Fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.
A framework for hierarchical feature learning and selection from whole genome sequencing data. Contribute to cmlh-gp/harvestman-public development by creating an account on GitHub.
A tool for analyzing NGS datasets form pooled haploid mammalian cell screens. It is used to identify insertion locations in the whole genome, map them at the level of genes, and classify insertions according to their effects on gene function.
Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile. A tool for core-genome MLST typing for bacterial data. This has been initially developed for Clostridium difficile, but could be adpated to other bacteria. Singularity - instructions can be found here https://github.com/sylabs/singularity/blob/master/INSTALL.md. This workflow will run on systems that support the dependencies above. It has been tested on MacOS, Ubuntu and CentOS. Minimal system resources are required to generate hash-cgMLST profiles alone, however generating assemblies using SPAdes is the main resource constraint for the whole pipeline, the amount of memory to use per core can be set in the nextflow.config file, e.g. 8 Gb. Java version 8 or later (required for nextflow).
HashSeq infers true biological 16S rRNA sequence variants from sequence errors generated from an Illumina sequencing instrument.
Fast Hybrid Assembly of Long Reads. HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. HASLR is capable of assembling large genomes on a single computing node. Our experiments show that it can assemble a CHM1 human dataset in less than 10 hours using 64 CPU threads.
Server designed as a scientific tool for researchers to visualize their phylogenetic, biochemical, and immunological HA data in the three-dimensional context of the HA structure, in the hopes that the context may help researchers better interpret their data and generate new hypotheses.
Accurate Haplotype-Resolved Assembly Reveals The Origin Of Structural Variants For Human Trios. Partition stLFR reads based on trio-binning algorithm using parentally unique markers.
Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit. Client for the HASTE Storage Engine. Smart middleware for working with a variety of storage media with Scientific Computing datasets. Supports Python 2.7 and Python 3.*.
A collection of software components that can be used to build intelligent streaming pipelines for scientific data streams.
HASTEN is a tool that makes it easier to run machine learning boosted virtual screening workflows. It is written in very general Python without relying in non-standard libraries so it is easy to run in any Python environment Currently only chemprop is supported as machine learning method, but it is easy to write Shell-scripts to plug-in your own methods. Glide from Schrodinger is supported in this version, but the same applies here: it should be easy to plug-in your own docking program. Do note that the HASTEN assumes that the smaller the docking score, the better the score. There is also simulation mode, which allows you to run benchmarks using existing docking_scores without in reality doing anything in 3D. This mode can be useful when adjusting the machine learning parameters.
HATK(HLA Analysis Tool-Kit) is a collection of tools and modules to perform HLA fine-mapping analysis, which is to identify which HLA allele or amino acid position of the HLA gene is driving the disease. HLA fine-mapping analysis is an indispensable analysis in studies of autoimmune diseases.
Increased specificity for analysis of tiling-array data in comparison with alternative methods, and that it accurately detected regions-of-interest in different applications of tiling-arrays.
C-program for the identification of attC sites in any type of DNA data. It uses a hidden Markov model (HMM) to describe each part of the attC site in a probabilistic manner.
Bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. HAVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples.The pipeline is ideal for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks.
An interactive visual analytics tool for genome assemblies.
Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline.
Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis. Hierarchical Bayesian Analysis of Differential Expression and ALternative Splicing (HBA-DEALS).
HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis of potential hydrogen bonds and similar type of weak interactions in macromolecular structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric approach to identify molecular interactions by analysing distance and angular criteria. HBAT 1.1 was released in 2007 as closed source Windows binary and continue to be available via SourceForge. HBAT 2.0 was introduced in 2025 and a completed rewrite of original implementation with cross-platform support. HBAT 2.0 is open sourced under MIT License.
hBayesDM (hierarchical Bayesian modeling of Decision-Making tasks), which offers computational modeling of an array of reinforcement learning and decision-making tasks and social exchange games.
The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.
HCA-Vision is an automated image analysis software package developed by CSIRO that rapidly and reproducibly measures and reports on important cell features for drug discovery.
Hilbert-Curve Assisted Structure Embedding Method. Hilbert-Curve Assisted Structure Embedding (HCASE) Method. This repository contains source code of the Hilbert-Curve Assisted Structure Embedding (HCASE) method. The method and a proof-of-concept study has been published as a preprint and can be accessed here: https://chemrxiv.org/articles/Hilbert-Curve_Assisted_Structure_Embedding_Method/11911296 .
Features an nnU-Net based segmentation tool capable of performing HCC segmentation for both arterial and portal venous phase in polyphasic contrast-enhanced abdominal CT. Please be mindful that the usage instructions below are for the image in the EUCAIM Harbor.
HCC segmentation tool for contrast-enhanced abdominal CT
HCDT (Highly Confident Drug-Target Database) is a combined database that provides validated associations between drugs and target genes.
Validation of an online tool for early prediction of the failure-risk in gestational trophoblastic neoplasia patients treated with methotrexate. hCG trophoblastic tumor or neoplasia.
A novel statistical method for phenome-wide association studies. We derived a novel and powerful multivariate method, which we referred to as HCLC-FC (Hierarchical Clustering Linear Combination with False discovery rate Control), to test the association between a genetic variant with multiple phenotypes for each phenotypic category in phenome-wide association studies (PheWAS). The R package HCLCFC is a novel tool that allows users to partition a large number of phenotypes into disjoint clusters; applicable to electronic medical records (EMR)-based PheWAS.
Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.
Hi-C Matrix Balancin (HCMB) is a Python package for processing the normalization of highly sparse Hi-C contact data.
hCoCena is an R-package that allows you to integrate and jointly analyse multiple transcriptomic datasets or simply analyse a single dataset if you don't want to do any data integration.
A genetic and proteomic database for the SARS-CoV, MERS-CoV, and SARS-COV-2.
An efficient docking method for modeling covalent protein-ligand interactions.
HCP Suite is a software collection consisting of (1) a Python-based framework for connectome-based analysis (CPM) using Ray to parallelize CPM which has become the main focus of this project and (2) a set of scripts to perform common operations and analyses on the Human Connectome Project's neuroimaging data with a focus on task-based fMRI.
HCS is an algorithm for simulating omics datasets that preserves the correlation structure of the original data using hierarchical clustering and principal components. The code and data are available on GitHub and described in a peer-reviewed publication.
HCS-hierarchical algorithm for simulation of omics datasets
Decompose given hierarchical clustering tree into non-overlapping clusters in a semi-supervised way by using available patients follow-up information as guidance. Contains functions for snipping HC tree, various cluster quality evaluation criteria, assigning new patients to one of the two given HC trees, testing the significance of clusters with permutation argument and clusters visualization using sample's molecular entropy.
HCTSA is a tool for highly comparative time series analysis, used to extract features from oxygen saturation and heart rate data in preterm infants to predict respiratory outcomes. It leverages existing code from multiple disciplines and includes documentation and installation instructions on its GitHub repository.
A specialized and medically-oriented database of published variations observed within the internal ribosome entry site (IRES) variants in hepatitis C virus.
A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. A web server for predicting the bioactivity of HCV NS5B inhibitors. Enter your input molecule(s) in SMILES notation Insert example data.
Visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering. Please select ONE file to upload. You may select up to 5 files to upload.
A simple and transparent application for virtual screening of histone deacetylase 1 inhibitors.
A Machine Learning-based Computational Tool to Screen for HDAC3 Inhibitors. HDAC3i-Finder is a python GUI application for virtually screening for HDAC3 inhibitors with a thoroughly validated machine-learning model 'XGBoost_Morgan2', i.e. the model built with XGBoost as the algorithm and Morgan2 fingerprints as features. It was designed to run on any Windows-based machine.
A resource of human disease associated mutations from next generation sequencing studies.
This package implements a class for manipulating HDF5 datasets.
Software for flexible high structural resolution of hydrogen/deuterium-exchange mass spectrometry data.
A novel GUI based application for gene selection and classification in high dimensional datasets.
A Web-Based Interactive Program for High-Dimensional Analysis of Molecular Alterations in Cancer. HDMAC is a web-based shiny App that provides high-dimension regression analysis for both survival (Cox PH regression) and binary outcomes (logistic regression), including ridge, lasso, adaptive lasso regression analysis. Users can use this App to do high dimensional regression analysis online without downloading or installing any software. In ad….
HDMC (Hierarchical Distribution Matching and Contrastive learning) is a novel deep learning based framework for batch effect removal in scRNA-seq data.
The Health Data Nexus is T-CAIREM's unique online platform for health data sharing & analytics that emphasizes patient privacy and security, provides transparent and speedy access, and simplifies data discovery and analysis.
Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking.
Characterization of intra-individual variability generates physiology-measurement data that can be written as a matrix with the different subsamples in the columns and the different phenotypic units in the rows. These datasets are called high-dimensional transposable data. The package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.
A Comprehensive Hepatitis D Virus Database. Welcome to Hepatitis Delta Virus Database (HDVdb). The Hepatitis D Virus (HDV) Database, HDVdb contains comprehensive data on HDV genetic sequences that allows the researchers to investigate the genetic variability of the virus. The HBV database strives to present HDV-associated sequences,as well as providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.
hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular and can construct co-expression networks across multi-scale cellular and spatial hierarchies. hdWGNCA identifies robust modules of inerconnected genes, and provides context for these modules through various biological knowledge sources. hdWGCNA requires data formatted as Seurat objects, one of the most ubiquitous formats for single-cell data.
Integrated software platform for HDX data analysis.
HDXer is a Python package that can be used to: compute Hydrogen-Deuterium exchange (HDX) data from an atomistic ensemble of protein structures and reweight a candidate ensemble by applying a maximum-entropy biasing scheme, so that the computed HDX data conform to a target experimental set of HDX-MS data, within a defined level of error.
HDXfit is a package for fitting the site exchange probabilities to peptide mass envelopes from hydrogen/deuterium exchange of a protein.
Allows ready access to the hematopoietic expression data, enhancing our ability to analyze and to identify genes that may be important in hematopoiesis, stem cell biology or blood malignancies among other uses.
HEA-PSP is a hybrid evolutionary search framework with various crossover implementations for Ab-initio protein structre prediction
A growing collection of highly realistic synthetic medical datasets that can be freely accessed to prototype, evaluate, and compare machine learning algorithms, with a specific focus on reinforcement learning.
Box plots of measured quantity in healthy vs. disease in two cohorts
Highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.
Data-Intensive AI platform with a Feature Store. Open-source PaaS for distributed data management, data analysis, and machine learning based on Hopsworks: https://www.hopsworks.ai/ https://docs.hopsworks.ai/latest/ Deployed at CSC– IT Center for Science: https://heap-hopsworks.csc.fi/login
Automatic peak-picking pipeline for targeted proteomic data powered by 2D heatmap transformation and convolutional neural networks.
Heart Disease detection by Multi-SVM and other classifiers: SVM, KNN, etc.
Heart Disease detection by Multi-SVM and other classifiers
A tool for transferrable, automated measurement of heart rate and heart rate variability in transparent animals.
Web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain.
Freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface.
This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.
Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.
Tool for simulation of bacterial (more exactly prokaryotic) communities. It is based on the original modeling approach investigated in the Laboratory of molecular-genetic systems at the Institute of Cytology and Genetics (Novosibirsk, Russia).
The human Ensemble Cell Atlas (hECA) a database.
A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.
A computational model for predicting potential lncRNA-disease associations based on multiple heterogeneous networks.
Linear mixed model based approach to partition the total heritability into the contributions of genomic regions.
Tool for single-species active module discovery.
iTOL is a web-based tool for displaying, annotating, and managing phylogenetic trees. It allows users to visualize trees, add annotations, and share results online.
HELIQUEST calculates the physicochemical properties and amino acid composition of an ��-helix and screens databank to identify protein segments possessing similar features. This server is also dedicated to mutating helices manually or automatically by genetic algorithm to design analogues of defined features.
Open-source LINUX software package intended for use in analyzing data produced by the HeliScope Single Molecule Sequencer.
The Human Early Life Exposome (HELIX) cohort study gathers longitudinal population-based birth cohort data from six European countries. It includes biomarkers, omics signatures, and health outcomes. Researchers can get access to this data upon request.
HelixCorr is a software to predict correlated mutations specifically for the transmembrane parts of membrane proteins. It includes predictions obtained by several individual prediction algorithms and combines them to a consensus prediction.
Deep Learning to predict gene annotations
HelixPSO (Particle Swarm Optimizer) is a multi swarm algorithm that searches the conformation space of an RNA sequence for low lying structures. Fitness is a combination of free energy and agreement with the centroid structure in the thermodynamic ensemble. HelixPSO has been used on sequences of up to 1500 nucleotides.
Identify nucleic acid-binding motifs in protein sequences.
Visualize α-Helical Peptides in Python. Create 2-dimensional visualizations of alpha-helical peptide sequences. helixvis: Visualize alpha-helical peptide sequences in Python.
HELLO is a Deep Neural Network-based small variant caller that can call variants for Illumina, PacBio, and hybrid Illumina-PacBio settings. HELLO uses customized Deep Neural Networks which provide accurate variant calls with relatively small model size.
Translates bedtools command-line invocations to R code calling functions from the BioConductor *Ranges infrastructure. This is intended to educate novice BioConductor users and to compare the syntax and semantics of the two frameworks.
The package contains a modular pipeline for analysis of microarray data, and includes graphical and mathematical tools with more general applications.
HelPredictor is a tool that models single-cell transcriptome to predict human embryo lineage allocation.
Functions for working with X-ray data measured in the Industrial Mathematics Computed Tomography Laboratory at the University of Helsinki.
This package fits heterogeneous error models for analysis of microarray data.
This tool provides a plot of gene expression in hematopoietic cells at different maturation stages based on curated microarray data.
A family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction.
HEMnet is a deep learning automated cancer diagnosis software using molecular labelling to improve pathological annotation of Haematoxylin and Eosin (H&E) stained tissue.
Plugin for continuous conformational flexibility analysis containing HEMNMA and StructMap
Database of experimentally determined hemolytic and non-hemolytic peptides.
HemoMIPs-Automated analysis and result reporting pipeline for targeted sequencing data. The hemoMIPs pipeline is a fast and efficient analysis pipeline for the analysis of multiplexed and targeted NGS datasets created from Molecular Inversion Probes (MIPs). It runs highly automated using conda und snakemake and can be set to use GATK v4 or GATK v3 for variant calling. It reports benign and likely pathogenic variants in a userfriendly HTML report that shows detailed performance statistics and results.
Predicting Hemolytic Activity with Integrated Feature Learning A neural network that perdict hemolytic activity classification of a peptide sequence along with inforamtion of N/C terminal modifications.This network captures context of amino acid with SeqVec embedding, Circular Fingerprint repersatation of N/C terminal modification's SMILES.
Allows user to predict predict hemolytic or hemotoxic or RBC lysing potential of a peptide. It allow users to perform various functions that includes virtual screening of peptides, analog-based peptide design.
A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure. HemoPI-MOD is an in silico method, which is developed to predict hemolytic or hemotoxic or RBC lysing potential of a peptide. The main dataset used in this method consists of 582 modified hemolytic peptides and 582 non-hemolytic peptides. This full dataset was divided into two parts (i) Training dataset and (ii) Validation dataset.
BrainSpace is a software package used to analyze functional connectivity patterns in resting-state fMRI data, particularly focusing on psychosis spectrum disorders. It allows for the calculation of entropy-based measures of connectivity and investigates their relationships with cognitive performance and other neurobiological factors.
Druginteractions Effect of comedication on ombitasvir/paritaprevir/ritonavir ± dasabuvir ± ribavirin therapy in chronic hepatitis C. Cookies help us deliver our services. By using our services, you agree to our use of cookies. OK Learn more. Access our free, comprehensive and user-friendly drug interaction charts.
A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Providing Bioinformatics Data For The Study Of Liver Diseases. a liver disease microarray database, visualization platform and data-mining resource. Hepamine was designed as a web-based repository of pre-analyzed microarray data for various liver diseases. Among these are HCC, CCC, liver cirrhosis, chronic hepatitis B and C, or biliary atresia. In contrast to public microarray repositories our website offers open and easy access to the respective, pre-analyzed gene expression profiles and support to compare samples, experiments and various liver diseases. Genes may be searched on the basis of specific expression patterns across diverse samples. All may be obtained as a simple three color table indicating up-, down-, or no differential expression in multiple experiments. Alternatively, users may choose to obtain a detailed, comparative expression data table.
Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies. deal_with_data_tg_invitro.R plays the code for feature selection of open_tggate_liver_single_rat_invitro. deal_with_data_tg_invivo.R plays the code for feature selection of open_tggate_liver_single_rat_invivo. deal_with_data_dm_invivo.R plays the code for feature selection of drug_matrix.
an atlas of enhancer RNAs across human tissues. The H uman e nhancer R NA A tlas (HeRA) provides the expression Landscape of enhancer RNA (eRNA) across 54 human tissues. An eRNA is a type of non-coding RNA transcribed from the enhancer region of DNA and plays important roles in shaping complex human traits and diseases. In this data portal, we provide four modules to explore eRNAs: Expression , associated Traits , potential Regulators , and potential Target Genes across human tissues.
HerbKG, a knowledge graph that bridges herbal and molecular medicine
HerceptinR is a database of assays performed to test sensitivity or resistance of Herceptin Antibodies towards breast cancer cell lines.
Hermes introduces a new “describe once, run anywhere” paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach.
RHermes is a broad-scoped targeted metabolomics software designed to analyse LC-MS and LC-MS/MS data to identify compounds in biological or environmental samples.
HERON is an R package designed for analyzing peptide binding array data, identifying epitopes, and calculating significance at the probe, epitope, and protein levels across multiple samples. It leverages meta p-value methods and spatial clustering techniques to estimate antibody targets.
HESML is an efficient, scalable and large Java software library of ontology-based semantic similarity measures and Information Content (IC) models based on WordNet, SNOMED-CT, MeSH or any other OBO-based ontology.
An R package for Gaussian graphical model-based heterogeneity analysis. Gaussian Graphical Model-Based Heterogeneity Analysis.
A heterogeneous ensemble algorithm which is the voting of multi-expert classifiers, SVM, kNN, and RF, in the task of pre-miRNA classification. Our model is trained on both human and plant pre-miRNA data and utilize robustness derivative features which has shown to be well distinquishing both plant and animal pre-miRNA hairpins from other non pre-miRNA hairpin-forming sequences.
Python package for matrix storage and operations on hetnets
HETTMO is an R package presenting a Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models, incorporating features like incomplete case ascertainment adjustment and flexible transmission rate modeling.
Heu-MCHC is a fast and accurate heuristic for the Minimum-Change Haplotype Configuration (MCHC) problem, i.e. a combinatorial formulation of the haplotype inference problem on pedigree data where the total number of recombinations and point mutations has to be minimized.
Accurate and Fast Detection of Genetic Variations with a Novel Heuristic Amplicon Aligner Program for Next Generation Sequencing.
Information on diverse sources of chemicals with the aim to explore human health risk from chemical exposure.
HexSE is a Python module designed to simulate sequence evolution along a phylogeny while considering the coding context of the nucleotides. The ultimate porpuse of HexSE is to account for multiple selection preasures on Overlapping Reading Frames.
A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.
Harmonic Feature Activation for Few-Shot Semantic Segmentation. Few-shot semantic segmentation remains an open problem because limited support (training) images are insufficient to represent the diverse semantics within target categories.
A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms.
A biomarker knowledge database for heart failure heterogeneity and personalized applications.
Heart Failure Integrated Platform (HFIP) is an integrated multi-omics data and knowledge platform for the precision medicine of heart failure.
A MATLAB-based graphic user interface for high frequency oscillations marking.
The LANL hemmorhagic fever virus database, a new platform for analyzing biothreat viruses.
Fast hierarchical clustering for large-scale single-cell data. The core function of HGC takes a graph G as the input. Here G is the adjacency matrix of a graph of cells, where the element in G are the weights of edges in the graph, and zero means no link between the corresponding node pairs. G should be a dgCMatrix supported by the R package Matrix.
The Human Gene Coexpression Analysis tool (HGCA) is based on the coexpression analysis of 55431 Human genes from gene pair correlation data of 3500 RNASeq samples from the GTEx Project
Prioritizing disease-causing gene variants by biological distance.
The Hymenoptera Genome Database is a comprehensive model organism database for insect species of the order Hymenoptera. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains.
An integrated homologous gene database across multiple species.
HGDiscovery is an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase.
A heterogeneous graph embedding model for predicting interactions between transcription factor and target gene.
A collective database of helmeted guinea fowl genomics. Helmeted guinea fowl (HGF; Numida meleagris) is vigorous, hardy, and mostly disease-free game birds. The rearing of HGF is a potential alternative poultry system. Because of the characteristics of the HGF, the study of HGF is valuable, so we conduct an improved domesticated HGF genome de novo assembly generated by long and short read sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds including domesticated animals, wild progenitors, and closely related wild species. The data are important to provide valuable genetic resources for researchers and breeders to improve production in this species. For this purpose, we have developed a comprehensive and easy-to-use web-based database, HGFDB.
Hierarchical Guided Genome Assembler (HGGA) a framework to guide genome assembly with additional data.
Heterogeneous graph inference with matrix completion for computational drug repositioning. Inspired by the low-rank completion of BNNR and the guilt-by-association principle of HGBI, we propose a heterogeneous graph inference with matrix completion (HGIMC) method to predict potential indications for drugs. Overview This repository contains data and code for HGIMC method, which is based on the model at https: github.com BioinformaticsCSU HGIMC. November 23, 2020 Software Open Access.
The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications including searching for an overview of known mutations associated with a particular disease, interpreting clinical test results or looking for the likely causal mutation in a list of variants.
Database of unique and meaningful names for all human genes.
Identification and correction of invalid gene symbols for human and mouse. Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols.
Human Gene and Protein Database: presents SDS-PAGE patterns and other informations of human genes and proteins. Stores info on a set of human Gateway entry clones in addition to protein expression and protein synethesis data.
Henry Gas Solubility Optimization-based Random Forest for C-Section prediction and XAI-based cause analysis.
A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks.
Identifies the integration of viruses into the human genome using the sequencing data.
Computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics.
Tool for facilitating the identification and phylogenetic analysis of horizontal gene transfer.
A comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.
A standard pipeline to study horizontal gene transfer.
A tool for measuring interspecies conservation scores.
The tool detects significant single- and multi-locus SNP associations in case-control studies.
This tool identifies which SNPs create amino-acid changes in the specified coding regions.
This tool provides functional annotation for a list of genes by connecting with DAVID database.
The tool detects significant single-SNP associations in case-control studies at a user-specified FDR.
This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus.
This tool creates a link to the g:GOSt tool (Gene Group Functional Profiling), which provides functional profiling of gene lists.
A tool for LASSO-Patternsearch algorithm. The LASSO-Patternsearch algorithm fits your dataset to an L1-regularized logistic regression model.
A tool that detects significant transcription factor binding sites from ChIP data.
Attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.
For general help inquiries and site feedback
For study authors to request data updates or submit new data
Protein motif discovery method that combines hidden Markov model (HH-) comparisons with a hierarchical representation of identified SLiMs in motif trees.
Open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
Useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.
The first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, it greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.
Database of human heterochromatin regions.
Pipeline for HMM-HMM comparison based hierarchial clustering and analysis of potential paralogues in sequence set.
Database which focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. It incorporates 43 location-specific histone modifications in human. The database can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. Database also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown.
Web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, it builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.
Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.
Tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).
Tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, it is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.
HH-suite is a remote protein homology detection suite.
Program for haplotype reconstruction from paired-end reads.
A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.
A software to predict Hi-C matrices based on ChIP-seq histone data using a cGAN approach.
Hi-ChIP-ML is a machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features.
Novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.
High-performance python and apache spark packages for feature selection with high-dimensional data.
Set of functions to annotate a GRanges object with custom set of annotations. This package takes two GRanges objects (query & subject) with a common set of seqnames (i.e. chromosomes) and returns associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands).
It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. It can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging (improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection), an ensemble classifier method, with haplotype inference for SNPs and HLA types.
HIBAG is a Bioconductor package that imputes HLA classical alleles using GWAS SNP data, utilizing an attribute bagging approach. It predicts psoriasis and its associated phenotypes in Taiwanese populations, incorporating polygenic risk score analysis.
HIBLUP is an user-friendly software that provides estimated genetic value of each individual by maximizing the usage of information from pedigree, genome, and phenotype.
Interactive and dynamic browser for synchronous Hi-C data visualization.
A systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Software tool for Hi-C HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework
A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C. This will install the python package (and its cli command) hic_hiker.
This tool was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, it can analyze data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C. The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler.
A computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization.
Framework to extract various one-dimensional features from chromosome structure data.
HiC4D is a tool for forecasting spatiotemporal Hi-C data with residual ConvLSTM (ResConvLSTM).
hicGAN infers super resolution Hi-C data with generative adversarial networks | Hi-C data super-resolution with generative adversarial networks | We proposed hicGAN, an open-sourced framework, for inferring high resolution Hi-C data from low resolution Hi-C data with generative adversarial networks (GANs)
Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Koren N, Walenz BP, Rhie A, Vollger M, Grothe R, Logsdon GA, Eichler EE, Phillippy AM, Koren S. HiCanu: precise assembly of segmental duplications and haplotypes using high-fidelity long reads. Biorxiv. (2020). Canu is a hierarchical assembly pipeline which runs in four steps:. Detect overlaps in high-noise sequences using MHAP.
Probe design and proximity detection for targeted chromosome conformation capture applications.
HiCARN: Resolution Enhancement of Hi-C Data Using Cascading Residual Networks
Hi-C data analysis tool. Importantly, HiCat is focussed on analysis of larger structural features of chromosomes and on comparative studies.
HiCBin is a new open-source metagenomic Hi-C-based binning pipeline to recover high-quality MAGs. HiCBin employs the HiCzin normalization method and the Leiden community detection algorithm, and includes the spurious contact detection into binning pipelines for the first time.
It provides functions for joint normalization and difference detection in multiple Hi-C datasets. It operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources.
identifying long range chromosomal contacts in Hi-C data. Scripts for prediction of long-range interactions between regions/domains based on Hi-C maps. Establish contact!. HiCEnterprise takes a list of regions/domains and searches for their significant interactions on given Hi-C maps. Package consists of two types of analyses: regions and domains. HiCEnterprise is a software tool for identification of long-range chromatin contacts based on the Hi-C experiments.
A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. HiCExplorer — HiCExplorer 3.6 documentation. scHiCExplorer — scHiCExplorer 7 documentation. Free document hosting provided by Read the Docs.
a package to correct and analyze the diploid Hi-C data. An integrated package to process diploid Hi-C data. HiCHap is a Python package designed to process and analyze Hi-C data, primarily the diploid Hi-C data for phased haplotypes.
A comprehensive database of HiChIP regulatory interactions.
A Python package for HiChIP data processing and quality control pipeline.
A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data.
HiCMC is a compression tool designed to efficiently reduce the size of Hi-C data by modeling underlying structural properties. It outperforms existing methods and provides a pathway for speeding up downstream analyses.
HiCNorm is a parametric model to remove systematic biases in the raw Hi-C contact maps. It relates chromatin interactions and systemic biases at the desired resolution level,resulting in a simple, yet accurate normalization procedure. Compared to the exiting Hi-C normalization method, our model has only a few parameters, is much easier to implement, can be interpreted intuitively, and achieves higher reproducibility in real Hi-C data
Python data visualization tool for integrating different data types with interaction matrixes.
HiCrayon is a tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. It is implemented using R shiny and python and available in both web or containerized format.
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth.
Fast comparison of Hi-C contact matrices in Python. A fast implementation of the HiCRep algorithm for computing similarities between pairs of Hi-C matrices. This repository is temporarily located at https://github.com/dejunlin/hicrep.
a computational method to estimate and predict the resolution of HiC libraries. Estimating and predicting HiC library resolution. The purpose of this container is to estimate the resolution of your HiC library and to predict the resolution the same library will reach when sequenced at deeper level. There are two main functionality to use HiCRes: you can either start from your analyzed library by providing a bam file containing the valid read pairs and the genome index you used (much faster option) or you can start from your raw sequencing data by providing the 2 fastq files, the enzyme you used, and the species (much slower, limited to human and mouse for now, and MboI, HindIII or Arima digestions).
a Hi-C super-resolution framework for producing highly realistic contact maps. Implementation of HiCSR framework described in this paper:. HiCSR is a Hi-C super-resolution framework written in python capable of producing enhanced contact maps which are both accurate and realistic. The HiCSR framework optimizes for a weighted combination of adversarial loss, pixel-wise L1 loss, and a feature reconstruction loss obtained from the latent representation of a task specific denoising autoencoder.
A lightweight library that generates and handles Hi-C contact maps in either cooler-compatible 2Dbedgraph or instaGRAAL format.
Blazing fast toolkit to work with .hic and .cool files
Python bindings for hictk: read and write .cool and .hic files directly from Python
R bindings for hictk: read .cool and .hic files directly from R
Interactive visualization of multiscale and multimodal Hi-C and 3D genome data.
A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts.
HiCzin is a tool for normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression.
a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data. Time-series hidden state visualization toolkit based on JavaScript, Python and ECharts framework.
Software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species. It takes as input a collection of unrooted gene trees along with a rooted species tree.
HIDECAN is an R package for generating visualizations that summarize genome-wide association studies (GWAS), differential expression analyses, and manually curated candidate genes. It is available on CRAN and GitHub and is part of the VIEWpoly tool for polyploid data exploration.
HiDeF (Hierarchical community Decoding Framework). HiDeF is an analysis framework to robustly resolve the hierarchical structures of networks based on multiscale community detection and the concepts of persistent homology.
Orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root. This concept reduces the total runtime complexity from a quadratic to a linear function of the number of species. The tree hierarchy provides a natural structure in multi-species ortholog groups, and the aggregation of multiple sequences allows for multiple alignment similarity searching techniques.
It is an implementation of hierarchical (a.k.a. multi-scale) Kalman filter using belief propagation.
Hierarchical Kalman Filter for clinical time series prediction
We developed an algorithm that deals with Hierarchical Feature Spaces, with focus on relative abundances of microbial communities but with the potential to be expanded to a wide range of Machine Learning tasks were features have an underlying hierarchical structure.
Hierarchicell is an R-package for estimating power for tests of differential expression with single-cell data.
REST Web service to get parents, children or siblings of an ontology term from a BioPortal ontology.
A multi-level clustering scheme for population assignments based on core genome MLST. HierCC (Hierarchical clustering of cgMLST). HierCC is a multi-level clustering scheme for population assignments based on core genome Multi-Locus Sequence Types (cgMLSTs). HierCC has been implemented in EnteroBase since 2018.
Hierarchical Random Forest for Information Transfer. Release First release of HieRFIT. There is an increasing demand for data integration and cross-comparison in the single cell genomics field. This release is a working version of HieRFIT with full functionalities.
Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.
High-throughput FISH detection of endogenous pre-mRNA splicing isoforms.
Estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution. A tool for high-resolution estimation of DNA-DNA interaction frequency from Hi-C data. HIFI is a set of tools to infer true intra-chromosomal interaction frequencies at restriction fragment (RF) resolution from Hi-C data. It uses adaptive kernel density estimation and Markov Random Field approaches to provide accurate estimates of interaction frequency matrices from sparse read-count matrices.
Efficient COI barcoding using high throughput single-end 400 bp sequencing. The BGISEQ-500 platform has launched a new test sequencing kits capable of single-end 400 bp sequencing (SE400), which offers a simple and reliable way to achieve DNA barcodes efficiently. In this study, we explored the potential of the BGISEQ-500 SE400 sequencing in DNA barcode reference construction, meanwhile provided an updated HIFI-Barcode software package that can generate COI barcode assemblies using HTS reads of length >= 400 bp.
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
HiFiBGC is a command-line workflow for identifying biosynthetic gene clusters (BGCs) in PacBio HiFi metagenomes. The workflow leverages an ensemble of assemblies to improve BGC recovery and is available on GitHub under the MIT license.
Integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs.
The software package HiFiX implements the novel algorithm for HIgh FIdelity Clustering of Sequences.
HIFU-beam is a free open source software with graphical user interface for modeling nonlinear axially symmetric focused ultrasound beams with account for possible formation of shock fronts.
Homology independent protein function prediction by a novel protein-language self-attention model.
Hierarchical Representations of Gene Ontology and Genes in the Poincaré Ball. Preprint version available here https://www.biorxiv.org/content/10.1101/2020.07.14.195750v1. git clone https://github.com/JaesikKim/HiG2Vec.git. Simply clone this repository via.
Bacteriological, clinical, genomic and proteomic database of H. influenzae.
Simulates high intensity focused ultrasound beams and heating effects in layered media
High intensity focused ultrasound simulator
A double-viewed hierarchical graph learning model, HIGH-PPI, to predict PPIs and extrapolate the molecular details involved.
An integrated resource for High-Altitude associated genes and proteins, interacting networks and semantic-similarities. Around 140 million people live in High Altitude (HA) conditions and even a larger number visit it for tourism, adventure-seeking or sports training.
A library that provides high-level DICOM abstractions for the Python programming language to facilitate the creation and handling of DICOM objects for image-derived information, including image annotations, and image analysis results.
Software suitable for genetic map. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably.
A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention.
How to compute longitudinal GWAS data in population designs. Implementing Lasso methods to identify significant SNPs and estimate joint genetic effects for non-longitudinal traits or longitudinal traits in GWAS. The HiGWAS package is developed to identify significant SNPs that control phenotypic variation and estimate their additive and dominant genetic effects based on the Bayesian Lasso or Group Lasso model. The package provides two statistical models, BLS can detect the association using one single time measured phenotypc and GLS solve the association based on the longitudinal phenotype. [1]. Li, J., Das, K., Fu, G., Li, R., & Wu, R. (2011). The Bayesian lasso for genome-wide association studies. Bioinformatics, 27(4), 516-523. [2]. Li. J., Wang, Z., Li, R., Wu, R.(2015).Bayesian Group Lasso for nonparametric varying-coefficient models with application to functional genome-wide association studies. The Annals of Applied Statistics. 9(1).
HIHISIV is a database integrating gene expression data associated with HIV and SIV infection in both hosts and pathogens, designed to facilitate research on lentiviral pathogenesis and host immune response.
New Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different cell types, developmental stages, even multiple species) using genome-wide histone modification data.
HIV-1 incidence and infection time estimator, which processes envelope gene sequences using hierarchical clustering algorithms and informs the stage of infection, along with time since infection for incident cases.
Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.
Functions to visualize long vectors of integer data by means of Hilbert curves.
An interactive tool to visualize long vectors of integer data by means of Hilbert curves.
Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks.
Web server for predicting rigid protein parts and the flexible hinge regions connecting them in the native topology of protein chains by employing elastic network (EN) models.
HMM-based Identification of TF Footprints
human integrated Pathway DataBase with facile visualiztion: an integrated pathway databasethat combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta, and KEGG.
Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.
Using mechanistic models for the clinical interpretation of complex genomic variation. The sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caused by a unique or a few genes. However, the discovery of causal genes in complex diseases has been far less successful. Many complex diseases are actually a consequence of the failure of complex biological modules, composed by interrelated proteins, which can happen in many different ways, which conferring a multigenic nature to the condition that can hardly be attributed to one or a few genes.
Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.
hiphop is an R package for paternity assignment among close relatives using a simple exclusion method for biallelic markers.
Make NGS data analysis quick and easy with high performance pipelines and intuitive web GUI.
Hiplot (https://hiplot.org) provides concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Hiplot (ORG) is maintained and updated by the Openbiox open-source community.
HipMCL: A High-Performance Parallel Algorithm for Large-Scale Network Clustering
Workflow for analyzing Hi-C paired-end reads in FASTQ format and predict enhancer–target gene interactions. HIPPIE streamlines the entire processing phase including reads mapping, quality control and enhancer–target gene prediction as well as characterizing the interactions.
HippoMaps is an open-access toolbox and online data warehouse for mapping and contextualizing hippocampal data in the human brain. It utilizes hippocampal unfolding and shape intrinsic registration to allow for cross-subject and cross-modal data aggregation.
A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. This package contains validation tests for models of hippocampus, based on the SciUnit framework and the NeuronUnit package. The purpose of this repository is to provide examples on how to run the validation tests of HippoUnit on models of the hippocampal CA1 pyramidal cell available in the literature and on ModelDB. Current tests cover somatic behavior and signal propagation and integration in apical dendrites of hippocampal CA1 pyramidal cell models. Feature errors: Z-score (the difference of model feature value from the exerimental mean feature value in the unit of the experimental SD.). git clone https://github.com/KaliLab/hippounit.git.
Hipsec is a tool for predicting high-level protein production in Aspergillus niger. The software predicts if gene overexpression of an extracellular protein will lead to successful high-level production in Aspergillus niger. The prediction is based on a protein’s amino acid sequence. One or more protein sequences can be pasted into the the text area (fasta format) or uploaded as a fasta file.
Haplotype inference and phasing for Short Tandem Repeats (hipSTR) is a haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data. It also enables genome-wide analysis and validation of de novo STR mutations.
Contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.
Database of HIV-1 resistance to broadly neutralizing antibodies.
HiRise is a software pipeline that can identify poor quality joins and produce accurate, long-range sequence scaffolds.
Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
leveraging higher-order structures for clustering analysis in biological networks. MOTIVATION:Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into the understanding of complex biological systems. Existing clustering techniques make use of lower-order connectivity patterns at the level of individual biological entities and their connections, but few of them can take into account of higher-order connectivity patterns at the level of small network motifs. RESULTS:Here, we present a novel clustering framework, namely HiSCF, to identify functional modules based on the higher-order structure information available in a biological network. Taking advantage of higher-order Markov stochastic process, HiSCF is able to perform the clustering analysis by exploiting a variety of network motifs
Hierarchical Structured Component analysis of microRNA-mRNA integration model is a novel statistical method to find biological relationship, efficiently study and identify such integrated markers. It could use subgroup information, it yelded more results, as related to phenotypes, than those of other existing methods that lack network information. It can be easily applied to other cancer studies to identify miRNA-mRNA integration sets for early diagnosis and prognosis.
Efficient all-vs-all long read aligner for SMRT sequencing data.
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. HiSIF - HiC Significant Interacting Fragments. HiSIF was implemented by using C++/C with parallel processing being written in C. It has been compiled and run exclusively on Linux operating systems. This tool only requires the g++ compiler and a reference genome for HG19. Standalone CERN ROOT C++ framework is used to extract fit parameters of the CTS interactions. A small C tool is provided to process the initial data from NCBI. HiSIF supports all of the available three Hi-C protocols (Hi-C, TCC and in situ Hi-C). The tool is named from the fact that it is designed to find the significant interactions from a given sample of Hi-C reads.
A bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Protein and nucleic acid interactions play a vital role in many biological processes such as DNA replication, repair and processing, as well as RNA processing and translocation.
HisPhosSite is a comprehensive database of histidine phosphorylated proteins and sites.
Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.
An interactive molecular scRNA-Seq reference of the human testis.
A user-friendly tool for cloud-based whole slide image segmentation. Histo-cloud (HistomicsTK-deeplab) is a modified version of HistomicsTK by Brendon Lutnick. HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI.
Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively.
Open-source Software for Histological Image Pre-processing and Augmentation to Improve Development of Robust Convolutional Neural Networks.
Federated learning for computational pathology on gigapixel whole slide images.
A browsable, manually curated, and relational database of human histone proteins and histone modifying enzymes. It contains 55 human histone proteins, 106 distinct sites of their post-translational modifications (PTMs) and 152 histone-modifying enzymes. Entries have been grouped into 5 types of histones, 8 types of post-translational modifications and 14 types of enzymes that catalyze addition and removal of these modifications.
HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI.
Python package for training Multiple Instance Learning models on histopathology slides.
Count the number of MS/MS ions in a given spectrum to determine the unambiguous localization of a post-translational modification (PTM). The software lists number and type of site determining ions found between the assigned PTM localization by Mascot (Matrix Science) and the closest other amino acids which can host the modification. The PTMs included in the script are phosphorylation (S,T,Y), acetylation (K), mono- and dimethylation (K,R) and trimethylation (K).
The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of interactive 3D slides that dissect the structural mechanism underlying the recognition of specific sequences and histone marks.
Structural Genomics of Histone Tail Recognition
Analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples.
Accurate reconstruction of ancestral sequences and evolutionary rates.
A Tool to Identify Nucleosome Free Regions from ChIP-Seq of Histone Post-Translational Modifications. A Tool to Identify Nucleosome Free Regions from ChIP-Seq Against Histone Modifications. USAGE: perl HISTRADER.pl --bedGraph ChIP.bedGraph --peaks ChIP.bed.
A comprehensive and fully curated database for Herb Ingredients’ Targets. Molecular target information involves those proteins being directly/indirectly activated/inhibited, protein binders and enzymes whose substrates or products are those compounds. Those up/down regulated genes are included under the treatment of individual ingredients. The experimental condition, observed bioactivity and various references are provided. The database can be queried via keyword or similarity search.
Hierarchical Taxonomic Classification of Fungal ITS Sequences. Abstract Motivation Fungi are key elements in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human microbiome and can be causative agents of human infections. An accurate and robust method for fungal ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight of the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them consider the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors
This package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.
HiTE is a dynamic boundary adjustment approach for fast and accurate full-length transposable element detection and annotation. It outperforms existing tools and has identified novel transposons with well-defined structures, with a Nextflow version also available.
A computational pipeline to identify non-reference transposable element insertions in Hi-C data. computational tool to identify trasposable element insertions using Hi-C data. HiTea (Hi-C based Transposable Element Analyzer) is geared to idenify non-reference transposable elemenet insertions from the Hi-C data. It uses split Hi-C read information and read coverage to detect insertions of three major classes of active human transposable elements (TE) - Alu (SINE), L1HS(LINE) and SVA.
An algorithm for correcting reads produced by high-throughput sequencing methods.
HiTIPS is a flexible and open-source high-throughput image processing software platform designed to expand image analysis capabilities and incorporate new image processing algorithms. It provides a graphical user interface and supports automated cell and nuclei segmentation, spot signal detection, nucleus tracking, and quantification.
HitPredict is a database with quality assessed PPIs in nine species. HitPredict assigns a confidence level to interactions based on a reliability score that is computed using evidence from sequence, structure and functional annotations of the interacting proteins.
HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis) web server uses command line MATLAB scripts to analyze input high throughput capillary electrophoresis data.
Software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. It provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.
Prioritizes patient variants relative to their weighted proximity to functional assay results in a protein-protein interaction network. It is highly extensible, allowing incorporation of diverse data types to refine prioritization.
HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file.
The HIVbio is the home page of various informations that are provided here for Human Immunodefeciency Virus (HIV) life cycle and Infection.
Web-server for predicting HIV protease cleavage sites in proteins.
HIVcoPRED: is a web server developed for predicting the coreceptor usage by HIV-1. It takes amino acid sequences of Variable loop (V3) of gp120 protein of HIV and predicts the coreceptor used by the HIV strain.
High-performance integrated virtual environment: a robust infrastructure for next-generation sequence data analysis.
An interactive network visualization tool. Update: Interactive hive panels can be easily built using different data formats. A wiki tutorial will be up soon. Stay tuned!. Welcome to the Hive Panel Explorer wiki!. Hive Panel Explorer is a Python script that takes a network and creates a static HTML page with interactive SVG graphics in D3. The visualization produced is a matrix of hive plots plotted using attributes of the nodes and edges (such as degree and centrality). The interactive features let users explore their network and discover patterns in their network. For more information on the design of the tool and on the kind of patterns it can reveal, check out Sarah Perez's Master Thesis.
An accurate tool to detect virus integrations in the host genome. After obtaining the integration sites, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations.
First integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. It is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation.
The Human Immunodeficiency Virus is a retrovirus and has a genome size of about 9.5 Kb with repertoire of only 15-20 proteins.
A python-based tool for HIV-1 genome intactness inference.
The HIVoligoDB is a comprehensive on-line resource with curated datasets of oligonucleotides for the human immunodeficiency virus (HIV). The database provides a curated and regularly updated list of oligonucleotides and a description of the genetic diversity across the HIV-1 and HIV-2 genomes to facilitate the design of accurate diagnostic methods and therapeutic approaches.
HIVoligoDB - The HIV oligonucleotide database
In this server, user can predict the IC50/Percent inhibition of given compounds against three HIV proteins namely reverse transcriptase, protease and integrase.
Portable resource for NGS and sample metadata integration for HIV-1 drug resistance analysis.
A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. A customizable environment for the structural modeling and analysis of peptide-HLA complexes.
A user-friendly tool to analyse HLA class I and class II compatibility on the amino acid level. HLA-EMMA is a software package designed to perform HLA class I and class II compatibility analysis on the amino acid level. HLA-EMMA predicts & analyses HLA antibody formation.
A new EPIsode in exploring donor/recipient epitopic compatibilities.
Distribution of the HLA-DPB1 alleles in a Russian population living in the Chelyabinsk region (South Ural of Russia). Tools for handling and analysing data with ambiguities. These programs expect plain text files in UNIFORMAT v3 as input. A download link to the results file is provided once the execution is completed (on screen and/or by email). Read more about these tools (and see examples of input files) in the usage overview.
A Natural Language Processing based resource for curating HLA association from PubMed abstracts. HLA Web Resource for SNPs, Populations, Resources, ADRs, Diseases.
An integrated structure-based computational toolkit for immunotherapy.
Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.
HLA class I clustering based on 3D structure.
Unraveling the glycosylated immunopeptidome with HLA-Glyco.
TheHLA-DR4Pred is an SVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction method. The accuracy of the SVM and ANN based methods is ~86% and ~78% respectively.
HLA-DR4Pred 2.0 is the update of the older version HLA-DR4Pred, which was a SVM and ANN based method to predict the HLA-DRB1*04:01 bindind peptides.
HLAncPred is a webserver for the prediction of promiscuous binders of non-classical HLA-G and HLA-E alleles (HLA-G*01:01, HLA-G*01:03, HLA-G*01:04, HLA-E*01:01 and HLA-E*01:03).
HLA Typing and Quantification of Expression with Personalized Index. HLApers integrates software such as kallisto, Salmon and STAR. Before using it, please read the license notices here. The first step is to use hlapers prepare-ref to build an index composed of Gencode transcripts, where we replace the HLA transcripts with IMGT HLA allele sequences.
HLAreporter (HLA reporter) is a novel tool for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads.
Patient-specific predictions of HLA restriction elements and optimal epitopes within peptides.
A MATLAB code for Human Learning Optimization(HLO) algorithm
Human Learning Optimization(HLO) algorithm
HLP is a server developed for predicting half-life of peptides in intestine like environment. It generates all possible mutants (single mutation at each position per cycle) for a peptide and predict/calculate half-life and physicochemical properties (e.g. charge, polarity, hydrophobicity, volume, pK) of mutant peptides.
Improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. Welcome to the Home Page of HLPpred-Fuse. HLPpred-Fuse could be established according to the following steps: (i) feature representation scheme was employed to generate 54 probabilistic features derived from 54 prediction models that utilized nine different types of peptide features, i.e. AAC, DPC, amino acid index (AAI), binary profile (BPF), composition-transition-distribution (CTD), conjoint triad (CTF), quasi-sequence order (QSO), grouped dipeptide composition (GDPC), and grouped tripeptide composition (GTPC), and six ML classifiers, i.e. SVM, RF, gradient boosting (GB), extremely randomized tree (ERT), k-nearest neighbor (KNN), and AdaBoost (AB); and (ii) those 54 probabilistic features were fused and inputted to ERT to develop a final predictor separately for both layers. For a given peptide sequence, HLPpred-Fuse predicts HLPs activity and probability values.
Database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, 2585 genes and 212 miRNA have been collected with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.
Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction.
Hierarchical multi-task deep learning for annotating antibiotic resistance genes.
Head-mounted display-based egocentric marker-less tool and hand pose estimation for augmented surgical guidance.
Human microbe-disease association prediction using network consistency projection.
Human Microbe-Disease Association Database (HMDAD)
Freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.
A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background.
Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).
Database for experimentally supported human microRNA-disease associations.
A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry. Upload a list of template interfaces. TM-align Score Threshold (0 to 1):.
Algorithm which uses distribution and centroid information to cluster a sample and was applied to biological data.
Protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. It corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors.
HMM-TM is a tool that takes a protein sequence as input and predicts the transmembrane regions of alpha-helical
Profile HMM construction from multiple sequence alignments.
Convert between profile HMM file formats.
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for further analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.
This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.
HMMER3 hmmscan is used to search sequences against collections of profiles.
HMMER3 nhmmer is used to search one or more nucleotide sequences against a nucleotide sequence database.
HMMER3 phmmer is used to search one or more sequences against a sequence database.
Supervised classification of superfamily protein sequences with a reliable cut-off threshold.
An ensemble method for multiple sequence alignment.
Prediction of vertebrate and C. elegans genes.
A hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data.
Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.
Scan a protein sequence against a database of HMM profiles (e.g. TreeFam or Pfam-A).
Search sequence(s) against a profile database.
Search profile(s) against a sequence database.
Collect profile HMM score distributions on random sequences.
Splice junction discovery in RNA-Seq data
Display summary statistics for a profile file.
Prediction of transmembranes helices and topology of proteins.
HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.
Calculate and plot hydrophobic moment for protein sequence(s).
A database of hormones and their receptors
Hidden Markov random field based Bayesian peak caller to identify long range chromatin interactions from Hi-C data.
The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the conversion of data IDs using the corresponding tables in HMS.
A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data. DNA methylation (5mC) and hydroxymethylation (5hmC) are chemical modifications of cytosine bases which play a crucial role in epigenetic gene regulation.
Database of human mitochondrial genomes from primary INSDC databases, personal submissions and application of MtoolBox to NGS data.
Houston Methodist Variant Viewer. Houston Methodist Variant Viewer (HMVV) is an application to support interpretation of Next Generation Sequencing (NGS) variants. The bioinformatics pipeline scripts associated with this application is uploaded to github - please see https://github.com/hmvv/ngs_pipelines. Setup a cron job to run the MAIN_runPipelines.sh script.
A hybrid network based on MLP-Mixer for protein-protein interaction site prediction.
HnaTyping is a software for genotyping of human neutrophil antigens (HNA) from whole genome sequencing data
Development, international multi-institutional validation, and web implementation of clinic-ready model-based risk stratification for head and neck cancer', 'clinic-ready'
A web tool for the prediction of gas sensing H-NOX proteins from amino acid sequence.
HNSCPred - A Package To Predict Head and Neck Squamous Cell Carcinoma Using Single Cell Data
Hybrid computational model combing network and sequence information for predicting protein-protein interaction.
Software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). It accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.
Machine learning model for predicting Human Oral Bioavailability
HOmo sapiens transcription factor COmprehensive MOdel COllection contains transcription factor (TF) binding models (motifs) as position weight matrices for human and mouse transcription factors.
Open-source tool for host contamination removal. It offers a one-step option for genome indexing. The tool employs a variety of well-known mapping, classification, and alignment methods to classify reads.
A Manually Curated Database of Human Ophthalmic Diseases with Symptom Characteristics and Genetic Variants Towards Facilitating Quick and Definite Diagnosis.
This is a simulation of Hodgkin-Huxley equations using simulink blocks.
It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.
A set of webservices allowing to browse Hogenom 4 evolutionary scenarios.
Set of webservices allowing to browse Hogenom 4 phylogenetic trees.
Higher-order genetic interaction discovery with network-based biological priors.
Unambiguous prediction of multiple double minute chromosome architectures.
Holomics is an R shiny application designed for user-friendly multi-omics data integration and analysis. It provides a well-defined workflow for feature selection, correlation identification, and biomarker discovery, leveraging methods from the mixOmics package.
A robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes.
Web-based interface that can create homology models of a protein with unknown structure (the target or query protein) based on a homologous protein with known structure (the template protein).
CABM Structural Bioinformatics Laboratory
HOMDscrape is a Python tool that retrieves and processes amino acid sequences and identifiers from the expanded Human Oral Microbiome Database (eHOMD). It was developed to analyze bacterial motility related genes within the human oral microbiota, and enables phylogenetic analysis of relevant protein components.
A unified and modular interface to homology modelling software
Fast and effective solution to disentangle homologous sequences based on a maximum likelihood optimization.
HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.
A comparative modelling server for protein structure prediction. Automatic template selection.
A comparative modelling server for protein structure prediction. Manual template selection.
Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.
Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data.
This is a command line tool for sampling related sequences from Ensembl. It requires PyCogent, Numpy, SQLAlchemy, PyMysql, Click and SciTrack. At present, this tool provides capabilities to support sampling one-to-one orthologs from protein coding genes stored in an Ensembl MySQl database. It can either write out the protein coding sequences from the canonical CDS, or it can write out the Ensembl multiple sequence alignment of the entire gene with annotated features masked.
A web server tool to incorporate 'homologous' water molecules into GPCR structures. Program to incorporate internal water molecules to GPCR models. A free access tool to incorporate internal water molecules to GPCR structures. available at http://lmc.uab.cat/homolwat.
Homopolish is a method for the removal of systematic errors in nanopore sequencing by homologous polishing.
A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.
Accelerating open modification spectral library searching on tensor core in high-dimensional space.
Homozygous stretch identifier from next-generation sequencing data.
A template for reproducible psychophysiological tasks for clinic, laboratory, and home use.
A tool designed for assessing and measuring homophily in networks whose nodes have categorical attributes, namely when the nodes of networks come partitioned into classes.
hoodscanR is an R package for analyzing cellular neighborhoods in spatial transcriptomics data. It facilitates neighborhood identification, colocalization analysis, and cell clustering based on spatial proximity within single-cell resolution data.
Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images. A platform for end-to-end development of machine learning solutions in biomedical imaging. Upload medical imaging data easily and securely.
This algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. It uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster.
The HawkEYE Orbital Fracture Prioritization and Evaluation (HOPE) algorithms are clinical decision-making tools developed to identify orbital fracture patients needing urgent ophthalmology evaluation, improving resource utilization and reducing healthcare costs. An online tool implementing the HOPE+CT algorithm is undergoing prospective validation.
HawkEYE Orbital Fracture Prioritization and Evaluation (HOPE)
HoPhage (Host of Phage) is a computational tool that integrates two modules respectively using the deep learning and the Markov chain model to identify the host of a given phage fragment from metagenome or metavirome data at the genus level. HoP demonstrates a superior performance on short fragments within a wide candidate host range at every taxonomic level when testing on the artificial benchmark dataset of artificial phage contigs and the real virome data.
Boosting protein functional dynamics with colored contact maps. A tool to boost protein functonal dynamics with colored contact maps. HOPMA is intended to help to define elastic network representations of protein structures. NOn-Linear rigid Block NMA approach (NOLB) a new conceptually simple and computationally efficient method for non-linear normal mode analysis.
Automated detection and authentication of pathogen DNA in archaeological remains. HOPS is a java pipeline which focuses on screening MALT data (see Table of Contents) for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison. To use HOPS you will need a config file, which specifies some key parameters for MALT and MaltExtract. You can have multiple config files to quickly redo a previous analysis or archive them to remember parameters you used in an analysis. HOPS will in every case create a log that tells you which command was sent to Slurm, in case you encounter problems, that log file is a very good place to start looking for the problem
High-performance library for (non-)uniform sampling of convex-constrained models. The Highly Optimized Polytope Sampling toolbox is an open-source C++17 library for efficient and scalable MCMC algorithms for sampling convex-constrained spaces possibly equipped with arbitrary target functions.
HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.
HORDB a comprehensive database of peptide hormones.
HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in vertabrates. ORs are G-Coupled Protein Receptors with a 7-transmembrane structure. The ORs are responsible for triggering the olfactory signal transduction pathway. You will find here information on the entire human OR repertoire, including a rich annotation on genomic variations, classification, orthologs and other features. Also available are OR repertoires of other mammalian species.
The Human Olfactory Data Explorer (HORDE)
HormonomicsDB is a tool and database for the untargeted analysis of plant growth regulators and hormones, facilitating hormone identification and characterization through LC-MS data analysis and retention time prediction.
Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use.
Hostile removes host sequences from short and long reads, consuming paired or unpaired fastq[.gz] input.
Canadian whole genome sequencing and clinical data resource.
A versatile pipeline to remove host contaminants from metagenomics raw datasets, using BBMap and Kraken2.
The Helsinki O2 Pathway Tool (HO2PT) is a desktop application that models the O2 pathway based on the Wagner diagram, integrating the Fick principle and Fick's law of diffusion for calculation and graphical display.
Free software to detect genomic regions unusually rich (hotspot) in a given pattern via scan statistics.
Pipeline for transferring annotations between proteins beyond globular domains.
Algorithm for finding significanlty altered subnetworks in a large gene interaction network.
A tool identifies significantly mutated groups of interacting genes from large cancer sequencing studies.
HotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface, output includes an interactive 3D visualization of the hot spots.
Database of predicted hot spot clusters. Hot spots are energetically important residues at protein interfaces, clustered across the interface. HotRegion provides the hot region information of the interfaces by using predicted hot spot resides, and structural properties.
HotSpot is a software of prediction of hot spot residues through physicochemical characteristics of amino acid sequences
An integrated resource for mutation analysis in protein 3D structures. Analyse Mutations in Protein 3D Structures. Analysing Your Own Mutation Data for Clusters. No need to screen for mutation types provided. Any variant classifications can for HotSpot3D, not just missense mutation.
Software to support sperm-typing for investigating recombination hotspots.
An automated design of mutations and smart libraries for engineering of protein function and stability and annotation of protein structures.
Database for hotspot mutations and annotations in cancer. Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes like BRAF, IDH1, KRAS and NRAS among many other genes. Hotspots are attractive because provide opportunities for biomedical research and novel treatments. Nevertheless, recent evidence, such as DNA hairpins for APOBEC3A, suggests that a considerable fraction of hotspots seem to be passengers rather than drivers. To document hotspots, the database HotSpotsAnnotations is proposed. For this, a statistical model was implemented to detect putative hotspots, which was applied to TCGA cancer datasets covering 33 cancer types, 10 182 patients and 3 175 929 mutations
Software for identifying recombination hotspots from population SNP data.
Web server to predict the host spots in RNA binding proteins (RBPs)
Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data. The program uses a residual deep learning model to predict water hot-spots on the surface of proteins. Supply a pdb file (or just the accession code) and rank the water molecules within it or scan the surface of the whole protein for most likely water hot spots. Note: This tool relies on EDTSurf, therefore runs only on Linux. If you have a linux system, install via pip from PyPi (recommended):.
This database allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.
Homologous vertebrate genes database (HOVERGEN)
Python package for testing strandedness of RNA-Seq fastq files.
Developing an Innovative System of Open and Flexible, Patient-Family-Centered, Virtual Visiting in ICU During the COVID-19 Pandemic.
A simple interface to and data from the Human Protein Atlas project.
A Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas. HPAStainR package to be submitted to Bioconductor. HPAStain.R is an R package/Shiny app used to query the Human Protein Atlas for staining data. The purpose of this tool is to test if a list of proteins/genes is associated with a certain cell type in a HPA tested tissue. E.g. you have a list of protein coding genes from a differential expression single cell analysis and want to see if these proteins are associated with a known cell type. Instead of querying HPA multiple times you can load your list in HPAStainR which will return a ranked table of the cell types with the most protein staining.
A Novel HPC-aware Tool for Improved Large Scale RNA-editing Analysis. REDItools2 is the optimized, parallel multi-node version of REDItools. REDItools takes in input a RNA-Seq (or DNA-Seq BAM) file and outputs a table of RNA-Seq editing events. Here is an example of REDItools's output:. The following image explains the high-level architecture.
Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-seq data to identify protein-interacting genomic regions.
Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a high proportion of polyunsaturated fatty acids (PUFAs). We produced 40 in-house RNA-seq datasets from 10 different tissues and performed de novo transcriptome assembly to obtain a complete transcriptome. Moreover,we had constructed the co-expression network database, HpeNet, which contains transcriptome data, gene information, the co-expression network, and so forth. Furthermore some analytical tools, such as blast, gene expression profiling analysis and gene set enrichment analysis (GSEA), were supported for network analysis and functional annotation. We hope that the HpeNet database will be beneficial to future work on Paeonia lactiflora Pall.
Blind protein–peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, it considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program.
An ultrafast, friendly tool for DMR detection and visualization. If you want to use this tool just now, there is an executable file for Linux x86_64 systems. This compressed file is available at releases page. But, previously, CUDA and Nvidia drivers must be installed in your system. For that, you can go to System requirements section. HPG-Dhunter is an interactive tool for detecting Differentially Methylathed Regions (DMRs) and visualizing DNA methylation signals. It is based on building a methylation signal from the information yielded by HPG-HMapper, and using a NVidia GPU and the CUDA programming model to compute the Discrete Wavelet Transform (DWT) of this methylation signal. The transformation of the signals in turn allows the comparison of different signals at low resolution levels, easily identifying DMRs with a low workload, when compared to other strategies. HPG-Dhunter is part of the HPG-MSuite.
Ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping.
Toolkit to explore and analyze nanopore sequencing data that can run both on a single computer and on the Hadoop distributed computing framework.
An R/Bioconductor package for predicting host-pathogen protein-protein interactions from protein sequences using ensemble machine learning approach.
Host-pathogen interactome prediction with phenotypic scoring.
A general tool for simulating and optimizing HPLC gradients.
Automated tool for computing pK values of ionizable groups in macromolecules and adding missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties.
HPM (Haplotype Pattern Mining) is a program for gene mapping in case-control haplotype data.
The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. It can be used for clinical diagnostics in human genetics, bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes and for providing a standardized vocabulary for clinical databases. All the data is available for download and can be browsed online.
Deep graph convolutional networks for predicting human protein-phenotype associations.
HPOFiller is a tool for identifying missing protein-phenotype associations by graph convolutional network.
Improving prediction of human protein-phenotype associations by learning to rank. Predict human protein-HPO term associations using Learning to Rank.
Centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in it is curated by experts, who manually extract it from published literature.
The Human Protein Reference Database (HPRD)
A comprehensive database for human proteome repeats. Human Proteome Repeats Database. HPREP : HUMAN PROTEOME REPEATS.
An online database for ligand binding sites in human proteome.
hPSCreg is a global registry for human pluripotent stem cell lines (hPSC lines). It aims to provide to the community: 1) a central and searchable hub for available hPSC lines; 2) a central registry of clinical studies based on hPSC-lines; 3) a standardized identifier for hPSC lines and register of these standard names; 4) a trustworthy data source for hPSC lines by verifying the ethical and biological conformity of registered lines based on community standards; 5) comparability of quality standards in hPSC research; 5) certification of quality and ethical provenance of hPSC lines; 6) a platform where any scientist or institution generating or working with human PSC lines can register their cell lines, projects or clinical studies
HPTT is a a visualized and expandable webtool for whole-genome-based Helicobacter pylori geographic surveillance. HPTT is a genomic typing tool based on SNP (single nucleotide polymorphism) of bacterial pathogens, which can facilitate not only H. pylori isolates, but also other pathogens that highly related to the public health.
Usage of the Sea Urchin Hemicentrotus pulcherrimus Database, HpBase. Hemicentrotus pulcherrimus Genome Resources. Hemicentrotus pulcherrimus Genome and Transcriptome database. Hemicentrotus pulcherrimus (A. Agassiz, 1863) (Animaria: Echinodermata: Echinoidea: Echinoida: Strongylocentrotiae: Hemicentrotus) is the most widely distributed sea urchin in Japan and important marine food resources in eastern Asia. This species has a long history as a model organism in the field of developmental and cell biology since the mid 1900s. The web site provides information on H. pulcherrimus genome and transcriptome for a wide range of biologists. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/insdc (NIG.AC.JP), bio.tools/dfast (NIG.AC.JP), bio.tools/ddbj (NIG.AC.JP), bio.tools/cibex (NIG.AC.JP) ||| CORRECT NAME OF TOOL COULD ALSO BE 'H pulcherrimus'
Java application to run on a laptop, cluster or even a supercomputer for cross-checking the sequences with the HPV viruses from the database.
A pipeline to detect human papillomavirus (HPV) transcripts in RNA sequencing (RNA-seq) data. Designed to enhance the accuracy of HPV detection and minimise false positives due to contamination, HPV-meta is particularly valuable in cancer genomics research. Ure A, Mukhedkar D, Arroyo Mühr LS. Using HPV-meta for human papillomavirus RNA quality detection. Scientific Reports. 2022 Jul 29;12(1):13058. doi:10.1038/s41598-022-17318-5.
Sensitive and specific genotyping of human papillomavirus in metagenomic DNA.
HPVsim is an open-source agent-based model for simulating HPV transmission and cervical disease, designed for flexible parameterization and adaptation to new screening methods. It is implemented in Python and offers tools for simulating interventions and runs quickly on standard hardware.
Tissue registration and exploration user interfaces in support of a human reference atlas.
The Human Reference Atlas (HRA) Knowledge Graph (KG) provides a data resource for HRA v2.2, supporting cross-scale biological queries using SPARQL. It is constructed and deployed following Linked Open Data principles, and provides APIs and interfaces for querying and retrieving data.
hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context.
Filter pruning based on High Relevance between activation maps and class labels.
Hyperbolic relational graph convolution networks plus (HRGCN+) is a simple but highly efficient QSAR-modeling web application.
High-throughput analysis of bacterial ribosome profiling data. High-throughput annotation by Ribo-seq. We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.
General statistical inference framework for stochastic transcription-translation networks.
Perform differential expression tests for RNASeq at scale with a configurable interface and visualize results with tunable control over p-value thresholds.
Deep High-Resolution Representation Learning for Visual Recognition. HigherHRNet-Human-Pose-Estimation.
A manually-curated database about the regulatory relationship between HPV and host RNA. 2.HRRD contains the map of HPVs, the regulation relationship between HPV and RNA. 1.The relationship between HPV and host RNA has been identified with biological function.
The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory modules for the co-occurring transcription factor binding motifs, which are within a binding locus. It also contains individual binding sites whose regulatory action has been verified by in vitro experiments.
Hierarchical approach to removal of unwanted variation for large-scale metabolomics data. hRUV is a package for normalisation of multiple batches of metabolomics data in a hierarchical strategy with use of samples replicates in a large-scale studies. The tool utilises 2 types of replicates: intra-batch and inter-batch replicates to estimate the unwatned variation within and between batches with RUV-III.
HRVanalysis is a free software that can be used to analyze cardiac autonomic activity.
Predicting Potential Efficacious Drug Combination Based on Hypergraph Random Walk with Restart.
Nucleotide-Nucleotide aligner that searches nucleotide queries against a large nucleotide database.
Software of testing association using tightly linked markers in nuclear pedigrees.
Fexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome.
The MicroRNA Target Prediction Database is a resource that provides tools for microRNA target prediction and functional studies. The database enables users to explore predicted miRNA targets and analyze their functional relationships within the context of Epstein-Barr virus-associated febrile diseases.
Database of highly similar duplicate genes from plants, animals, and algae.
An integrated tool for predicting highly similar duplicates (HSDs) in eukaryotic genomes. HSDFinder aims to become a useful platform for the identification and analysis of HSDs in the eukaryotic genomes, which deepen our insights into the gene duplication mechanisms driving the genome adaptation.
HSEpred is a web server to predict the HSE(Half-Sphere Exposure) measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset.
Allows predicting the subcellular localization of human proteins. This is based on various type of residue composition of proteins using SVM technique.
A high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching. HSM6AP is a machine-learning framework to predict m6A based on Sequence and Gnomic coordinates. DNA methylation is an important epigenetic modification, which is closely related to the development and progression of cancer. As a cancer-related biomarker, the effective identification of DNA methylation sites has import implications in understanding the pathogenesis of cancer, cancer diagnosis and drug development.
Identification of motifs in sequences composed of non-single-letter elements.
A hybrid semantic network for polyp segmentation.
A computational repository of heat shock protein modulators. A bird's-eye view of Heat Shock Proteins. HSPMdb will assist the scientific community working in the area of chaperone biology for designing novel inhibitors. It will also be useful for creating datasets for developing novel scaffold using in silico prediction algorithms.
Homology-derived secondary structure of proteins database.
Framework to determine optimal parameter selection for a generic spike sorting algorithm. Heuristic Spike Sort Tuner Readme. Novel paradigm for optimal parameter selection of a generic spike sorting algorithm. Full code base written for Matlab 2018a is available here. Full documentation along with a getting started guide is in the HSST Manual.pdf.
Symmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule.
Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging.
Aggregation and fully automated clinical interpretation of genetic variants in heritable thoracic aortic aneurysm and dissection.
HTCA is an interactive web-based healthy human single-cell transcriptome landscape, containing 19 adult tissues and their matching fetal tissues, demonstrating diverse and in-depth transcriptomics profiles of all cell types across tissues.
Heterogeneous Task Decoupling for Two-Stage Object Detection.
High Throughput Experimental Materials Database
R package and shinyR application for quality controls of HTG EDGE-seq protocols.
HTHmotif is a novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
HTM-ONE takes single amino acid sequence as input and returns residue-wise prediction of several one-dimensional structural properties of helical transmembrane regions.
Create a html report from a blast result.
Novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image.
Exploiting maize haplotype-tag polymorphisms for germplasm resource analyses and genomics-informed breeding.
Created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries.
HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.
Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science, etc. It handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features.
A new tool to facilitate public health field visits and electronic data capture. HTrack (Household Tracking) is an application built in R-Shiny for use on encrypted Android devices. This app was created to allow for offline data collection in studies where stringent data-security requirements must be met (see https://doi.org/10.1371/journal.pone.0244028), though it can also be run online if needed. The application allows for field navigation and secure field-level data capture. It also serves as a bridge to an alternate software, like EpiInfo, to collect participant-level questionnaire data. This repository houses:.
An R package for learning non-contiguous haplotypes associated with a phenotype.
This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.
Implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).
Python framework to process and analyse high-throughput sequencing (HTS) data
htseq-clip, a python package developed for preprocessing, extracting and summarizing crosslink site counts from i/eCLIP experimental data.
This script takes an alignment file in SAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it.
A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. Quality control analysis for high-throughput sequencing data (HTS). HTSeqQC Quick Start — HTSeqQC Quick Start documentation. The Open Science Workspace for Collaborative Data-driven Discovery.
We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.
This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.
Python package used to create gene sets for the study of high-throughput sequencing data.
The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.
Represents the structure of signals in the screen using linear mixed models, normalizes and summarizes the phenotypes to make them comparable across samples, and outputs a list of hits while controlling the False Discovery Rate. The methodology is appropriate for experimental designs with at least two control samples profiled throughout the screen.
An end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening.
HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.
The tool functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).
HTStream is a quality control and processing pipeline for High Throughput Sequencing data. The difference between HTStream and other tools is that HTStream uses a tab delimited fastq format that allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data and makes it fully interoperable with other standard Linux tools.
Exploratory data analysis and visualization of arrayed high-throughput screens.
HTT-OMNI (HTT OMics and Network Integration) a web-based application for HIP network analysis, visualization, and omics data exploration.
Package designed for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree.
Humanization of antibodies using a machine learning approach on large-scale repertoire data.
Human Antigen Receptor Consortium (huARdb) is a comprehensive database of single cell immune profiling and V(D)J T cell and B cell analysis, enhanced with advanced visualization of single-cell data.
Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.
Probe design for simultaneous, targeted capture of diverse metagenomic targets.
An ensemble predictor for human ubiquitination sites using convolutional and recurrent neural networks
The Human BioMolecular Atlas Program (HuBMAP) Data Portal provides access to single-cell, spatial, and molecular data, along with tools and visualizations for exploring the human body at multiple scales. It aims to construct a reference atlas of the healthy adult human body.
Human BioMolecular Atlas Program Data Portal
This tool uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.
A Novel Tool for Hub-centric Visualization. hubViz (a novel tool for hub-centric Visualization) is a novel tool for hub-centric visualization which is based on a latent space joint model (LSJM) for visualization. ‘hubviz’ package provides computationally efficient and user friendly interface to fit the hubViz models. The following help pages provide a good start point for the genetic analysis using the ‘hubviz’ package, including the overview of ‘hubviz’ package and the example command lines:.
The HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus.
Atlas pages that are unique in containing digital 3D models of human developmental stages, organ specific gene expression datasets as well as annotated histology sections.
HuDSeN atlas and spatial gene expression database
An R package for creating mirrored Manhattan plots
HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences.
Database of the human cDNA project at the Kazusa DNA Research Institute, covering various sets of large human proteins of hitherto unidentified functions.
Reconstruction of human protein-coding gene functional association network based on machine learning.
An international, open and dynamic library for up-to-date clinical information. Collect information about clinic management and research projects.
Human-gpDB is a publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function.
Human IRES Atlas is an integrative platform for studying IRES-driven translational regulation in humans.
Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
Comprehensive characterization of human-virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs.
Interactive spatio-temporal visualization and database of human archeogenomics.
Retrieves expression matrices and metadata from the Human Cell Atlas.
A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue.
Collection of human microbiome sequencing data that pairs subject metadata with relative abundance data derived from amplicon and shotgun metagenomic sequencing processed via uniform pipelines.
The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).
A public repository of curated and standardized metadata for human metagenomes. Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”
HUMAnN 2.0 is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or capable of doing)?”
An improved database of human gene networks for disease research.
Humess is an analysis pipeline using Snakemake to automatically generate specific human metabolic models from 3'SRP RNA-seq dataset. It depends on a modified version of CarveMe which uses a top-down approach to build specific metabolic models from a universal model. Humess can also perform an optional analysis on the generated metabolic models using a sampling procedure.
Web Services, Tools and Databases for Exploring Human microRNA Data. The Chair for Clinical Bioinformatics at Saarland University has developed numerous tools to aid microRNA researchers. HumiR is here to match you with the perfect tool for all your miRNA analysis needs.
Hummingbird is a Python framework that gives a variety of optimum instance configurations to run your favorite genomics pipeline on cloud platforms.
HUMOS (How to Understand My Orbitrap Spectrum?) is a web application based on Dash framework. It helps to teach and learn more about Orbitraps and shotgun proteomics.
An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition. A very simple framework for state-of-the-art NLP. Developed by Humboldt University of Berlin and friends. A powerful NLP library. Flair allows you to apply our state-of-the-art natural language processing (NLP) models to your text, such as named entity recognition (NER), part-of-speech tagging (PoS), special support for biomedical data, sense disambiguation and classification, with support for a rapidly growing number of languages.
Hungarian algorithm for linear sum assignment. Works for square and rectangular cost matrices.
Hungarian Algorithm for Linear Sum Assignment Problem
Online web resource for recovering information about human phosphatases.
An integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses.
Database for skin permeation of xenobiotics. Jupyter Notebook which leads through the code used to create huskinDB publication Figures. huskinDB is a human skin permeation database containing information on experimental protocols used. It provides an interactive access to the data, filtering options and a possibility to search for structures.
Python module for Humphrey Visual Field (HVF) report data extraction. The package can taken in HVF single field analysis report images (from HFA2 or HFA3), and using OCR (tesseract) and image processing techniques (openCV), extracts data into an object oriented format for further processing.
A comprehensive database for human-virus protein-protein interactions. Here, we introduce a comprehensive human-virus PPI database, HVIDB (http://zzdlab.com/hvidb/), which is based on (i) multiple data resources associated with human-virus PPIs and provides (ii) an integrative, computational platform to predict interactions between human and virus proteins.
HVRLocator is a workflow to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). It aligns query sequences to a reference E. coli full-length 16S rRNA gene and identifies the spanning region through alignment.
We have developed HVSeeker, a deep learning-based method for distinguishing between bacterial and phage sequences. HVSeeker consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. This method has shown promising results on sequences with various lengths, ranging from 200 to 1500 base pairs. Tested on both NCBI and IMGVR databases, HVSeeker outperformed several methods from the literature such as Seeker, Rnn-VirSeeker, DeepVirFinder, and PPR-Meta. Moreover, when compared with other methods on benchmark datasets, HVSeeker has shown better performance, establishing its effectiveness in identifying unknown phage genomes
Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction.
Test if a locus is under Hardy Weinberg Proportion
An Excel spreadsheet for analysis of H/D exchange mass spectra.
hyb is a bioinformatics pipeline for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.
A hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction.
Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.
A workflow for the detection and phasing of hybrids in target capture datasets.
Containerization and additional options for assembly and paralog detection in target enrichment data.
Enabling scalable, automated, complete and accurate bacterial genome assemblies.
De novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs.
Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids.
An algorithm for error correction of the reads from various DNA sequencing platforms
MATLAB script for Hybrid Skin Lesion Segmentation Tool using PCA and Iterative Canny Edge.
Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. Automatic set up of Molecular Mechanics/Coarse-Grained (MM/CG) simulations for human G Protein-Coupled Receptor (GPCR)/ligand complexes.
Software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer.
Improved sequence-based prediction of dna-binding amino acids using annotations from structured complexes and disordered proteins.
HybridExpress is an R/Bioconductor package designed for comparative transcriptomic analyses of hybrids and their progenitors, providing tools for data normalization, gene expression classification, and functional analyses.
Pipeline for allele inheritance and gene copy number prediction in industrial yeast hybrids. Fast and accurate parental allele inheritance prediction tool for hybrid species.
Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation.
Dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. hybridPBRpred - web server from Biomine lab. HybridPBRpred combines prediction of protein-binding residues generated by SCRIBER (predictor that was trained using structures of protein-protein complexes) and DisoRDPbind (predictor that was trained using disordered protein-binding residues), with the underlying goal to produce complete set of the protein-binding residues.
A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. a hybrid-learning architecture for succinylation site prediction.
Improved blood velocity measurements with a hybrid image filtering and iterative Radon transform
A hybrid single particle tracking software using manual and automatic detection of dim signals.
Python-based program for prediction of rotational correlation time of folded protein domains in the context of flexible multidomain proteins and protein complexes with long disordered tails and/or interdomain linkers as well as intrinsically disordered proteins.
Provides access to an accurate classifier for hydrogenase sequences and a curated database of hydrogenases by known type.
Program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).
Novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease.
New approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques.
HYDRA is a multi-objective optimization-based de novo protein design method, which is implemented in a new quantified and continuous sequence space.We use two different energy functions to evaluate the decoy sequences simultaneously, and aided by the prior information collected from DSSP and PDB data base, a space transformation procedure is conducted in each iteration.In the new ordered sequence space, the searching process will be boosted dramatically.
A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. There is a need for more flexible gene expression analyses for precision oncology applications. We developed an unsupervised clustering approach for identifying clinically relevant expression patterns. The hydra analysis framework uses state-of-the-art Bayesian non-parametric statistics to learn which genes are differentially expressed without the need for matched normal expression data. This is very useful in the pediatric oncology setting where matched normal tissue is usually not available. ||| NAME (hydra) SIMILAR TO (PUB. DIFFERENT) bio.tools/hydra (HyDRA), bio.tools/hydra_sv (Hydra)
Detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. It can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments.
Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. Predict potential water molecules in the protein binding pocket. HydraMap V1.0 - Automatic Tailoring and Transplanting. We developed an empirical method for predicting the favorable hydration sites in a protein binding pocket.
PyMOL script for retrieving hydrogen bond characteristics from protein structures.
Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomes. Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein co-translational folding. In this work, we explore how codon variants affect the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA. By analyzing over 14,000 bacterial, archaeal, and fungal ORFeomes, we found that Bacteria and Archaea exhibit an exponential ramp of hydrogen bonding at the 5′-end of CDSs, while a similar ramp was not found in Fungi. The ramp develops within the first 20 codon positions in prokaryotes, eventually reaching a steady carrying capacity of hydrogen bonding that does not differ from Fungi
Hydrophobicity Grapher graphs the hydrophobicity/hydrophilicity of a sequence of amino acids, using a sliding window. The window size can be specified by the user, and several hydrophobicity scales can be used to determine the plot.
A open-source architecture which is inspired by previously reported DEFactor architecture and based on hydrogen labeled graphs.
Identifies primer and microarray probe binding sites in genomic DNA.
A Hybrid approach for Detection of Insertions and Deletions.
A semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia. HyLength: a semi-automated digital image analysis pipeline to measure total fungal hyphal and root lengths.
HyMM is a hybrid method for disease-gene prediction by integrating multiscale module structures.
Insights from incorporating quantum computing into drug design workflows.
Deep Proteome Profiling Enabled Functional Annotation and Data-Independent Quantification of Proline Hydroxylation Targets.
Helps in the identification and classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs.
An R Package for Geneset Enrichment Workflows | Please visit https://montilab.github.io/hypeR-docs/ | hypeR currently requires the latest version of R (>= 3.6.0) to be installed directly from Github or Bioconductor. To install with R (>= 3.5.0) see below. Use with R (< 3.5.0) is not recommended
An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search.
HYPER is a simple, flexible, and efficient pooled testing strategy for group testing via hypergraph factorization applied to COVID-19.
HyperBeta is a tool for the automatic identification and visualization of beta-structures in molecular dynamics files produced using the MARTINI force field. HyperBeta explots graph theory to identify the beta sheets, and was specifically designed to investigate the emergence of regular structures and patterns in self-assembly polypeptides.
HyperChIP for calling hypervariable ChIP-seq signals across samples
The hypertextual version of the Cell Line Database (CLDB), which is not directly accessible, a collection of information on human and animal cell lines available from some of the main European cell banks and many Italian research laboratories
A python package and SnakeMake pipeline for flexible, parallelized unsupervised clustering optimization. A package for clustering optimization with sklearn. Example jupyter notebooks for hypercluster.
HyperEx (pronounced "Hyper Ex" for Hypervariable region Extractor) is a tool that extracts 16S ribosomal RNA (rRNA) hypervariable region based on a set of primers.
HyperGen is a software tool for genome sketching that utilizes hyperdimensional computing to efficiently estimate Average Nucleotide Identity (ANI) for large-scale genome collections. It improves accuracy, runtime performance, and memory efficiency compared to existing methods.
HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures.
Hypergeometric cumulative distribution (left, right and two-tailed) including permutation testing.
Hypergeometric cummulative distribution with permutation testing
A package that implements some simple capabilities for representing and manipulating hypergraphs.
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction.
Efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs.
Software of simultaneous analysis of many SNPs and covariates.
HyperMorph: amortized hyperparameter learning for image registration.
Regression-based scoring functions for predicted Hi-C matrices to enhance hyperparameter optimization.
Tools for hyperpolarized MRI acquisition and reconstruction methods
Hypergraph-based semi-supervised learning algorithm to classify gene expression and arrayCGH data using biological knowledge as constraints on graph-based learning.
Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. HyperQuant A Pipeline for integrating identification and quantitation results for Hyperplexing experiment © Suruchi Aggarwal, Dr.
High-throughput, nondestructive, and precise measurement of seeds is critical for the evaluation of seed quality and the improvement of agricultural productions.
Hyperspectral CARS microscopy and spectroscopy toolbox
HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.
A flexible R package for the analysis of differential RNA editing.
Exploring time series of hyperspectral images for cold water coral stress response analysis.
HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.
Deep learning-based approach for high-throughput hypocotyl phenotyping.
Manually-curated non-redundant catalogue of human hypoxia-regulated proteins with a goal of collecting proteins whose expression patterns are altered in hypoxic conditions.
A software for analyzing and denoising 5D hyperspectral time-lapse data.
A processing tool for scanning probe microscopy and other n-dimensional datasets.
New R package that we have developed for detection, quantification, and visualization of homozygous segments/ROH in high-density SNP datasets.
Semi-Automatic Analysis of Invasion and Migration Transwell Assays.
A highly sensitive software tool to detect degenerated homology relations within and between different genomes.
The Comprehensive Antibiotic Resistance Database (CARD) is a resource providing curated resistance information for bacterial pathogens. It integrates genomic data and resistance mechanisms and is linked to ontologies and other resources.
Comprehensive Antibiotic Resistance Database (CARD)
Web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).
Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model. Information embedded in ligand-binding residues (LBRs) of proteins is important for understanding protein functions. How to accurately identify the potential ligand-binding residues is still a challenging problem, especially only protein sequence is given. In this paper, we establish a new query-specific computational method, named I-LBR, for the identification of LBRs without directly using the information of protein 3D structure. I-LBR includes two modes, named as I-LBRGP and I-LBRLS, for the general-purpose and ligand-specific LBR identification
Neural Network based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Structure.
Predictor of effects of single point protein mutation on its stability from protein sequences or structures.
Software that uses Circos to render interactive images for protein sequence visualization.
Method for predicting initiation sites of folding protein sequences.
I-Spin is an open-source software that performs real-time decoding of motor neurons using a blind-source separation approach for multichannel EMG signal processing. It provides a framework and guidelines for researchers studying movement control at the motor neuron level.
Best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information.
Automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation
For quantitative proteomics using iTRAQ.
An open source, freeware tool to simulate river water temperature coupled with HEC-RAS. This method paper explains the i-Tree Cool River model algorithms for simulating the response of river water temperature to urban greening. The model captures the warming and cooling impacts of urban development and restoration through a water and energy budget. The water budget includes river inflows from urban storm sewers and reservoirs, and the associated water temperatures. The energy budget adjusts radiation fluxes due to riparian shading and evapotranspiration, and propagates temperature downstream. Restorative cooling of the river can be simulated through algorithms for cool groundwater, either as direct inflows or by river water replacement called hyporheic exchange
a computational approach called i2APP that can identify APPs using a two-step machine learning framework
i2b2-etl provides a command line interface and api interface to import, delete concepts and facts and encounters.
To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.
An R package for simulating data from images and the implications in biomedical research. The R package i2d is a novel tool that allows users to transform an image into a simulated dataset that can be used to extract and analyze the complex information in biomedical and biological research. The package also includes three novel and efficient methods for image clustering based on finding minimum spanning tree by Prim's algorithm, detecting communities by modularity optimization, and finding the branches of the backbone of minimum spanning tree.
Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results. Interactive & iterative dashboards in R. Iterative and Interactive Dashboards.
Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.
Completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique.
3plex enables deep computational investigation of triplex forming lncRNAs.
Bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome. i4mC-ROSE is available for public
Improved identification of DNA N4-methylcytosine sites in the mouse genome using multiple encoding schemes. i4mC-Mouse is available for public.
A CapsuleNet-based framework for identifying DNA N6-methyladenine sites.
i6mA-DNCP is a computational tool for identifying 6mA sites in rice genome.
A stacking ensemble-based computational prediction of DNA N6-methyladenine (6mA) sites in the Rosaceae genome. Welcome to Our Bioinformatics Lab!.
i6mA-VC is a multi-classifier voting method for the computational identification of DNA N6-methyladenine sites.
Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. iAcetyP : Identify acetylation protein via Chou's 5-steps rule and general pseudo components : Read Me : Supporting Information : Citation :. Enter the sequences of query proteins in FASTA format (Example), and select Submit button for identifying acetylation protein. The number of proteins is limited at 5 or less for each submission
An efficient multi-label classifier for recognizing anatomical therapeutic chemical (ATC) classes of drugs. Recognizing the Anatomical Therapeutic Chemical (ATC) classes of first level for given drugs. Functions : Recognizing the Anatomical Therapeutic Chemical (ATC) classes of first level for given drugs.
Modular Open-Source Software for Digital Radiography. A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices.
A public access, broad coverage resource. NIH Office of Portfolio Analysis. iCite is a tool to access a dashboard of bibliometrics for papers associated with a portfolio. Users type in a PubMed query or upload the PubMed IDs of articles of interest. iCite has three modules: Influence, Translation, and Open Citations. iCite: Influence delivers metrics of scientific influence such as the Relative Citation Ratio (RCR), which is field- and time-adjusted, and benchmarked to NIH publications as the baseline. Read about how RCR is calculated at PLOS Biology. Bulk data can be accessed at the iCite database snapshot repository
Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts. Solution to iDASH'19 challenge track 1.
Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor | Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%
Integrated web application for differential expression and pathway analysis of RNA-Seq.
Identifying DNase I hypersensitive sites with balanced dinucleotide-based detrending moving-average cross-correlation coefficient.
Identification of DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC.
A Computational Tool for Detecting N6-Methyladenine Sites in Rice | Home About us Web-Server Contact us Download Citation | 6mA is formed by transferring methyl groups to the 6th position of the adenine ring catalyzed by methyl-transferases. It is a non-canonical DNA modification that is present at low levels in different eukaryotes. 6mA possesses similar characteristics between prokaryotes and eukaryotes. Its functions display diversity, such as guiding the discrimination between original and newly synthesized DNA strand after replication, regulating gene transcription and repressing transposable elements; in the cell cycle, reducing the stability of base pairings for opening DNA duplexes. Strikingly, the protection from methylation is an inherited state that, however, can be modified by environmental conditions
Validation of an integrated dermoscopic scoring method in an European teledermoscopy web platform | EADV-iDScore project “European web platform for the development of a Scoring Classifier for Early Melanoma detection” (EADV PPRC project number 2016-012)
Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. integrative analysis of (epi-)DNA and gene expression data for the identification of candidate cancer drivers. iEDGE is an R-package for performing integrative analysis of (epi-)DNA and gene expression data that builds upon, and significantly expands, the methodology first described in Monti, Chapuy, et. al., Cancer Cell (2012). This package provides the generalized pipeline to perform integrative analysis of epi-genomic data (methylation, copy number alteration, mutation, microRNA, etc.) and gene-expression data from paired samples, and consists of 3 major modules:. Integrative analysis of (Epi-)DNA and Gene Expression Data.
An open-source multifunction GUI-based Matlab toolbox for localization and visualization of human intracranial electrodes. Localization and Visualization of Intracranial Electrodes.
Identifying enhancers and their strength using ensembles of convolutional neural networks. BACKGROUND:Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength.
Developing Evidence to Decision Frameworks and an Interactive Evidence to Decision Tool for Making and Using Decisions and Recommendations in Health Care | Evidence-informed health care decisions and recommendations need to be made systematically and transparently. Mediating technology can help manage boundaries between groups making decisions and target audiences, enhancing salience, credibility, and legitimacy for all. This article describes the development of the Evidence to Decision (EtD) framework and an interactive tool to create and use frameworks (iEtD) to support communication in decision making. Methods: Using a human-centered design approach, we created prototypes employing a broad range of methods to iteratively develop EtD framework content and iEtD tool functionality
An integrative resource for investigating genetic model of drug response in cancer. An integrative database for investigating genetic model of drug response in cancer. iGMDR database collects predictive models of response for anti-cancer drugs. The efficacy of anticancer drugs usually varies from individual to individual, mainly due to genetic heterogeneity
Improved pipeline for analyzing CRISPR cleavage specificity.
Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS. This repository consists of set of exeamples to showcase the ways of interacting with iLINCS API. The examples are implemented in the RStudio notebook usingIlincsApis.Rmd and the "knitted" html output of the notebook is provided in usingIlincsApis.html.
Integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Mapping RNA-chromatin interactions by sequencing with iMARGI. Overview — iMARGI Pipeline 1.1 documentation.
Integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes.
Program to identify novel mobile genetic elements inserted in individual genomes.
An R package to impute microRNA expression using protein-coding genes. imputed miRNA activity from gene expression (Title Case). iMIRAGE: imputed microRNA activity from gene expression. As the name stands, iMIRAGE a set of tools that facilitates imputation of microRNA or miRNA expression using protein-coding genes. With a growing repertoire of publicly available transcriptomic data, it is now possible to study miRNA expression in several phenotypes
Methods for broad-scale plant phenology assessments using citizen scientists’ photographs | iNaturalist.org is a joint initiative of the California Academy of Sciences and the National Geographic Society | Explore and share your observations from the natural world
A PyMOL plugin for an efficient 3D protein structure superimposition approach. Background:Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures. Results:We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles.
A deep learning framework for improving protein interaction prediction using sequence properties. Abstract Motivation Almost all critical functions and processes in cells are sustained by the cellular networks of protein-protein interactions (PPIs), understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack high-quality PPI data for constructing the networks, which makes it challenging to study the functions of association of proteins. High-throughput experimental techniques have produced abundant data for systematically studying the cellular networks of a biological system and the development of computational method for PPI identification.
Identification of Sigma70 promoters using multiple windowing and minimal features.
Identifying protein-DNA binding residues using capsule neural networks. Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of post-genomic where data on protein sequences have expanded very fast. In this study, we propose iProDNA-CapsNet -- a new prediction model identifying protein-DNA binding residues using an ensemble of Capsule Neural Networks (CapsNets) on position specific scoring matrix (PSMM) profiles. The use of CapsNets promises an innovative approach to determine the location of DNA-binding residues. In this study, the benchmark datasets introduced by Hu et al. (2017), i.e., PDNA-543 and PDNA-TEST, were used to train and evaluate the model, respectively. To fairly assess the model performance, comparative analysis between iProDNA-CapsNet and existing state-of-the-art methods was done
Integrated feature-based webserver in silico prediction of protease substrates and their cleavage sites for 38 different protease types, covering four major protease families: Aspartic (A), Cysteine (C), Metallo (M) and Serine (S).
A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties. A sequence-based tool for the prediction and analysis of quorum sensing peptides using informative physicochemical properties. Enter your input sequence(s) in FASTA format Insert example data
Identifying N2-methylguanosine Sites Based on Sequence-Derived Information. iRNA-m2G: identifying N2-methylguanosine sites. The benchmark datasets that uesed to train and test the proposed model are provided on this page. Benchmark dataset S1 contains 143 m2G site containing sequences and 143 non-m2G site containing sequences from H. sapiens, M. musculus and S. cerevisiae, respectively. Benchmark dataset S2 contains 143 non-m2G site containing sequences (same as dataset S1) and 1246 non-m2G site containing sequences from H. sapiens, M. musculus and S. cerevisiae, respectively
Identifying N7-methylguanosine Sites by Fusing Multiple Features. N7-methylguanosine (m7G) is an essential RNA modification and participates in a series of biological processes. However, our knowledge about its biological functions is very limited. In order to reveal its new functions, it is necessary to develop various methods to identify m7G sites. Since experimental methods to detect m7G sites are still expensive, we proposed the first computational method, called iRNA-m7G, to detect m7G sites in Homo Sapiens. iRNA-m7G is developed by fusing multiple features, i.e., nucleotide property & frequency, pseudo dinucleotide composition, and secondary structure composition. The framework of iRNA-m7G is shown as following
Computational tool for identifying D modification sites in RNA sequence.
Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition. : Server : ReadMe : Supporting Information : Citation : Contact Us :
Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow.
iS-CellR (Interactive platform for Single-cell RNAseq) is a web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data.
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. Streptococcus mutans is a Gram-positive bacterium that thrives under acidic conditions and is a primary cause of tooth decay (dental caries). To better understand the metabolism of S. mutans on a systematic level, we manually constructed a genome-scale metabolic model of the S. mutans type strain UA159. The model, called iSMU, contains 675 reactions involving 429 metabolites and the products of 493 genes. We validated iSMU by comparing simulations with growth experiments in defined medium. The model simulations matched experimental results for 17 of 18 carbon source utilization assays and 47 of 49 nutrient depletion assays. We also simulated the effects of single gene deletions. The model's predictions agreed with 78.1% and 84.4% of the gene essentiality predictions from two experimental data sets.
A National-Scale Framework for Visualizing Riverine Concentrations of Microplastics Released from Municipal Wastewater Treatment Incorporating Generalized Instream Losses. iSTREEM® is an in-stream environmental exposure model which predicts the concentration of a chemical used in "down-the-drain" products. It is a tool to promote product stewardship and regulatory compliance for chemical suppliers and manufacturers of formulated products of all sizes across commodity groups. Predicted environmental concentrations are calculated for the continental United States and several watersheds in Canada:.
An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. Support Vector Machine and Random walk Graph Kernel for Protein Interface Scoring. Welcome to iScore’s documentation! — iScore documentation. Support Vector Machine on Graph kernel for protein-protein conformation ranking. Install iScore using pip install iScore. Minimal information to install the module. iScore offers simple solutions to classify protein-protein interfaces using a support vector machine approach on graph kernels. The simplest way to use iScore is through dedicated binaries that hide the complexity of the approach and allows access to the code with simple command line interfaces. The two binaries are iscore.train and iscore.predict that respectively train a model using a trainging set and use this model to predict the near-native character of unkown conformations. Free document hosting provided by Read the Docs
A Tool for Expression-Based Quality Control in RNA Sequencing | A Quality control analysis tool for NGS technologies | iSeqQC: An Expression based Quality Control tool | 'American Typewriter'; color:#081d58">iSeqQC- An Expression based Quality Control tool | Please wait while the server is working.. | iSeqQC- An Expression based Quality Control tool | iSeqQC displays the results in a form of a summary table and several plots: Summary statistics, counts distribution, Mapped read density, Housekeeping gene expression, Principal Component variances, Hierarchical relationship between samples and correlations (Pearson and Spearman)
MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery. A free resource for expression-based gene discovery in the eye
Sequence-based tool for predicting bacterial transcriptional terminators.
Integrated text-mining system for large-scale knowledge extraction from the literature.
Web-based application that provides variant assessment, interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis.
A transcriptome atlas and interactive analysis platform for autoimmune disease.
This web-server was developed to identify the anticancer peptides based on the sequence information.
Anticancer peptides prediction with deep representation learning features. Anti-Cancer Peptide Prediction with Deep Representation Learning Features. This repository contains the source code and links to the data and pretrained embedding models accompanying the iACP-DRLF paper: Anti-Cancer Peptide Prediction with Deep Representation Learning Features.
Computational prediction of anticoronavirus peptides (ACVPs) using their sequences.
Program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)
A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides. Welcome to the Home Page of iAMAP-SCM.
This web-server is a two-level multi-label predictor. It can be used to identify an uncharacterized peptide as antimicrobial peptide (AMP) or non-AMP according to its sequences information alone.
IAMSAM is a web-based tool for analyzing spatial transcriptomics data using the Segment Anything Model to accurately segment tissue images and perform downstream analysis like differential gene expression and enrichment analysis.
Iamxt is an array-based max-tree toolbox implemented in Python using the NumPy library for array processing. It can be used in mathematical morphology research and image processing.
Improved prediction and analysis of amyloid proteins using a scoring card method with propensity scores of dipeptides. This is the website for predicting Amyloid Proteins from the publication called ... iAMY-SCM: Improved Prediction and Analysis of Amyloid Proteins Using Scoring Card Method.
A cross-species omics knowledgebase for animals.
A neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
AnVILWorkflow is an R package that simplifies the execution of bioinformatics workflows hosted on the AnVIL platform, enabling convenient access to cloud-based genomics data and analysis tools.
iapi provides an instrument API for Thermo Fisher Scientific Orbitrap family (Tribrid, Exactive, and Exploris series) of mass spectrometers.
Apocryptovirus RdRp Assembler is a software resource used to assemble and analyze RNA viruses, specifically focusing on the identification and characterization of Apocryptoviruses within parasitic systems, as demonstrated by its use in the discovery of Apocryptovirus odysseus infecting Toxoplasma gondii.
Curated atlas of the biogenesis of spliceosome machinery during RNA splicing.
A web server for machine learning-based prediction of protein-protein and antibody-protein antigen binding affinities.
Collection of tools to reconstruct evolutionary histories which include recombination and back/recurrent mutation events.
Joint intraclassly adaptive GAN and segmentation network for unsupervised cross-domain in neonatal brain MRI segmentation.
The Integrated Aging Studies Databank and Repository (IASDR) IASDR serves as a resource for the scientific community to foster new scientific questions and analyses
It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.
Standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs.
Identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell-cell crosstalk network.
Global Context-Aware Feature Learning for Person Reidentification. This repository contains the code for the paper:. IAUnet: Global Context-Aware Feature Learning for Person Re-Identification. Person re-identification (reID) by CNNs based networks has achieved favorable performance in recent years.
A bi-clustering algorithm which is optimizes for binary data analysis. It is applied to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. The tool does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes.
This open source tool benchmarks IBD detection tools with multiple measurements.
Inflammatory Bowel Disease (IBD) Database (IBDDB) is a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease.
Aids the identification of regions of Identity By Descent (IBD) in inbred individuals, by plotting and collating runs of homozygous SNP genotypes, ordered by physical or genetic distance.
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP).
fast estimation of kinship coefficients from identity by descent segments. IBDkin is a software for IBD-based kinship estimation. IBDkin scales to hundreds of billions of IBD segments detected in hundreds of thousand individuals.
Factorial HMM based algorithm. Several models are supported in this implementation, including both the standard model and the 4-track model which uses a first order Markovian model for the LD process in a subset of the founders.
Software program for detecting segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data. IBDseq can analyze large data sets with thousands of individuals, and it can analyze data with multi-allelic markers.
Computer package for the simulation of genotypic data under general isolation by distance models.
Manually curated transcriptomic database for inflammatory bowel disease.
Aligning images acquired with the IBEX microscopy imaging technique
This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.
Web-based tool for building and visualizing interaction network of gene and gene set.
Concomitant prediction of environmental fate and toxicity of chemical compounds. Welcome to SVM Biodegradability predictor. This is a tool for predicting biodegradability and/or toxicity, based on the different definitions provided for some of the most popular compound databases. It is easy to use, just introduce a compound in SMILES format or draw its structure with the JSME editor, select the databases that you want to obtain a prediction for and press GO button.
interactive visualization and analysis of compound bioactivity space. iBioProVis has its own in house bioactivity dataset curated from ChEMBL (v25) having 15,506,670 data points (i.e., bioactivity measurements). Several filtering and pre-processing steps were applied in order to generate a reliable compound-target dataset.
Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology
A web server for a phylogeny-driven coevolution analysis of protein families.
NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. It provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query.
Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features
Identification and characterization of bitter peptides using a scoring card method with propensity scores of dipeptides. This is the website for predicting Bitter peptides from the publication called ...
iBLAST is tool which performs incremental BLAST of new sequences via automated e-value correction.
An XGBoost-Based Predictor for Identifying Bioluminescent Proteins. The role of this page is a brief introduction to iBLP. Bioluminescent proteins are a class of proteins that widely distributed in many living organisms with various mechanisms of light emission including bioluminescence and chemiluminescence from luminous organisms.
Predict outcomes faster using a platform built with data fabric architecture. Collect, organize and analyze data, no matter where it resides.
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.
IBM Bioinformatics and Pattern Discovery Group
An R package for benchmark dose estimation. The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper's objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R.
Integrated Bayesian Modeling of eQTL data.
A sequence-based predictor package for identifying ion binding protein in phage.
Integrated Benchmarking Single-cell RNA-sequencing Analytical Pipeline.
IBRENA (Insilico Biochemical REaction Network Analysis) is a software to aid the analysis of complex biological reaction networks. In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis.
IBRtools is an R package for calculating Integrated Biomarker Response (IBR) and Integrated Biological Responses version 2 (IBRv2) indexes, providing a user-friendly platform for environmental degradation assessment.
This resource provides a web-based platform for Multilocus Sequence Typing (MLST) and cgMLST analysis of *Brucella* spp. isolates, enabling epidemiological investigations and phylogenetic analysis.
Software package that can be used for representing the organization of either protein or nucleotide sequences, in a convenient, efficient and precise manner.
The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS.
A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.
Interactive Visualization of Cytoplasmic Heteroplasmy.
Identification & Classification of Aminoacyl tRNA Synthetases
Interpretable Classification and Regression with Feature Attribution for Mapping Neurological Phenotypes in Individual Scans.
Interpretable cross-attention network for identifying drug and target protein interactions.
A tool for identifying cancer and its type using DNA methylation.
Snakemake Pipeline for a long non-coding-RNA search and annotation in transcriptomic sequences.
A Web Server for Predicting Cardiotoxicity of Small Molecules.
An R package to compute Individualized Coherent Absolute Risk Estimators.
A computational tool for identifying protein carbonylation sites by novel encoded features. The role of this page is a brief introduction to iCarPS. to view more scientific achievements. iCarPS is a server for the prediction of carbonylation sites based on omputational method.
Novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool. Icarus consists of two major contig viewers: Contig alignment viewer and Contig size viewer.
Icarus is a method which uses the Protein Peeling algorithm (Gelly et al. (2006a), Gelly et al. (2006b), Gelly et al. (2011), Postic et al. (2017), Cretin et al. (2022)) to identify compact regions i.e Protein Units (PUs). PUs define rigid regions to be aligned to the target and delimit hinge positions in the structure.
ICARUS (Interactive single cell RNA-seq analysis with R-shiny using Seurat) a interactive web server.
iCAT: Immune Cells Analysis software Tool. High throughput sequencing of immune cell receptor sequences presents a unique opportunity to inform our understanding of immunological response to infection and how we can detect it. iCAT is a user-friendly, graphical-interface software that takes exposed and non-exposed samples of T-cell receptor (TCR) clonotypes as input and identifies pathogen-specific TCR sequences. Using these sequences, iCAT can also classify independent samples of TCR clonotypes. iCAT was able to identify vaccine-associated TCR sequences with up to 95% prediction accuracy in mice.
A novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes.
Web server that could predict methylation sites in proteins. With the assistance of FKNN, the highlight of this tool is to employ amino acid sequence features extracted by incorporating the sequence evolution information into PseAAC via a grey system model (Grey-PSSM).
An integrative database of cancer-associated viruses.
Visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.
Immune Checkpoint Blockade therapy Atlas (ICBatlas) is a database providing comprehensive expression resources and functional analysis for patients with ICB therapy. It also compares the expression between ICB groups of Response versus Non-Response (R vs NR), as well as groups between Pre-treatment and On-treatment (Pre vs On).
Comprehensive expression database for immune checkpoint blockade combination therapy.
Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures. ICBM-OCEAN — Carl von Ossietzky Universität Oldenburg. ICBM - Institut für Chemie und Biologie des Meeres. ICBM-MPI Brückengruppe für Marine Geochemie. ICBM-Webmaster (Stand: 21.08.2020).
R package that implements algorithms for parameter estimation and model selection for Isotonic Conjunctive Bayesian Network (I-CBN) models. It combines isotonic regression on a partially ordered set with CBNs for estimating order constraints among events. The model has been developed to jointly estimate mutational order constraints among genetic events and a genotype-phenotype mapping (such as a fitness landscape) that is non-decreasing along the lattice of genotypes.
ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.
Compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.
ICD-10 is the 10th revision of the International Classification of Diseases (ICD). It is a medical classification list published by the World Health Organization (WHO) and it is designed to promote international comparability in the collection, processing, classification and presentation of mortality statistics. This system includes codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.
An international classification of diseases for the twenty-first century.
ICD9_GROUPS assigns each code in the input vector to an ICD-9 class and displays the results.
International Classification of Diseases 9 (ICD-9) Classifier (Unofficial)
Independent predictor using Fuzzy K-Nearest Neighbor algorithm, used to predict ion channel-drug interactions. It can be used to identify a pair as Ion channel-drug pair or non-Ion channel drug pair according to the sequence of protein and the molecular fingerprint of drug.
Cloud-based freely open-source DNA part, plasmid, microbial strain, and Arabidopsis seed repository with physical sample tracking capabilities.
Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.
An intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition. IceBear is a research data management tool for structural biology. It currently covers crystallization trials, crystal fishing and shipping, as well as linking crystals, datasets, and PDB depositions for full chain of custody. It gives you a highly task-focused interface and a flexible access rights system. And it's FREE to download and install in your lab.
Web-based resource for integrative and conjugative elements (ICEs) found in bacteria.
An interactive online tool for calculating initial rates from continuous enzyme kinetic traces. An Interactive Continuous Enzyme Kinetics Analysis Tool (ICEKAT) was developed for semi-automated calculation of initial rates from continuous enzyme kinetic traces with particular application to the evaluation of Michaelis-Menten and EC50/IC50 kinetic parameters, as well as the results of high-throughput screening assays. ICEKAT allows users to interactively fit kinetic traces using convenient browser-based selection tools, ameliorating tedious steps involved in defining ranges to fit in general purpose programs like Microsoft Excel and Graphpad Prism, while still maintaining simplicity in determining initial rates. As a test case, we quickly analyzed over 500 continuous enzyme kinetic traces resulting from experimental data on the response of the protein lysine deacetylase Sirt1 to small-molecule activators.
a transcriptome-based framework to dissect intercellular communication. Floriane Noël and Lucile Massenet-Regad. To install it, the easiest way is to use the R package devtools and its function install_github. If you don't have all the dependancies needed to use ICELLNET package, run the commands below:.
Combined Coverage Correction and Principal Component Alignment for Batch Alignment in Single-Cell Sequencing Analysis. iCellR is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq and CITE-seq). Index of /results/external/iCellR/data. Analyzing High-Throughput Single Cell Sequencing Data. News (July 2020): See iCellR version 1.5.5 with new cell cycle analysis for G0, G1S, G2M, M, G1M and S phase, Pseudotime Abstract KNetL map (PAK map) and gene-gene correlations. See below for how to. A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq.
Visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. The unique advantages compared to other sequence logo creating tools is that this tool has a more dynamic nature and is more correct and complete in the analysis of conserved sequence patterns.
Many functions for computing the NPMLE for censored and truncated data.
IceR improves proteome coverage and data completeness in global and single-cell proteomics. IceR - Quantitative Label-Free Proteomics Workflow. Label-free proteomics enables the unbiased quantification of thousands of proteins across large sample cohorts.
A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.
The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alterations, structural rearrangements, gene expression, miRNAs). Easy to search and analyze data, construct queries across multiple data sets.
Resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.
A comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types. Iterative Comparison of Gene Epigenetic Circumstance (ICGEC). Function: This script is to simultaneously estimate the epigenetic conservation of genes and the conservation of histone modifications between two cell lines or two conditions. It was purely written by R.
QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.
A toolkit to detect, analyze and compare protein-ligand interactions.
Streamlining Expansive Chemical Space Evaluation of Molecular Sets. If you would like to reference chespa in an academic paper, we ask you include the following:. chespa, version 1.0.0 http://github.com/pnnl/chespa (accessed MMM YYYY).
ChewieSnake is an end-to-end cgMLST based workflow for analyzing a set of assemblies (or reads) and obtaining an easy-to-interpret cgMLST report.
This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.
Application for Unsupervised Analysis of Chromosome Movements in Meiosis.
iCircDA-LTR is a tool for the identification of circRNA-disease associations based on learning to rank.
Identification of circRNA-RBP interaction sites using deep hierarchical network. The tool is developed for circRNA-RBP interaction sites identification using deep hierarchical network. The 37 training sets of circular RNA (circRNA) and 31 testing sets of linear RNA are provided to evaluate our iCircRBP-DHN and compare with other methods.
A comprehensive analysis platform for cardiovascular-relavant cis-regulation in human and mouse.
The Citrus Pan-genome to Breeding Database (CPBD) provides a resource for analyzing transposable elements in the genomes of *Citrus* and related genera. It allows users to explore data and contributes to genetic breeding and agronomic trait research.
CPBD: Citrus Pan-genome to Breeding Database
The on-line catalogue of the Interlab Cell Line Collection of human and animal cell lines.
Interlab Cell Line Collection Catalogue (ICLC)
The ICTV Taxonomy Browser provides access to the current virus taxonomy, updated with new releases approved by the ICTV. It provides documentation, support resources, and versions.
A tool for accurate prediction of potential lncRNA disease associations. Potential lncRNA-disease association prediction. ICLRBBN, a tool for accurate prediction of potential lncRNA-disease associations using internal confidence based local radial basis biological network.
Integrative clustering of multiple genomic data using a joint latent variable model.
The Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.
Extracting interconnected communities in gene Co-expression networks. This is an implementation of ICN detection for gene co-expression network (GCN) in Matlab. In constrast to the community structure, we consider a pair of communities be interconnected if a subset of genes from one community is correlated with a subset of genes from another community. Please refer to the paper "Extracting Interconnected Communities in Gene co-expression Networks" for details.
From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode.
Integrative copy number variation (CNV) detection from multiple platform and experimental design.
This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results.
ICODE Hip US Calculator is a cross-platform mobile application that aids examiners in screening for hip dysplasia using Graf’s sonographic technique. The application calculates hip type based on patient data and provides management recommendations.
iCodon is a tool for ideal codon design for customized gene expression.
The Icolos tool is a workflow manager for structure-based workflows in computational chemistry, that abstracts execution logic from implementation as much as possible.
iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis along with Machine Learning tools, cTaG and NBDriver for cancer related data analysis.
ComplexHeatmap is an R package providing a highly flexible way to arrange multiple heatmaps and supports various annotation graphics for complex visualization of data associations. It allows for the efficient discovery of patterns and connections in diverse datasets within bioinformatics and other related fields.
consICA is an R package that implements consensus independent component analysis (ICA) for robust deconvolution of multi-omics data, separating biologically relevant signals from technical effects and providing insights into cellular composition and biological processes.
Allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).
Iteratively align deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.
A Python package to calculate, visualize and analyze correlation maps of proteins.
The Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins.
iCPAGdb is an atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility.
Tool for processing and analyzing ICPL LC-MS/MS (ESI) data.
Tool for processing and analyzing ICPL LC-MALDI data.
Predict regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. It reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.
Generating interoperable electronic case report forms using online codebooks. Semantic interoperability of clinical data requires the use of a common vocabulary, such as SNOMED-CT. Unfortunately, mapping data to such a terminology is time-consuming and requires expert knowledge of both the dataset and the terminology. A viable alternative can be the reuse of codebooks - published dataset definitions which, in some cases, have already been mapped to a terminology. We designed the iCRF Generator, a tool which makes it easy to generate interoperable electronic Case Report Forms for (currently) three major EDCs: OpenClinica 3, Castor and REDCap. The tool currently provides access to several codebooks stored online in Art-Decor, such as:.
An integrative analysis of CRISPR screen by reducing false positive hits.
Iterative consensus spectral clustering improves detection of subject and group level brain functional modules. Iterative consensus spectral clustering for brain functional modules. The code repo for the iterative consensus spectral clustering that performs detection of subject and group level brain functional modules. We obtained the following group level modularizations for normal healthy samples:. The proposed algorithm can also be used to obtain subject-level modules from multiple scans (of the same subject). For more details refer to the paper.
Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information for research in regenerative medicine. Searching fields (16641 cell lines). All SKIP ( 5615 ) RIKEN BRC ( 4111 ) eagle-i ( 3548 ) hPSCreg ( 3367 ).
Identify conserved structural features at sequentially degenerate locations in transcription factor binding sites. ICSF uses base-pair step parameters obtained from a collection of high-resolution DNA crystal structures to discover structural conservation that exists in the sequentially degenerate areas within a binding site and produce profiles of the structural features along the entire site.
ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways.
An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors. Identifying the ion channel-targeted conotoxins using reduced amino acid alphabet composition. Conotoxins are small peptide toxins which are rich in disulfide and have the unique diversity of sequences.
Integrated Complex Traits Networks. Database that allows researchers to build heterogeneous networks by integrating a variety of biological interactions, thus offering a systems-level view of human complex traits.
Committee for developing, refining, and maintaining a universal virus taxonomy. The goal is to categorize the multitude of known viruses into a single classification scheme that reflects their evolutionary relationships, i.e. their individual phylogenies.
Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs.
Icy provides the software resources to visualize, annotate and quantify bioimaging data.
Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding.
Rapid browser-based visualization for phylogenetic trees and networks.
Aligns metabolite data from multiple files to single spreadsheet.
Metastable decomposition at the peptide C-terminus. "iD-plus" MS-based search engine for protein identification. Copyright© 2017-2020,IPR Osaka Univ.
Integration of ecological responses to a soil bacterial 16S rRNA gene database. Abstract High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalising syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterise taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from the survey metadata.
IDACombo is a web application built on the R Shiny platform that predicts drug combination efficacy using monotherapy data and the Independent Drug Action (IDA) model. It provides a user-friendly interface for researchers to explore drug combination predictions without requiring programming expertise.
Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties.
IDAM provides a framework for the identification of microbial disease-associated biomarkers based on metagenomic and metatranscriptomic data. The raw sequencing data (matched metagenomic and metatranscriptomic data) or the expression matrix is required. The output is gene modules consisting of gene and sample subsets.
A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.
Locus-specific databases for immunodeficiency-causing mutations.
Immunodeficiency mutation databases (IDbases)
A server for the identification of DNA binding proteins.
Sequence-based Detection of DNA-binding Proteins using Multiple-view Features Allied with Feature Selection. DNA-binding proteins play essential roles in many molecular functions and gene regulation. Therefore, it becomes highly desirable to develop effective computational techniques for detecting DNA-binding proteins. In this paper, we proposed a new method, iDBP-DEP, which performs DNA-binding prediction by using the discriminative feature derived from multi-view feature sources including evolutionary profile, dipeptide composition, and physicochemical properties with feature selection. We evaluated iDBP-DEP on two benchmark datasets, i. e., PDB1075 and PDB594 by rigorous Jackknife test. Compared with the state-of-the-art sequence-based DNA-binding predictors, the proposed iDBP-DEP achieved 1.8 % and 3.0 % improvements of accuracy (Acc) and Mathew's Correlation Coefficient (MCC), respectively, on PDB1075 dataset; 7.4 % and 14.8 % improvements of Acc and MCC, respectively, on PDB594
This tool was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure
An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution.
Isotope distribution and theoretical spectrum calculation with GUI.
A converter between pepXML and mzIdentML formats for peptide identifications from tandem mass spectrometry. Developed by the ProteoWizard team.
A pipeline for quick clade identification of SARS-CoV-2 isolates. idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud.
A comprehensive resource featuring genes, variants and characteristics associated with infertility. Infertility Disease DataBase (IDDB) provides a versatile resource for genes, experiments and clinical records related with the infertility diseases, data in IDDB is annually updated and freely served for biologists and doctors interested in reproduction and infertility.
idDMR is an R package for detecting differentially methylated regions (DMRs) that uses a normalized kernel-weighted model and is array-adaptive to account for differences in probe spacing between Illumina platforms. The tool allows for convenient implementation of the array-adaptive DMR method.
IDDRRA is a software that allows the user to design and model a DNA molecule, irradiate it with various types of radiation included in the Geant4 physics models, and then analyze the simulation outcome in terms of Single Strand Breaks (SSB), Double Strand Breaks (DSB), Cluster Damage Sites (CDS) and energy deposition. IDDRRA, combines powerful tools in a single platform, providing the ability to quantify DNA damage and DNA damage repair using MC forecast algorithms.
A decision tree-based method for the refinement of variants in FFPE DNA sequencing data.
Collection of experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites.
This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.
IDEAS (Individual level Differential Expression Analysis for Single cells) an R package for differential expression analysis using single cell RNA-seq data of multiple individuals.
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
RNA-binding protein recognition based on multi-view deep feature and multi-label learning. RNA-binding protein (RBP) is a class of proteins that bind to and accompany RNAs in regulating biological processes. An RBP may have multiple target RNAs, and its aberrant expression can cause multiple diseases. Methods have been designed to predict whether a specific RBP can bind to an RNA and the position of the binding site using binary classification model. However, most of the existing methods do not take into account the binding similarity and correlation between different RBPs. While methods employing multiple labels and Long Short Term Memory Network (LSTM) are proposed to consider binding similarity between different RBPs, the accuracy remains low due to insufficient feature learning and multi-label learning on RNA sequences
identification of protein submitochondrial localization with deep learning.
Deep learning interactive tool for alignment-free clustering of DNA sequences.
Aa ranking framework for miRNA-disease association identification.
Identifiability and experimental design in perturbation studies. Interaction strengths between nodes in directed networks can be quantified from observations of the network's response to perturbations. This package reveals the identifiability of the inferred network parameters and optimizes experimental design for network perturbation studies. See our publication for details. You can install the IdentiFlow package with pip:.
Identifiability and experimental design in perturbation studies. Interaction strengths between nodes in directed networks can be quantified from observations of the network's response to perturbations. This package reveals the identifiability of the inferred network parameters and optimizes experimental design for network perturbation studies. See our publication for details. You can install the IdentiFlow package with pip:. The package is easy to use and we demonstrate its most relevant features in the example below. You find the example script in identiflow/examples. This folder also contains the scripts that were used to analyse the KEGG pathways, as described in our paper.
IdentPMP is a web application that predict plant moonlighting protein.
Plots data associated with arbitrary genomic intervals along chromosomal ideogram.
Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.
The goal of iDESC is to identify differential expressed gene signatures between two groups in single cell RNA-seq considering subject effect with zero-inflated negative binomial mixed model.
Gene knockout cell lysates are the cell homogenate in RIPA buffer made with double-knockout cell lines. The Gene knockout cell lines are developed by CRISPR. The protein concentration was determined with BCA assay. A vial of lysate from the parental cell line was also included as an internal control.
identifying DNase I hypersensitive sites based on LASSO and stacking learning. Enter the query DNA sequences in FASTA format (Example):.
iDHS-Deep is an integrated tool for predicting DNase I hypersensitive sites by deep neural network.
Identification of dihydrouridine sites through ensemble learning models.
An integrative signal extractor for data-independent acquisition proteomics.
A pipeline for automated configuration and processing of diffusion MRI data. iDIO is a software toolkit for processing diffusion-weighted MRI data. It integrates the functionalities of modern MRI software packages to constitute a complete data processing pipeline for structural connectivity analysis of the human brain.
A package for plotting genomic data by chromosomal location.
Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface.
iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks
An Integrated Application for Differential Splicing Analysis and Visualization.
Identifier mapping performance analysis.
Data retrieval for identifier mapping performance analysis.
Federated generalized linear mixed models for collaborative genome-wide association studies.
Network-based approach for integrating differential analysis of cancer metabolomics.
An alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data.
Gene-Focused Networks Underlying Phenotypic Convergence in a Systematically Phenotyped Cohort With Heterogeneous Intellectual Disability. The broad spectrum of intellectual disability (ID) patients' clinical manifestations, the heterogeneity of ID genetic variation, and the diversity of the phenotypic variation represent major challenges for ID diagnosis. By exploiting a manually curated systematic phenotyping cohort of 3803 patients harboring ID, we identified 704 pathogenic genes, 3848 pathogenic sites, and 2075 standard phenotypes for underlying molecular perturbations and their phenotypic impact. We found the positive correlation between the number of phenotypes and that of patients that revealed their extreme heterogeneities, and the relative contribution of multiple determinants to the heterogeneity of ID phenotypes
Multi-scale deep biological language learning model for the interpretable prediction of DNA methylations.
A generic webserver for predicting DNA methylation sites
This web-server is according to its genetic codes by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample. And by means of the approach of optimizing training datasets for predicting DNA methylation sites. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed their counterparts in the existing prediction methods.
iDNA-OpenPrompt is a software resource utilizing an OpenPrompt learning framework for identifying DNA methylation sites. The model combines prompt templates, a BERT tokenizer, and pre-trained language models to improve accuracy and efficiency compared to traditional methods.
iDNA6mA-Rice-DL is a local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method. Accurate detection of N6-methyladenine (6mA) sites by biochemical experiments will help to reveal their biological functions, still, these wet experiments are laborious and expensive. Therefore, it is necessary to introduce a powerful computational model to identify the 6mA sites on a genomic scale, especially for plant genomes. In view of this, we proposed a model called iDNA6mA-Rice-DL for the effective identification of 6mA sites in rice genome, which is an intelligent computing model based on deep learning method. Traditional machine learning methods assume the preparation of the features for analysis. However, our proposed model automatically encodes and extracts key DNA features through an embedded layer and several groups of dense layers.
iDog is a multi-omics resource for domestic dogs and wild canids, integrating genomic, transcriptomic, and epigenomic data. It offers a 15-fold increase in genomic samples and incorporates data for breed-specific SNPs, disease trait-associated variants, and genotype-to-phenotype associations.
"IDOPS IDentification of Pesticidal Proteins", a profile HMM-based tool to detect pesticidal sequences and compare their genetic context
Identification of Intrinsically Disordered Regions based on Sequence to Sequence Learning. Identification of Intrinsically Disordered Proteins and Regions. based on Sequence to Sequence Learning. The datasets used in this study can be downloaded from below links:.
A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States.
Characterization and Identification of Lysine Phosphoglycerylation Sites Based on Sequence-Based Features. iDPGK is a web server for identifying phosphoglycerylation sites. Protein phosphoglycerylation is the reaction in which a 1,3-bisphosphoglyceric acid (1,3-BPG) is attached to a lysine residue of a protein molecule, and thus to form a 3-phosphoglyceryl-lysine (pgK). Phosphoglycerylation is a reversible and non-enzymatic post-translational modification (PTM). It has been shown that the process of lysine phosphoglycerylation plays important regulatory roles in glucose metabolism and glycolytic process. However, studies in this field have been limited by the difficulty of experimentally identifying modified site specificity in lysine phosphoglycerylation (PGK). To facilitate this process, several tools have been proposed for the computational identification of PGK sites.
Ontology used to describe disordered regions in intrinsically disordered proteins.
A Sequence-Based Predictor for Identifying and Analyzing Dipeptidyl Peptidase IV (DPP-IV) Inhibitory Peptides Using a Scoring Card Method.
Illuminating the Dark Phosphoproteome Through PubMed Mining.
A package for profiling and analyzing Intrinsically Disordered Proteins in R.
A repository of binding sites for intrinsically disordered proteins complexes with known 3D structures.
The IDR (Irreproducible Discovery Rate) framework is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provide highly stable thresholds based on reproducibility.
IDR2D identifies reproducible genomic interactions. Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https: idr2d.mit.edu
Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework.
Identifying DNA- and RNA- binding proteins based on hierarchical ensemble learning.
IDRBP-PPCT is a web application for identifying nucleic acid-binding proteins based on position-specific score matrix and position-specific frequency matrix cross transformation.
Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network. A new sequence-based computational predictor for identifying DNA-binding proteins and RNA-binding proteins. In which, multi-label learning and a novel motif-based convolution neural network were employed. It reduced the cross prediction between DNA-binding proteins and RNA-binding proteins and improved the predictive perfermance for identification of DNA-binding proteins and RNA-binding proteins. It is a useful tool for nucleic acid binding protein prediction. The framework and working process of iDRBP_MMC are shown in Fig.1.
An interactive version of DREM software, which enables to integrate static protein-DNA interaction data with different types of time series data for reconstructing dynamic regulatory networks. It also allows users to interactively visualize a gene, TF, path or model-centric view of each of these data types, their interactions and their impact on the resulting model.
Predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. IDRMutPred is a specific and accurate computational approach to prioritizing disease-associated nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions (IDR). IDRMutPred is specifically trained on the IDR nsSNVs, and is specifically utilized to the IDR nsSNVs. IDRMutPred outperforms other general-purpose predictors for the IDR nsSNVs. This web server will serve as a valuable tool in the research community that focuses on the study of nsSNVs, especially those located in intrinsic disordered regions (Go to Predictor).
Identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework.
Identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers.
Integration of drug repositioning and drug-target prediction via cross-network embedding. iDrug is a computational pipeline to jointly predict novel drug-disease and drug-target interactions based on a heterogeneous network. iDrug adpots cross-network embedding to learn lower dimensional feature spaces for drugs, targets, and diseases in the heterogeneous network. A paper describing the approach is currently under review. A link to the paper will be added once it is published.
By means of the approach of optimizing training datasets, this webserver was developed for predicting drug-target interaction. It contains four predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for indentying the interactions of drug compounds with GPCRs (G protein-coupled receptors), ion channels, enzymes, and NR (nuclear receptors), respectively.
Multi-layered network-based pathway activity inference using directed random walks. iDRW is an integrative pathway activity inference method using directed random walks on graph. It integrates multiple genomic profiles and transfroms them into a single pathway profile using a pathway-based integrated gene-gene graph.
IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring. Infectious Disease Sequencing Platform. IDseq is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.
IDSL.IPA Characterizes the Organic Chemical Space in Untargeted LC/HRMS Data Sets.
Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets.
Deep learning framework to predict molecular fingerprints from mass spectra.
an lncRNA functional similarity calculation model based on an improved disease semantic similarity method. BACKGROUND:It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting lncRNA functions and identifying potential lncRNA-disease associations. Nevertheless, among them, little effort has been attempted to measure lncRNA functional similarity, which is an essential part of association prediction models. RESULTS:In this study, we presented an lncRNA functional similarity calculation model, IDSSIM for short, based on an improved disease semantic similarity method, highlight of which is the introduction of information content contribution factor into the semantic value calculation to take into account both the hierarchical structures of disease directed acyclic graphs and the disease specificities
Suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.
idTarget is a web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. idTarget screens against protein structures in PDB.
iDVIP is a web server for identifying Viral integrase inhibitory peptides (VINIPs).
An R package for generating analysis-ready data from electronic health records-diagnoses and procedures. The proposed open-source dxpr package is a software tool aimed at expediting an integrated analysis of electronic health records (EHRs). The dxpr package provides mechanisms to integrate, analyze, and visualize clinical data, including diagnosis and procedure records.
Deep Learning-Based Segmentation of the Inner Ear's Total Fluid Space.
an atlas of HLA-presented immune epitopes derived from non-coding regions.
The Immune Epitope Database provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes.
The 3D structural component of the Immune Epitope Database (IEDB). It catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB).
The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools. peptide:MHC-I binding and T-cell epitope tools have been added, mapping of discontinuous epitopes onto 3D structures was also added.
Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens. Free epitope database and prediction resource. Free resource for searching and exporting immune epitopes. Includes more than 95% of all published infectious disease, allergy, autoimmune, and transplant epitope data.
a common data model for global HIV cohort collaboration. IeDEA International epidemiology Databases to Evaluate AIDS. REDCap Data Dictionaries for IeDEA. IeDEA is an international research consortium established in 2006 by the National Institute of Allergy and Infectious Diseases to provide a rich resource for globally diverse HIV/AIDS data.
iELM webserver predicts the function and positional interface for short linear motifs important in protein-protein interactions.
Interactive electrode localization utility (ielu) is a software package that provides a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images.
Inborn Errors of Metabolism Knowledgebase (IEMbase) accepts an array of biochemical and clinical symptoms from a user and returns a ranked list of possible IEM disorders that match the input profile. In addition, the system can explain the rationale of its results, suggest possible tests that would assist in narrowing down the differential diagnosis, and provide access to its database of biochemical, molecular, and clinical information if more evidence is desired.
A prediction method based on deep learning is proposed to identify enhancers and enhancer strength, called iEnhancer-DCLA
Predicting enhancers and their strength based on DenseNet and improved convolutional block attention module.
A novel two-layer predictor for identifying enhancer by position specific of nucleotide composition. An enhancer is a short region of DNA with the ability to recruit transcription factors and their complexes, thus increasing the likelihood of the transcription possibility. Considering the importance of enhancers, the enhancer identification was popular in computational biology. In this paper, we propose a two-layer enhancer predictor, called iEnhancer-KL. Kullback-Leibler (KL) divergence is taken into consideration to improve feature extraction method PSTNP. Furthermore, LASSO is used to reduce the dimension of features to get better prediction performance. Finally, the selected features are tested on several machine learning models to find the best model with great performance
iEnhancer-RD:Identification of enhancers and their strength using RKPK features and deep neural networks
Interpretable sequence-based enhancers and their strength predictor. The program is developed for enhaner prediction, including five individual feature-based models: spectrum profile, mismatch profile, subsequence profile, PSSM and PseDNC, and ensemble learning model. Before the prediction, please make sure your computer has installed the software: the python package: repDNA and shap. repDNA (http://bioinformatics.hitsz.edu.cn/repDNA/).
Calculate the isoelectric point of proteins.
Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning.
Robust outlier identification for DNA methylation data. The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta.
A package used as a classifier for determining the origin of a mutation, specifically for samples that have been preserved using formalin-fixation paraffin-embedding (FFPE).
Visualizing gene expression changes in time, space, and single cells.
ABC (Artificial Bee Colony) and IF-ABC (Internal Geedback Artificial Bee Colony) are algorithms for protein structure optimization using off-lattice model.
A novel isolation-forest-based package to detect copy number variations from various NGS datasets.
IFeaLiD is an interactive visualization for feature localization in deep neural networks.
Python Toolkit and Web Server for Calculating a Wide Range of Structural and Physicochemical Feature Descriptors from Protein and Peptide Sequences.
iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands.
findCPcli is a command line python-tool for the computation of chokepoint reactions in genome-scale metabolic models. The main purpose of the tool is to compute chokepoints by taking into account both the topology and the dynamic information of the network. In addition to the computation of chokepoints, findCPcli can compute and remove dead-end metabolites, find essential reactions and update the flux bounds of the reactions according to the results of Flux Variability Analysis. findCPcli takes as input an SBML files of genome-scale models, and provides as output a spreadsheet file with the results of the chokepoint computation.
An automated web tool for determining enzyme-kinetic parameters based on the high-curvature region of progress curves.
Flnc is software that can accurately identify full-length long noncoding RNAs (lncRNAs) from human RNA-seq data. lncRNAs are linear transcripts of more than 200 nucleotides that do not encode proteins.
This web server is developed for users working in the field of vaccine design. This server allows users to predict and design IFN-gamma inducing peptides. It have following three modules.
A webserver for the prediction and designing of interferon-gamma inducing epitopes.
Web portal for interactive RNA folding simulations.
Incorporating Find Occurrence of Regulatory Motifs.
Fast, free, and highly customizable genome browser for viewing and exploring big genomic datasets.
Web tool can be used to view the matches to germline V(D)J gene segments, details at rearrangement junctions, the delineation of Ig sub-regions as well as other commonly sought information. Ithas the capacity to analyze both nucleotide and protein sequences.
This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.
high-performance search for large-scale genomic interval datasets. IGD: A high-performance search engine for large-scale genomic interval datasets. Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions.
Integrated and curated repository of mutation data on common genetic diseases afflicting the Indian populations. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers.
Analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes).
An integrated genome decontamination pipeline for wild ciliated microeukaryotes.
IgemRNA is an open access toolbox for transcriptome data statistical and biochemical network topology-based analysis. IgemRNA was developed in the MATLAB environment in order to take advantage of the up-to-date and most commonly distributed GSM modelling tool Cobra Toolbox 3.0 and spreadsheet file capabilities.
Statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies.
IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.
An implementation of scale functions for setting axis breaks of a 'gg' plot.
Differential gene usage in immune repertoires. Decoding the properties of immune repertoires is key in understanding the response of adaptive immunity to challenges such as viral infection. One important task in immune repertoire profiling is the detection of biases in Ig gene usage between biological conditions. IgGeneUsage is a computational tool for the analysis of differential gene usage in immune repertoires. It employs Bayesian hierarchical models to fit complex gene usage data from immune repertoire sequencing experiments and quantifies Ig gene usage biases as probabilities.
The Immunoglobulin Intraclonal Diversification Analysis tool (IgIDivA) offers the opportunity for an in-depth analysis of high-throughput sequencing data, with the scope of studying the intraclona diversification process through the identification of the somatic hypermutations that take place within the IGV gene region, the detailed characterization of their connections, the establishment of the mutational pathways and the calculation of metrics that allow the objective determination of the level of ID in a sample, together with statistical analysis for the comparison of different features of the ID level for different groups of samples.
Web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region.
An integrative transcriptomic and epigenomic classifier for glioblastoma molecular subtypes.
Interpreting blood GLUcose data with R package iglu. iglu: Interpreting data from Continuous Glucose Monitors (CGMs). The R package ‘iglu’ provides functions for outputting relevant metrics for data collected from Continuous Glucose Monitors (CGM). For reference, see “Interpretation of continuous glucose monitoring data: glycemic variability and quality of glycemic control.” Rodbard (2009). For more information on the package, see package website. Interpreting Glucose Data from Continuous Glucose Monitors.
IgMAT is a tool for the automatic discrimination and annotation of antibody sequences, specifically designed to be integrated into analysis pipelines or being used as a cli tool. IgMAT is highly customizable, allowing the addition of custom antibody sequences datasets and generating a range of output formats including a bed file of FR and CDR coordinates allowing simple downstream analysis on individual regions.
A program to identify, characterize, and quantify molecular interactions.
Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling.
ignomonicM is an R-package to estimate natural mortality throughout different life stages.
Predicting interaction between GPCRs and drugs in the cellular networks.
The web-server IGPred was developed to identify the immunoglobulins (antibodies) based on the sequence information.
Performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.
Tool for simulation of antibody repertoire and Ig-seq library. It is designed for testing and benchmarking tools for reconstruction of Ig repertoires.
Intermolecular Graph Transformer (IGT) employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture.
An integrative genome database of traditional Chinese medicine plants. An Integrative Genome Database of Traditional Chinese Medicines. IGTCM (An Integrative Genome Database of Traditional Chinese Medicines) is a comprehensive database of traditional Chinese medicine (TCM) genome and is also an integrative database of TCM with modern molecular biology. It contains six diverse components including herb, ingredient, gene, protein, rna and cds, which integrate TCM with modern molecular biology not only by internal molecular mechanism, also by enhanced understanding of secondary metabolic processes.
IGUANA is a graph neural network built for colon biopsy screening. IGUANA represents a whole-slide image (WSI) as a graph built with nodes on top of glands in the tissue, each node associated with a set of interpretable features. The output of the pipeline is explainable, indicating glands and features that contribute to a WSI being predicted as abnormal.
High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.
An embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team. igv.js is an embeddable interactive genome visualization component written in JavaScript and CSS. It is based on the desktop Integrative Genomics Viewer (IGV), and developed by the same team. See the sidebar for detailed documentation.**. To create an igv.js browser supply a container div and an initial configuration defining the reference genome, initial tracks, and other state to the function igv.createBrowser(div, config). ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/igv ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/igvtools (GITHUB.COM/igvteam/igv) ||| CORRECT NAME OF TOOL COULD ALSO BE 'igv.js'
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
The igvtools utility provides a set of tools for pre-processing data files.
iHDSel is a software tool for detecting genomic patterns of selection using the price equation and the population stability index. It's designed to identify sites with divergent selection based on the distribution of allelic classes of haplotypes.
A online platform for identifying human enzyme classes via reduced amino acid cluster strategy. Enzyme, as a kind of biocatalyst, dominates many catalytic processes such as metabolism, nutrition and energy conversion, and most of the reactions closely related to human life process are also enzyme catalytic reactions. Identifying the 2-level antimicrobial peptides using reduced acid amino composition.
An interactive web server for large-scale and comprehensive discovery of genes of interest in hepatocellular carcinoma.
Curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis.
Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence.
Inferring lncRNA Functional Similarity Based on Integrating Heterogeneous Network Data. Long non-coding RNAs (long ncRNAs, lncRNA) are one of great importance non-coding RNA with exceeding 200 nucleotides which are involved in human crucial biological processes. Improved evidences has proved that lncRNAs with similar expression patterns, expression profile and associated with similar diseases may share similar functions. Using the available data to build networks that are able to systematically and comprehensively infer the functional similarity of lncRNA. Determining the functional similarity of lncRNAs is beneficial to clarify the mechanism of their in life activities and complex diseases. IHNLncSim is a freely and reliable computational model can calculate functional similarity between lncRNAs, it will be advantageous to discover their functions which are ambiguous.
It allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, it reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.
Text-mining methods used to identify information on specific genes and proteins, their physical interactions and regulatory relationships, their relevance in pathologies, and their interactions with chemical compounds. iHOP parses thousands of PubMed documents every day and collects information specific to thousands of different biological molecules.
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. IHP-PING: Integrated Human Protein-Protein Interaction Network Generator. Maintainer: Gaston K. Mazandu 1,2,3 <gaston.mazandu at uct.ac.za>, Bioinformatics and Genomics Informatics Tools. IHP-PING provides a flexible python package, which extracts and integrates heterogeneous PPI datasets to generate a unified PPI network on-the-fly, which is stored locally for further potential user applications through three main steps starting from user input as shown in the figure (Part A) below, with basic statistics and properties: power-law and small-world (Part B).
IHRW is an improved hypergraph random walk model for predicting triple drug therapy.
The integrated haplotype Score is a measure of the amount of extended haplotype homozygosity at a given SNP along the ancestral allele relative to the derived allele. This measure is typically standardized empirically to the distribution of observed iHS scores over a range SNPs with similar derived allele frequencies. Extended homozygosity for haplotypes on a high frequency derived allele relative to the ancestral background is a signature of a positively selected sweep.
This web-server was developed to identify the family of heat shock proteins by using reduced amino acid alphabet.
Iterative hard thresholding - a multiple regression approach to analyze data from a Genome Wide Association Studies (GWAS).
Multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.
New predictor which was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition.
An integrative database of the expression dynamics of proteins in response to hypoxia in animals.
Predicting drug-target interactions through interactive and independent features based on attention mechanism.
Improved prediction of IL-13 inducing peptides using popular machine learning classifiers.
iimi is an R package that uses machine learning to diagnose plant viral infections from high-throughput sequencing data, addressing challenges of parameter subjectivity and mapping artifacts. The package is available on CRAN and integrates with the virtool.ca web application.
iIMPACT is a statistical method for spatial transcriptomics analysis that integrates image and molecular profiles to identify spatial domains and detect domain-specific differentially expressed genes. It leverages AI-reconstructed histology images and spatial context of gene expression measurements.
An R Package for Online Item Calibration, Scoring, Evaluation of Model Fit, and Useful Functions for Unidimensional IRT.
Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools.
Dynamic Python-Based Method Provides Quantitative Analysis of Intercellular Junction Organization During S. pneumoniae Infection of the Respiratory Epithelium.
Heuristic framework for inference of kinase activities from Phosphoproteomics data.
IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis. IKAP – Identifying K mAjor cell Population groups in single-cell RNA-seq analysis. Note: IKAP will, by default, regress out the percentage of mitochondrial gene counts and total UMI counts and scale the expression matrix using Seurat ScaleData function. These two values should be save in Seurat metadata with column names 'percent.mito' and 'nUMI' respectively. If you want to regress out different confounding variables or use different column names, please save these variables in Seurat metadata and set 'confounders' (an IKAP parameter) as their column names in the Seurat metadata data frame.
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Kaptive reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies. You can also run a graphical version of Kaptive via this web interface (source code). Given a novel genome and a database of known loci (K, O or OC), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:. Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. BLAST for all known locus nucleotide sequences (using blastn) to identify the best match ('best' defined as having the highest coverage).
Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of file formats containing genomic and transcriptomic sequence data.
A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets. kernInt uses the kernel framework to unify supervised and unsupervised microbiome analyses, while paying special attention to spatial and temporal integration. If you find our package useful, please cite:.
This resource provides access to genomic data and typing definitions for isolates of the Klebsiella pneumoniae species complex based on various typing methods like MLST, cgMLST, and core genome MLST. It allows data retrieval and analysis for researchers studying antimicrobial resistance and transmission mechanisms.
Klebsiella pneumoniae MLST databases and software
The International Knockout Mouse Consortium database and web portal which serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority.
High-throughput tool for alignment-free phylogenetics.
Prediction of Interleukin-13 inducing peptides.
Computer-aided prediction and design of IL-6 inducing peptides. A webserver to predict and design interleukin-6 inducing peptides. IL-6Pred: Prediction of Interleukin-6 inducing peptides. Protein Scan: Identify IL-6 inducing peptides or regions within a protein sequence. Welcome to the Dataset Page of IL-6Pred.
Prediction of Interleukin-10 inducing peptides
IL-13Pred: Prediction of Interleukin-13 inducing peptides
In silico model for predicting IL-2 inducing peptides in human.
IL4predIn Silico Platform for Designing and Discovering of Interleukin-4 inducing peptides
IL5pred is developed for the prediction of IL5 inducing peptides. Interleukin-5 (IL-5) is one of the key cytokines released by several cellular elements, including T-helper 2 cells, mast cells, Type-2 innate lymphoid cells, basophils and eosinophils.
Prediction of Interlukin-6 inducing peptides
LaminaRGeneVis: a tool to visualize a tool to visualize gene expression across the laminar architecture of the human neocortex.
Tool for interactive bioimage classification, segmentation and analysis.
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. Identification of Linear B-Cell Epitopes. Input your epitope sequence here. The sequence should be in FASTA format. Example. Please be patient after submitting and do not close this page. Retrieval Job IDInput your job id here (e.g. 20180602221946).
Consensus predictor that combines the two complementary inverse ligand binding predictors implemented using FINDSITE and SMAP and Support Vector Machines.
A manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases. ILDGDB is a manually curated database that provides comprehensive experimentally supported associations between genes and interstitial lung diseases (ILDs). The current version of ILDGDB incorporates 20 ILDs and over 600 genes obtained from 3000 articles in four species. The database consists of 5 sections: regulation of mRNA level (1082 entries, more than 450 genes), regulation of protein level (391 entries, more than 200 genes), variants (425 entries, more than 100 genes), drug information (35 entries, 29 genes) and knockout information (85 entries, 72 genes).
iLearnPlus is a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization.
ILEE is an anguided algorithm for accurate and automated quantitative analysis of cytoskeletal images.
A computational microscope to scrutinize membrane properties at the organelle-level
Software for robust calculation of transfer functions.
R Library for preprocessing Illumina Whole Genome Expression BeadChips.
The Illumina BCL Convert is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina™ sequencing systems to FASTQ files. The DRAGEN™ product includes hardware accelerated BCL conversion on the DRAGEN™ platform, which results in improved run times compared to BCL Convert pure software execution. The DRAGEN BCL conversion is designed to output FASTQ files that match bcl2fastq2 v2.20 output. DRAGEN supports direct conversion from .BCL to the compressed FASTQ.ORA format in order to reduce FASTQ.GZ file size by a ratio up to 5. Refer to the section "DRAGEN ORA compression from BCL" for proper usage.
Tools for parsing Illumina's microarray output files, including IDAT.
Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics.
Software for machines running Windows to identify variants in Illumina short read data.
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.
A Learning to Rank (LTR)-based method called iLncDA-LTR to predict diseases related with newly detected lncRNAs
Identify lncRNA-disease associations by fusing biological feature blocks through deep neural network. A new predictor for identifying lncRNA-disease associations by fusing biological feature blocks through deep neural network.
Predictor for subcellular locations of human proteins with multiple sites.
Extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism.
Robust evaluation of genome content and organization for provisional and mature genome assemblies.
This tool uses protein structural features (protein loops as classified in ArchDB and/or domains as classified in SCOP) to determine whether any pair of proteins interact or not. To do that, it uses data from both known protein interactions and putative non-interacting proteins, assigning positive and negative scores to the structural features. The main result page displays a summary of the predictions for the given protein pairs with available detailed data for each prediction.
ILoReg enables high-resolution cell population identification from single-cell RNA-seq data. ILoReg is a novel tool for cell population identification from single-cell RNA-seq (scRNA-seq) data. In our study [1], we showed that ILoReg was able to identify, by both unsupervised clustering and visually, rare cell populations that other scRNA-seq data analysis pipelines were unable to identify.
LUCIDus is an R package implementing a novel statistical model for multi-omics data analysis, addressing list-wise missingness through an integrated imputation framework. It elucidates the influence of exposures on outcomes by integrating omics data within latent clusters.
Identifying the N6-Methyladenine Site in Multiple Tissues by Using the Convolutional Neural Network. im6A-TS-cnn is able to identify multi-tissues in Human, Mouse and Rat.
IMA method for identifying protein complexes in PPI network
A web-based software platform for tumour radiogenomic evaluation and reporting.
The IMAAAGINE server is a protein structural motif database searching program. Users can define an amino acid arrangment of 3 to 8 residues which will be converted into a search pattern. The search using the query is carried out against the PDB. 3D arrangements of amino acids in PDB structures that conform to the query will be returned to the user.
“Iterative Mapping and Assembly for Gap Elimination”. IMAGE closes gaps in a draft assembly using Illumina paired-end reads.
Acquire video and images from Matrox frame grabbers.
Image Acquisition Toolbox Support Package for Matrox Hardware
MathWorks Image Acquisition Toolbox Team
Acquire video and images from Point Grey cameras.
Image Acquisition Toolbox Support Package for Point Grey Hardware
Acquire video and images from QImaging cameras.
Image Acquisition Toolbox Support Package for QImaging Hardware
Image feature detection using-Phase-Stretch-Transform (PST). PST is an operator that finds features in an image.
Image feature detection using Phase Stretch Transform
Image Section Generator grabs cursor-designated linescans from microscope images
MATLAB script for a new distribution metric for image segmentation for active contours.
Active Contours: A New Distribution Metric for Image Segmentation
The program finds the membrane in a fluorescence image using a modified Dijkstra algorithm to find the maximum mean intensity path.
Image segmentation for fluorescence membranes
Spatially-resolved single cell sequencing guided by in situ and in vivo imaging.
Converts a single image (microscopy, topogrpahy) into array of images.
Image to Volume Conversion for Representing Materials Topography
A CLI tool for detecting duplicate DICOM images by analyzing pixel data, generating content-based hashes, and comparing them to identify identical images—even when metadata, file format, or size differs
Docker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of preclinical and clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.
Image Quality Assessment metrics (IQA) for XNAT platform
High-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Integrated Methylation QTL Mapping and Allele-Specific Analysis. Integrative Methylation Association with Genotypes. IMAGE is implemented as an open source R package for mQTL mapping in sequencing-based methylation studies.
Image SXM is a version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.
R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, it provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.
It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.
Public domain Java image processing program inspired by NIH Image for the Macintosh. It was designed with an open architecture that provides extensibility via Java plugins.
ImageM is a GUI for Image processing with Matlab.
ImageMagick is a free, open-source software suite, used for editing and manipulating digital images. It can be used to create, edit, compose, or convert bitmap images, and supports a wide range of file formats.
Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.
Description of a functional connectivity and omics analysis tool and case study identifying a race confound.
Python based image analysis software designed for the automated analysis of images of the animal S. mediterranea. This software allows the animals’s neoblasts to be quantified and tested for assymetries along its veritcal and hoizontal axes. ImagePlane also allows simple mophology categorizations to be made based on the overall shape of the animal.
Open-source, Python-based and platform-independent software package for bioimage analysis.
Image analysis software package for electron microscopy, which is also used to process images from other devices, spectra and other multi-dimensional data-sets.
Functions for reading and writing image files and STAR files for electron microscopy
An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. Imaging-AMARETTO: tools for interpreting multi-omics networks for relevance to radiographic and histopathology imaging-derived biomarkers of clinical outcomes. The *AMARETTO framework for network biology and medicine: linking diseases, drivers, targets and drugs via graph-based fusion of multi-omics, clinical, imaging and perturbation data. NIH NCI CBIIT ITCR Cancer Data Science Pulse Blog. Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression. Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer.
Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models.
Integration of multiple single-cell datasets by adversarial paired transfer networks. Wang, D., Hou, S., Zhang, L. et al. iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks. Genome Biol 22, 63 (2021). https://doi.org/10.1186/s13059-021-02280-8.
Chromosome-level genome assembler combining multiple de novo assemblies
Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.
An integrative platform for comparative and functional genomics of marmots. iMarmot: an integrative Marmot database. Marmots are large Holarctic rodents in the genus Marmota with 14 living species. Most marmot species occupy a harsh environment characterized by a long, cold season without food. Their physiology is highly adapted to cope with this condition by hibernating in burrows. Global warming since the last ice age has reduced the geographic distribution of some of the marmots. The plagues in some marmots are known to co-occur with human epidemics in the same area, which give rise to a unique surveillance and a major public health concern. MarmotDB database aims to collect the currently available marmots’ genomic data and to characterize the molecular mechanism of hibernating and plague infection by comparisons of the expression profiles from different hibernators and plague hosts or transmitters.
Integrative analysis of Multi-omics data for Alternative splicing.
MatchMaps is a Python-based command-line interface for calculating non-isomorphous difference maps in X-ray crystallography, allowing for the detection of conformational changes in macromolecules.
Content aware denoising pipeline to enhance Imaging Mass Cytometry.
Identifying Driver Genes for Individual Patients through Inductive Matrix Completion.
Data exploration and visualization in Excel.
Python library of pretrained generative models for medical image synthesis.
Multi-label classifier for identifying membrane proteins with single and multiple types via physical-chemical property matrix and grey-PSSM.
Homology-based method, which predicts a membrane protein’s position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user.
iMet-Q (intelligent Metabolomic Quantitation) is a software that quantifies metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data.
This package provide a graphical user interface to the metagene package. This will allow people with minimal R experience to easily complete metagene analysis.
Calculate if an intron enhances gene expression.
This consortium is an international collaboration between a group of major public interaction data providers.
A Web Application for Interactive Metabolic Flux Analysis and Visualization.
This tool, 'img2catalog', is built to extract metadata from imaging data repositories, map it to a model class, and export it to a catalog. The tool is set up to be modular, but it currently supports extracting metadata from an XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0), based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO (https://github.com/Health-RI/SeMPyRO), and either writing it to an RDF file, or pushing it to a FAIR Data Point (FDP).
Software to automatedly analyze structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.
The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context.
Database of plasmids from genomes and metagenomes with rich annotations and metadata. It provides an extensive collection of plasmids, identified across thousands of isolate genomes, SAGs, MAGs, metagenomes, and metatranscriptomes using the geNomad tool. These plasmids are presented within a structured framework encompassing functional annotation and extensive metadata, which includes host taxonomy, similarity to other plasmids, geographic coordinates, and ecosystem information, allowing users to investigate plasmid function and ecology thoroughly.
An expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.
Community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. It contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. It provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context.
IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.
IMGT, the international ImMunoGeneTics information system
IMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA). Annotation is based on the IMGT-ONTOLOGY concepts.
Provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.
Interactive sequence alignment tool with help page available.
IMGT/V-QUEST is the IMGT® tool for nucleotide sequence alignment and analysis of immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains, integrates IMGT/JunctionAnalysis, IMGT/Automat and IMGT/Collier-de-Perles. Analysis is based on the IMGT-ONTOLOGY concepts.
IMI-driver is a model that integrates multi-omics data into eight biological networks to identify cancer driver genes. It applies Multi-view Collaborative Network Embedding and has outperformed other methods when tested on 29 cancer types from TCGA.
Modular pipeline for comprehensive analysis of small RNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow.
Web application designed to selectively mutate predicted miRNA target sites while ensuring that predicted target sites for other miRNAs, termed illegitimate target sites, are not created in the process.
Package for integrative missing value estimation of microarray data sets with limited number of samples, high level of noise, or high rate of missing values. iMISS works by incorporating information from multiple reference microarray datasets to screen reliable neighbor genes used in basic local estimation algorithms such as the Local Least Squares (LLS) algorithm. In addition to the integrative algorithms, implementations of KNN and LLS based imputation algorithms are also provided.
ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction.
A multivariate mixture model approach to integrative analysis of multiple types of omics data. R package for integrative genomics analysis using a multivariate mixture model framework. Ziqiao Wang and Peng Wei. IMIX: A multivariate mixture model approach to integrative analysis of multiple types of omics data. bioRxiv 2020.06.23.167312; doi: https://doi.org/10.1101/2020.06.23.167312.
Machine learning framework for identifying severity of tomato yellow leaf curl virus and their experimental validation.
The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest.
Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.
Light transport modeling in highly complex tissues using the implicit mesh-based Monte Carlo algorithm.
ImmCancer - Portal For Cancer Immunothrerapy Tools And Repositories
A user-friendly web-based platform to infer metabolic function from omics data.
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier. Knowledge-based and lineage-driven immune cell classification in single-cell RNA-Seq data. ImmClassifier (Immune cell classifier), a knowledge-based and lineage-driven immune cell classification algorithm with fine annotation granularity yet high prediction accuracy. ImmClassifer seamlessly integrates the biology of immune cell differentiation, the strength of heterogeneous reference datasets and the state-of-art machine learning models. ImmClassifier cascades a machine learning module and a deep learning module. Maintainer: Xuan Liu xuan.liu.1@uth.tmc.edu Sara Gosline sara.gosline@sagebase.org.
Tool to merge VCF genotype files at scale
ImmQuant is a software tool allowing immunologists to upload transcription profiles of multiple tissue samples, apply deconvolution methodology to predict differences in cell-type quantities between the samples, and then inspect the inferred cell-type alterations using convenient visualization tools.
The regulon atlas of immune-related pathways across cancer types.
An open resource for exploring immunotherapy-related multidimensional genomic profiles in melanoma.
A tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction.
R package designed to analyse T-cell receptor (TCR) and B-cell receptor (BCR) repertoires
Tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking | The goal of the immuneSIM simulation is to in silico generate human and mouse B- and T-cell repertoires with user-defined properties to provide the user with custom native or aberrant immune receptor sequence repertoires to benchmark their repertoire analysis tools. The simulation algorithm implements an in silico VDJ recombination process with on-the-go annotation of the generated sequences and if enabled by the user somatic hypermutation (SHM) and motif implantation. With a wide range of user-modifiable parameters, a uniquely diverse set of repertoires can be created. The parameters include: Clone count distribution, Germline Gene Usage, Insertion and Deletion Occurrence, SHM likelihood and Motif Implantation
Deep-learning models for predicting the structures of immune proteins.
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology | Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://doi.org/10.1093/bioinformatics/btz363 | Comprehensive evaluation of cell-type quantification methods for immuno-oncology | A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) | immunedeconv - an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data | Sturm, G., Finotello, F., Petitprez, F., Zhang, J | The source code in this project can be used to reproduce the results described in the paper
ImmuneMirror is a machine learning-based pipeline and web server for neoantigen prediction, trained on a balanced random forest model. It is designed to prioritize neoantigens for immunotherapeutic targets, applied to gastrointestinal tract cancers.
Sandve Research Group for Biomedical Informatics
immuneML is a flexible platform designed for machine learning-based analysis and classification of adaptive immune receptor repertoires (AIRR). The platform is available in several formats, including a command-line tool and a Galaxy web interface, and is accessible to a wide range of users from data scientists to clinicians. immuneML offers comprehensive functionality for exploratory analysis of datasets, training machine learning models for repertoire or receptor sequence classification, simulating immune events, and applying trained ML models to new datasets with unknown class labels. The platform also provides developer documentation for extending functionality with new components.
Reference-based comparison of adaptive immune receptor repertoires.
Provides a convenient API for accessing data sets within ImmuneSpace, the data repository and analysis platform of the Human Immunology Project Consortium (HIPC).
An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The SARS-CoV-2 Immunoanalytics platform is an online tool for the visulisation and analysis of multiple genomic and immunoinformatic meta-analyses. The tool combines an extensive epitope mapping and prediction meta-analysis, with an updated variant database (55,944 non-synonymous mutations) based on 16,087 whole genome sequences, and an analysis of human coronavirus homology, combined with up-to-date annotations from the UniProt database. With this tool and the data we have generated, we hope researchers can perform their own further research, whatever it may be.
ImmunoAIzer is a deep learning-based computational framework to characterize cell distribution and gene mutation in tumor microenvironment.
Model based clustering and meta-clustering of Flow Cytometry Data.
A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
Enabling systems immunology with a manually curated intercellular immune interaction network. ImmunoGlobe is a map of the immune network that describes how different parts of the immune system work together to drive immune responses. By structuring our knowledge of immune interactions into a directed graph, ImmunoGlobe makes it easy to explore the relationships between components of the immune system.
A novel scoring method based on RNA-Seq immunograms describing individual cancer-immunity interactions. Because of the complexity of cancer-immune system interactions, combinations of biomarkers will be required for predicting individual patient responses to treatment and for monitoring combination strategies to overcome treatment resistance. To this end, the "immunogram" has been proposed as a comprehensive framework to capture all relevant immunological variables. Here, we developed a method to convert transcriptomic data into immunogram scores (IGS). This immunogram includes 10 molecular profiles, consisting of innate immunity, priming and activation, T cell response, interferon γ (IFNG) response, inhibitory molecules, regulatory T cells, myeloid-derived suppressor cells (MDSCs), recognition of tumor cells, proliferation, and glycolysis
UK Veterinary Immunological Toolbox Website is promoting vaccine research by facilitating communication and removing reagent barriers. Colorized scanning electron micrograph of a B cell from a human donor [Credit: NIAID]. Welcome to the Immunological Toolbox, a repository of antibodies, other reagents and resources to promote veterinary immunology research. The Antibody Hub has been established with the aim of improving animal and human health globally.
UK Veterinary Immunological Toolbox Website
Web-based computational pipeline for analysing and mining immunopeptidomic data.
High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Wellcome Trust Sanger Institute.
ImmunoSPdb is a repository of experimentally validated peptides which suppress the immune system. All information compiled in this database has been extracted from research papers and patents.
Set of image processing, modelling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
Explore the colletive motions of proteins and nucleic acids using NMA in internal coordinates.
A knowledgebase of microbial transcriptional regulation derived from machine learning. Independent Component Analysis of Bacterial Transcriptomes. iModulonDB is maintained by the Systems Biology Research Group at the University of California, San Diego.
iMOMLogit provides improved performance in identifying true models and reducing estimation and prediction error in a number of simulation studies.
A web server for interactive multiomics and pharmacological analyses of patient-derived cancer cell lines.
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
motifbreakR is a Bioconductor package that scans genetic variants against position weight matrices of transcription factors to predict potential disruptions in binding sites. It includes an R/Shiny graphical user interface and leverages DNA-binding sequencing datasets for evidence-based predictions.
Integrative Multi-species Prediction (IMP) is a webserver that enables biologists to analyze their experimental results in the functional context of gene networks from multiple organisms.
Modeling Biological Complexes Using Integrative Modeling Platform | Scripts to assess sampling convergence and exhaustiveness
Integrative Modeling Platform broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies. Detailed structural characterization of assemblies is generally impossible by any single existing experimental or computational method. This barrier can be overcome by hybrid approaches that integrate data from diverse biochemical and biophysical experiments.
Integrated Meta-omic Pipeline. Large-scale standardized integrated analysis of coupled metagenomic and metatranscriptomic data. Incorporates robust read preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations.
A Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. This software makes use of several known bioinformatics software, e.g., ConTest, Jmol, PhyML, ATV, etc.
Java swing based Graphical User Interface program for analyzing and/or combining several selection results from programs like, PAML (codeml), Datamonkey, TreeSAAP. Provides 3D homology modeling through Swiss Model and 3D mapping of selection results through Jmol.
IMPaLA is a web tool for the joint pathway analysis of transcriptomics or proteomics and metabolomics data.
Partial Annotations for Cell Instance Segmentation. Partial Annotations for MultiplexCell Instance Segmentation.
Genotype-phenotype annotations from knockout mouse strain for every protein coding gene in the mouse genome.
Package contains methods for data retrieval from IMPC Database.
Fast and comprehensive IMmune Paired-End Reads Merger for sequencing data.
Software package implementing methods for imputation from summary statistics and accompanying data. The software takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants.
Integrated medicinal plantomics is an integrated platform for organizing, analyzing, and sharing omics data of medicinal plantomics.
ImpLiMet is a Shiny application for missing data imputation that enables users to impute missing data using eight different methods and suggests an optimal approach. The tool’s effectiveness can be visually assessed through various analyses, and its code is openly available on GitHub.
An Integrated Method for Predicting Potential Associations Between miRNAs and Diseases. Background< h4>With the rapid development of biological research, microRNAs (miRNAs) have increasingly attracted worldwide attention. The increasing biological studies and scientific experiments have proven that miRNAs are related to the occurrence and development of a large number of key biological processes which cause complex human diseases. Thus, identifying the association between miRNAs and disease is helpful to diagnose the diseases. Although some studies have found considerable associations between miRNAs and diseases, there are still a lot of associations that need to be identified. Experimental methods to uncover miRNA-disease associations are time-consuming and expensive
McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level.
iMPP is a tool designed to predict and assemble peptides from short fragmentary reads. iMPP is written in C++ and has been tested on a 64-bit Linux system. The input for the software are FASTQ sequences, and the output comprises of 4 files: 1. predicted genes (nucl), 2. predicted peptides (prot), 3. gene predictions in gff format, 4. assembled peptide sequences (prot).
Immune Germline Prediction (IMPre), a tool for predicting germline Variable/Joining genes and alleles using deep-sequencing data derived from T-cell receptor/B-cell receptor repertoires.
improj3 generates 3D projections from image stacks
A flexible software platform for adaptive neuroscience experiments. A flexible software platform for real-time and adaptive neuroscience experiments. improv is a streaming software platform designed to enable adaptive experiments. By analyzing data, such as 2-photon calcium images, as it comes in, we can obtain information about the current brain state in real time and use it to adaptively modify an experiment as data collection is ongoing.
Integrating Multiple Phenotype Resources Optimises Variant Evaluation in genetically determined Developmental Disorders.
iRRBS is a Python package designed to correct the 3' trimming of reduced representation sequencing (RRBS) reads, which can lead to false positive differentially methylated site (DMS) identifications. It improves RRBS analysis by identifying and hiding non-trimmed cytosines.
The Integral Membrane Protein Stability Selector. Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites
This resource presents a comparative analysis of machine learning models for cancer detection and multiclass classification using platelet RNA data from 1397 cancer patients and 354 healthy donors. The code and data processing pipelines are open-sourced to serve as a baseline for further research.
This tool captures single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.
It is a differential expression algorithm for longitudinal count data sets which arise in sequencing experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq. It is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene.
impuSARS allows the imputation of viral whole genome sequences from partially sequenced samples. Additionally, impuSARS provides the lineage associated to the imputed sequence. impuSARS have been validated with a reference of SARS-CoV-2 sequences.
A fast and user-friendly calculation of genotype-imputation accuracy-measures.
Genotype imputation and haplotype phasing.
IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples.
A Visualization Tool of Imputation for the Prediction of Biomedical Data.
An R package for assessing imputation quality of genotypes and optimizing imputation parameters. imputeqc is an R package and accompanied scripts to estimate the quality of imputation of genotypes that was made with fastPHASE and BEAGLE softwares. Any other tools that support *.inp fastPHASE or VCF files can be also considered. The package is based on masked data analysis.
Web server and R package for missing values imputation in metabolomics data.
Load any size TIFF stack, even those larger than 4GB.
imread_big -- read in TIFF stacks larger than 4GB
ImReLnc accurately identified the irlncRNA characteristics in multiple cancers based on the heuristic correlation coefficient
A platform for simultaneously identifying multiple kinds of RNA modifications. iMRM is able to simultaneously identify m6A, m5C, m1A, ψ and A-to-I modifications in Homo sapiens, Mus musculus and Saccharomyces cerevisiae.
This is developed for designing a single-strand RNA sequence with desired immunomodulatory potentials in order to develop RNA-based therapeutics, immunotherapy and vaccine-adjuvants. This server also facilitates the users in computer-aided designing of siRNAs with desired toxicity.
Comprehensive database application and analysis platform that is capable of combining metabolic data, like IMS chromatograms, and heterogeneous biomedical data, like patient records, into a centralized data structure.
Fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments.
The software ImShot aims to identifying peptides obtained in MALDI-IMS.
Simulation of small-angle X-ray scattering data of biological macromolecules in solution. Biological small angle scattering. Simulation of 2-D SAXS patterns and 1-D profiles from biological macromolecules in solution. Post all your questions about IMSIM to the ATSAS Forum. ATSAS online : Forum : User information : EMBL Hamburg. Simulation of two-dimensional small angle X-ray scattering patterns and, further, one dimensional profiles from biological macromolecules in solution.
An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.
Multibatch Cytometry Data Integration for Optimal Immunophenotyping. iMUBAC: Integration of Multi-Batch Cytometry Datasets. The 'iMUBAC' package provides a structured framework for objective inter-batch comparisons and unbiased immunophenotyping of high-dimentional cytometry datasets.
Computational identification of multiple lysine PTM sites by analyzing the instance hardness and feature importance.
MUSTA is a Python-based command-line tool and end-to-end pipeline for accurate somatic mutation analysis in cancer, designed to simplify complex workflows and improve reproducibility.
A web application to identify the most similar mutational signature using shiny.
The IMvigor210CoreBiologies package provides methods and processed data for analyzing immunotherapy response in lung adenocarcinoma. It includes tools for identifying prognostic signatures (ICSMI) and analyzing tumor microenvironment characteristics.
An open-source Python library enabling efficient extraction and processing of ion mobility spectrometry-mass spectrometry data in the MZA file format.
imzMLConverter is a tool designed to convert various mass spectrometry imaging (MSI) data formats into the open standard imzML format, enabling cross-platform data sharing and compatibility with different software and instruments.
Exploiting deep learning embeddings of protein sequences to predict the localisation of peroxisomal proteins. In-Pero: Prediction of sub-peroxisomal localisation using deep learning embeddings and
Computational method for predicting DNA repair outcomes at DNA double strand breaks induced by CRISPR/SpCas9 resulting from non-homologous end-joining.
Cloud infrastructure deploying a series of genome oriented tools.
It provides an array of features useful in analysis of synonymous codon usage in whole genomes. In addition to computing codon frequencies and several usage indices, such as ‘codon bias’, effective Nc and CAI, the primary strength of INCA has numerous options for the interactive graphical display of calculated values, thus allowing visual detection of various trends in codon usage.
An R package for an integrated evaluation of statistical approaches to cancer incidence projection. Comparative analysis of model performance for rate data.
An efficient and incremental approach for calculating the differences in orbit counts when performing single edge modifications in a network. Calculating the differences in orbit counts is much more efficient than recalculating all orbit counts from scratch for each time point.
A set of algorithms for the standard representation of chemical structures that will be readily accessible to chemists in all countries at no cost. The standard chemical representation could be used as input into existing and newly developed computer programs to generate a IUPAC name and a unique IUPAC identifier.
R package for computation and visualization of epicurves from unaggregated linelist data.
Set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
NBC++ is an incremental Naive Bayes classifier designed for metagenomic taxonomic classification. It focuses on query performance and memory efficiency, utilizing canonical k-mer storage and adaptable memory allocation, and is available through GitHub with a Dockerfile for easy deployment.
NBC++ (Incremental Naive Bayes Classifier)
Powerful tool for pathway-based analysis or visualization of heterogeneous cross-platform microarray datasets (mRNA, miRNA, DNA methylation and protein).
IncucyteDRC is an R package for the analysis of data from live cell imaging cell proliferation experiments carried out on the Essen Biosciences IncuCyte ZOOM instrument.
IND-enzymes is a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.
A tool for generating primers suitable for CAPS or dCAPS analyses of sites with insertions or deletions as well as SNPs.
A first method to evaluate uniform/independent graph sampling.
3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.
Biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution.
Takes a NEXUS file containing aligned DNA sequences and recodes the gaps using the simple indel coding algorithm.
Database of indels in protein structures and their flanking regions. Contains indels with flanking regions extracted from structural alignment pairs of non-redundant domains from superfamilies. Provides access to information about indels and their flanking regions.
An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next-generation sequencing data.
indelPost is a Python library for indel processing via realignment and read-based phasing to resolve alignment ambiguities.
Tool for genome-wide identification of indels.
Predicting deleterious multiple point substitutions and indels mutations.
Integrated tool for in-depth pathway enrichment analysis based on single-cell sequencing data.
Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome.
This repository includes the official implementation of IndexNet Matting for deep image matting, presented in our paper:. Simple and effective: IndexNet Matting only deals with the upsampling stage but exhibits at least 16.1% relative improvements, compared to the Deep Matting baseline;.
There are different ways to create forecastive models. I used Curve Fitting Toolbox
India COVID-19 Patients Forecastive Model and Standalone App
Compute Chao, Simpson and Shannon values from Sabund and Rabund files.
A comprehensive resource of genetic variants from over 1000 Indian genomes. IndiGenomes Resource of Population Genomes from India.
IOS app for in-silico digestion and more.
INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles.
Identifies causal genes and their affecting risk pathways in cancer individuals by integrating data from genetic alteration, gene expression and the topology structure of KEGG pathway.
A 1st principles mathematical model of a 100,000 Litre penicillin fermentation
MenDeVAR is a software resource integrated within the PubMLST system that performs high-throughput phenotype-to-genotype testing for *Neisseria meningitidis* isolates, identifying genetic determinants of disease-relevant phenotypic traits.
Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR)
R package for fast implementation of nested cross-validation with embedded feature selection designed for transcriptomics and high-dimensional data.
iNetModels is an interactive visualization and database of multi-omics data.
A Transformer-Based Causal Inference Framework for Enhancing Pharmacovigilance.
Software of reconstructing contiguous regions of an ancestral genome.
Inferring copy number alterations from tumor single cell RNA-Seq data
Leveraging single-cell chromatin accessibility for the signal of chromatin loop.
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases (e.g. Rfam) for RNA structure and sequence similarities.
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants.
Simple but effective method to estimate purities from the DNA methylation 450k array data.
Web-Based Database and Predictor of Anti-Inflammatory Natural Products.
Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis.
R-package designed to give insight in clustering results and provide an optimal number of clusters
influx_si estimates metabolic fluxes and concentrations based on stationary or dynamic labeling experiments conducted on cultures held in a metabolically stationary state.
New Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.
INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
Display basic information about a multiple sequence alignment.
Information on a multiple sequence alignment.
An Emboss tool that writes statistics for a sequence assembly
Return information on a given nucleotide base.
Small script for calculating statistics that measure the ancestry information content of genetic markers.
Identifying flow modules in ecological networks using Infomap. Network community detection using the Map Equation framework. A a package for running Infomap, inspired by ecological networks. Infomap finds important patterns in complex networks by optimizing the map equation, which exploits the information-theoretic duality between the problem of compressing data and detecting patterns. This site is an extension of the paper Identifying flow modules in ecological networks using Infomap.
Return information on a given amino acid residue.
A novel computational method and its R and web-based implementations, to perform inference of gene network from transcriptome data and prioritization of key genes with central functional and topological role in the network.
Information-based similarity index is an analysis of measuring distance between symbolic sequences
Informeasure is an R/Bioconductor package for quantifying nonlinear dependencies in biological regulatory networks using information theory. It provides a comprehensive set of information measurements, allowing users to infer relationships between variables.
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR. This folder contains a Python port of MiXeR, wrapping the same C/C++ core as we previously used from MATLAB. This is work in progress, but eventually it should singificantly improve user experience, as Python allows much simpler installation procedures, makes it less error prone, allows to implement well-documented command-line interface (python mixer.py --help), and provide visualization. Input data for MiXeR consists of summary statistics from a GWAS, and a reference panel.
A suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer.
Predicting kinase inhibitors using bioactivity matrix derived informer sets | This repository implements in Matlab the Regression Selection method described in "Zhang, Huikun, Lee, Ching-pei, Ericksen, Spencer S., Mason, Blake J., Wlodarchak, Nathan, Mitchell, Julie C., Wildman, Scott A., Wright, Stephen J., Nowak, Robert, Gitter, Anthony, Hoffman, F. Michael, and Newton, Michael A. Minimally-supervised, chemogenomic strategies for effective compound prioritization on kinases." | This repository implements two experiments described in the manuscript: | Training a single model for prediction on new kinases | Conducting leave-one-out cross-validation and outputing the final leave-one-out prediction on each input kinase
Display basic information about sequences.
Declarative tree decomposition-powered framework for bioinformatics.
Interaction Network GO Annotator protein function predictor.
Integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.It does not have any read length restriction. It can handle 454 sequencing and/or Illumina Solexa sequencing and/or Sanger sequencing data sets.
Effective construction of full-length and non-redundant CDSs from unassembled transcriptomes.
inGAP-family is a tool for accurate detection of meiotic recombination loci and causal mutations by filtering out artificial variants due to genome complexities. inGAP-family provides an efficient and effective framework to discover, filter and visualize DNA polymorphisms and structural variants from alignment of short reads. Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. In addition, inGAP-family provides user-friendly graphical interface for detection of polymorphisms and structural variants, and for further evaluation of predicted variants and identification of mutations related to genotypes.
inGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to evaluate the quality of the predicted structural variation.
Software tool for constructing, simulating, and exploring models of gene regulatory networks. It is an open source, extensible Java application that allows users to rapidly build ordinary differential equation models of a gene regulatory network without requiring extensive programming or mathematical skills.
A web application that helps researchers studying human disease to identify causal variants.
Identification of bacteriophage genome sequences with representation learning.
A suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk. Redirecting to the new location... FluConvert and IniFlu (ver.1.0.0.0701).
MATLAB based matched filter is implemented for an Intravascular Near-Infrared Fluorescence (iNIRF) imaging method.
Intravascular Near-Infrared Fluorescence (iNIRF) Imaging
New predictor was developed by incorporating the position-specific dipeptide propensity into the general pseudo amino acid composition for discriminating the nitrotyrosine sites from non-nitrotyrosine sites in proteins.
Prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution. The Individual Meta Random Forest (InMeRF) is a tool to predict the pathogenicity of nonsynonymous SNVs (nsSNVs) using 150 independent models that were individually generated for all possible amino acid (AA) substitutions. This version is using 34 rank scores in dbNSFP v4.0a as feature values.
Web based tool designed to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments.
InMoose, the INtegrated Multi-Omic Open-Source environment, ports to Python state-of-the-art R tools for the analysis of transcriptomic data.
Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource.
Revealing mechanisms of infectious disease spread through empirical contact networks.
A python package with a command-line interface that implements the method for characterizing the noise and identifies statistically significant responding clones.
A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.
A software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.
InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning.
Alternative polyadenylation (APA) is an important post-transcriptional regulation mechanism which occurs in most human genes. This tool facilitates the discovery of novel APA sites from RNAseq data by leveraging cleanUpdTSeq to fine tune identified APA sites.
InPheRNo-ChIP is a computational framework for reconstructing phenotype-relevant gene regulatory networks associated with endoderm development. It integrates RNA-seq, transcription factor (TF)-specific ChIP-seq, and phenotypic labels to infer GRNs.
An R package for computing the number of susceptibility SNPs and power of future studies.
inpPDH is an improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties.
Predicting the impact of mutations on protein stability from sequence
Predicting the impact of mutations on protein stability from sequence and structure.
An intelligent network pharmacology platform unique for traditional Chinese medicine.
Wwo-level predictor. It can be used to identify an uncharacterized protein as nuclear receptor (NR) or non-NR according to its sequences information alone.
INSaFLU-TELEVIR is a free, open-source bioinformatics suite for viral metagenomic detection and routine genomic surveillance, designed for both web-based and locally installable use. It supports various sequencing technologies (Illumina, Ion Torrent, Oxford Nanopore) and includes modules for genome assembly, variant calling, and phylogeographic analysis.
Integrating millions of single cells using batch-aware triplet neural networks. INtegration of millions of Single Cells using batch-aware Triplet networks. insct is a deep learning algorithm which calculates an integrated embedding for scRNA-seq data. With insct, you can:. a, INSCT learns a data representation, which integrates cells across batches. The goal of the network is to minimize the distance between Anchor and Positive while maximizing the distance between Anchor and Negative. Anchor and Positive pairs consist of transcriptionally similar cells from different batches. The Negative is a transcriptomically dissimilar cell sampled from the same batch as the Anchor. b, Principal components of three data points corresponding to Anchor, Positive and Negative are fed into three identical neural networks, which share weights. The triplet loss function is used to train the network weights and the two-dimensional embedding layer activations represent the integrated embedding.
This database consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. It covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations.
Nucleotide Sequence Database Collaboration
Easy-to-use and powerful web server for biologists analysing genomic sequence data for in silico cis-regulatory modules prediction and analysis.
InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. Insect Olfactory Receptor Genome Wide Survey. Prediction of odorant receptor genes from newly sequenced insect genomes is a difficult task in absence of antennal transcriptome data. This tool will make it easier for you.
ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers.
A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data.
Interpretable sparse matrix decomposition for bulk RNA expression data analysis.
Web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.
Comparative analysis of open source in silico fragmentation tools.
InSilicoSeq is a software package that simulates realistic Illumina-like sequencing reads for amplicon-based sequencing, allowing for design and validation of sequencing experiments and benchmarking of bioinformatic workflows.
Provides tools for theoretical PCR amplification, AFLP-PCR and PFGE with all up-to-date public complete bacterial genomes (300+ genomes available).
In silico simulation of molbio experiments
Proteomics open-source project, aimed at implementing recurrent computations that are necessary for proteomics data analysis.
nsink is an R package that uses widely available GIS data to identify landscape sinks within catchments, estimate their nitrogen removal potential, and map the effect of those sinks on nitrogen movement. It facilitates data acquisition, processing, and visualization for decision-makers and resource economists.
Incorporating Network Structure Information for Single-Cell Type Classification.
Method for detecting insertions based on deep learning network.
INference of Synthesis, Processing and dEgradation rates in Course-Time experiments analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.
INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. de Pretis S., Furlan M. and Pelizzola M. Modeling RNA synthesis, processing and degradation with RNA-seq data. INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data. INSPEcT - INference of Synthesis, Processing and dEgradation rates from Transcriptomic data. GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse. 2 Run the application from an R session. 3 Presentation of the Graphical User Interface.
Inspect is a general purpose database search algorithm, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, Inspect implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.
INSPIIRED is a software suite designed to study viral integration sites and the longitudinal outcomes of gene therapy patients.
An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction.
2D prototype to integrate InSPIRE into Radiation Oncology treatment planning.
My challenge paper listed on my profile relies on reducing a multi-modal to mono-modal def reg.
Effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.
Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL. Large genome reassembly based on Hi-C data, continuation of GRAAL. Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries. This work is under continuous development/improvement - see GRAAL for information about the basic principles. sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal. Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)
A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Get in touch with Team InstaDock.
InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
An easy-to-use deep learning pipeline for image segmentation and classification. InstandDL: An easy and convenient deep learning pipeline for image segmentation and classification. InstantDL enables experts and non-experts to use state-of-the art deep learning methods on biomedical image data. InstantDL offers the four most common tasks in medical image processing: Semantic segmentation, instance segmentation, pixel-wise regression and classification. For more in depth discussion on the methods, as well as comparing the results and bechmarks using this package, please refer to our preprint on bioRxiv here.
InstaPrism is an R package that implements a fixed-point algorithm to accelerate BayesPrism, a Bayesian approach to computational cell-type deconvolution. It enhances speed and memory efficiency while maintaining accuracy compared to the original method and comes with precompiled reference sets for cancer types.
A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.
InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification
Integrating High-End Services for Translational Research in Structural Biology.
Browser that helps navigate among abundant homologies, syntenies and genes annotations.
Tool that will allow researchers to find genes and genetic variations that affect health and disease.
Calculates the residue Interaction Energy Matrix for any protein structure and offers comprehensive analysis of the interfaces in protein–DNA complexes.
Protein interaction database and analysis system.
IntAct App is a Cytoscape application for molecular interaction network visualisation and analysis.
The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.
This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.
Integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. IntAPT is a C++ package to identify alternatively spliced isoforms using multiple RNA-seq data. The user manual of IntAPT is available here. We have provided both precompiled binaries (require gcc 5.4.0 or newer) and source code.
An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix. IntAssoPlot: Visualize Genome-Wide Association Study with Gene Annotation and Linkage Disequiblism. GNU General Public License, GPLv3.
Data integration platform for molecular and clinical epidemiological analysis of tuberculosis.
The R package intCC (integrative Consensus Clustering) introduces intCC functions inspired by consensus clustering methods. The main function in this package is intCC. Users input a list of datasets, clustering methods, the number of clutsers for separate datasets and global, criterions and so on. Then consensus clustering will be applied to each dataset to derive consensus matrix.
This R package provides a benchmarking tools for quantitative comparison of cancer gene detection algorithms based on integrative analysis of DNA copy number and gene expression data.
Interactome of drug-metabolizing enzymes. Interactome of Drug-Metabolizing Enzyme. Search for the Drug-Metabolizing Enzyme (DME). Examples: CYP3A* ; UGT1A1 ; Apixaban ; Uterine cancer ; Shigella flexneri ... Search for DME Entries by DME Name:.
Produces numerical solution for integral equations of the type Z(t)=z(t) + \int_0^t f(y, Z(t-y)) dG(y).
INTEGRALL is a freely available, text-based search system developed to collect and organize information on integrons. There are more than 4800 integron sequences in the database.
Alexandra Moura (Website and database related issues)
Thomas Jové (Curation and In numbering attributions)
Comprehensive gene fusion visualization tool to help a user infer the potential consequence of a gene fusion event.
Unbiased detection and visualization of fusion-derived circular RNA.
Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information for research in regenerative medicine.
IntegratedPhasing is a tool integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes.
IntegrationMap can be used to determine and profile integration sites of viruses or viral vectors on a chromosomal and genomic level.
isma (integrative somatic mutation analysis) - R package for the integrative analysis of mutations detected by multiple pipelines.
R package for the integrative analysis of mutations detected by multiple pipelines.
integrative somatic mutation analysis (isma)
Laboratoire d’Excellence IBEID Integrative Biology of Emerging Infectious Diseases
A tool to detect Integron in DNA sequences.
integron_gene_fetch is developed to get integron genes from metagenomic sequencing reads. It is capable of getting the integron mobile genes more efficiently, as these genes are extremely difficult to be detected in whole-genome assembly. By assembling the dataset and traces all potential paths between any two contigs that consist of recombination sites, the integron_gene_fetch tool is able to get more integron genes given a pre-determined set of recombination site sequences.
A web-based intelligent system for fast chemical patent claim drafting. The first step of automating composition patent drafting is to draft the claims around a Markush structure with substituents. Currently, this process depends heavily on experienced attorneys or patent agents, and few tools are available. IntelliPatent was created to accelerate this process. Users can simply upload a series of analogs of interest, and IntelliPatent will automatically extract the general structural scaffold and generate the patent claim text. The program can also extend the patent claim by adding commonly seen R groups from historical lists of the top 30 selling drugs in the US for all R substituents. The program takes MDL SD file formats as inputs, and the invariable core structure and variable substructures will be identified as the initial scaffold and R groups in the output Markush structure
Graphical User Interface for automatic analyses of IntelliCage data in .xlsx file
Software package with a graphic user interface for automated sleep stage scoring in mice based on a light gradient boosting machine algorithm.
Pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads.
The recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.
interacCircos is an R package based on JavaScript libraries for the generation of interactive Circos plots.
This tool provides objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
InteractiveComplexHeatmap is a R package to make make heatmaps which are produced by the ComplexHeatmap package into interactive applications.
This package contains the methods needed to generate interactive Shiny-based display methods for BioConductor objects.
This package contains the basic methods needed to generate interactive Shiny-based display methods for BioConductor objects.
A web-based tool for the analysis of sets through Venn diagrams.
A wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites.
Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling techniques paramount. Interactome3D is a resource for the structural annotation and modeling of protein-protein interactions. Through the integration of interaction data from the main pathway repositories, we provide structural details at atomic resolution for over 12,000 protein-protein interactions in eight model organisms. Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner.
A tool to link genomic variant information with structural protein–protein interactomes.
A web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data. InteractomeSeq: a web server for the identification and profiling of domains and epitopes from Phage Display and Next Generation Sequencing data. InteractomeSeq is a webtool allowing either genomic or single gene domainome analysis of phage libraries generated and selected by following the interactome-sequencing approach. Home. Interactome Sequencing Platform. InteractomeSeq is a web server allowing domainome data analysis from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an interactome-sequencing approach. InteractomeSeq allows users to upload raw-sequencing data and to easily obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis procedure.
InterARTIC is an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses.
The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure.
InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data.
The Intercranial Meningioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of intercranial meningiomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis.
Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors.
Creates a new Gff output, which corresponds to the region of two successive Elements.
An R Package for High-Dimensional Interaction Analysis of the Repeated Measurement Data
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.
Database designed to explore 3D structures of homologous interfaces of protein complexes. Provides tools to retrieve and visualize these structures, including downloadable pre-computed multiple sequence alignments.
Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data | CancerDAP is a database molecularly characterizing subpathways involved in cellular response to 191 anticancer drugs | 1 Prospect the detailed information of each subpathway related to corresponding anticancer drug; 2 | CancerDAP has been formally launched and is freely available at:
Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. In recent years, increasing evidence has suggested that aberrant long non-coding RNA (lncRNA) copy number variation may contribute to the onset of human cancers. LncRNAs function in variety of biological pathways and processes. Investigating the functions of lncRNAs are important in uncovering the mechanisms of tumorigenesis and progression of cancers. Here we identified lncRNAs related subpathways (sub-regions of pathways) throughout 14 cancer types for characterizing functions of 4115 lncRNAs.
A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. Download the spreadsheet dataset template. Fill in as indicated (see the included notations for reference). interferENZY Copyright ©2019-2020 Maria Filipa Pinto, Pedro M. Martins. When using interferENZY, the user-provided dataset is only kept as long as interferENZY analysis by GNU Octave takes place; once the output page is presented the submitted dataset has been eliminated to ensure user data confidentiality.
Open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information.
Browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.
InterLabelGO+ is a hybrid protein function prediction tool that integrates deep learning and alignment-based methods, incorporating a novel loss function to address label dependency and imbalance. It achieved a strong performance in the CAFA5 challenge and is freely available on GitHub.
A program to interleave and deinterleave FASTQ files
improved ligand-based virtual screening using topologically independent structural alignments.
Prediction of interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.
A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information.
Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.
Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge.
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.
Automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and clusters of orthologous proteins. The tool can be downloaded or used through the web application.
Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes.
Assessment of Docked Peptide Conformations by a Deep Graph Network. Abstract Motivation Peptide-protein interactions between a smaller or disordered peptide stretch and a folded receptor make up a large part of all protein-protein interactions. A common approach for modelling such interactions is to exhaustively sample the conformational space by fast-fourier-transform docking, and then refine a top percentage of decoys. Commonly, methods capable of ranking the decoys for selection in short enough time for larger scale studies rely on first-principle energy terms such as electrostatics, Van der Waals forces, or on pre-calculated statistical pairwise potentials. Results We present InterPepRank for peptide-protein complex scoring and ranking
This software encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms.
Python API to access the HapMap dataset. It provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relavant human population datasets (e.g. Ensembl and UCSC Known Genes)
A pipeline to identify and model protein–protein interactions.
A freely available server for ADMET properties evaluation, model interpretation and chemical optimization.
Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
Scan sequences against the InterPro protein signature databases.
Tool that combines different protein signature recognition methods into one resource. It is a reimplementation of the traditional InterProScan 4.x series and adds features such as pathway annotations and signal peptide and transmembrane prediction using Phobius.
Intersection of two sets of positive integers (works much faster than built-in intersect)
InterSIM is a software application tool for simulating multiple interrelated data types with realistic intra- and inter-relationships based on the DNA methylation, mRNA gene expression, and protein expression from the TCGA ovarian cancer study.
INTER-Species Protein Interaction Analysis. Given a set of proteins of user's interest, it first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface.
Integration of Multi-Omics Data on Topological Associated Domains. InterTADs is an open-source tool written in R, for integrating multi-omics data (e.g. DNA methylation, expression, mutation) from the same physical source (e.g. patient) taking into account the chromatin configuration of the genome, i.e. the topologically associating domains (TADs).
Helps human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria.
Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.
A Shiny-based application to map the rolled intestinal tissue onto a line.
Integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
A manually curated database of inter-tissue communication molecules and their communication routes.
Identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements.
IntOGen is a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. The framework identifies cancer genes and pinpoints their putative mechanism of action across tumor types.
Tool for integrating secretomics and transcriptomics data in order to uncover paracrine cell crosstalk mechanisms.
IntOMICS: an efficient integrative framework based on Bayesian networks systematically analyses gene expression, copy number variation, DNA methylation, and biological prior knowledge to infer regulatory networks.
Structure-based predictor of protein–protein interaction sites.
Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila.
An Integrative Transcript Library to Enable Genome-Free Systematic Exploration of Bougainvillea. For better access experience, the webserver may take several minutes to initiate the working evironment at your first visit. Please be patient. The Bougainvillea is a genus of thorny ornamental vines, bushes, or trees.
INTeractive dna REPair prEDiction is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis.
The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.
Software package for mapping components of isolation in hybrids. It is an R-package that implements various methods for the analysis of gene introgression in hybrid zones.
Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.
A motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification
A comprehensive database of introns across human tissues.
Web tool for confidence scoring of biological interactions. Individual interactions are weighted according to the likelihood that they actually take place in the cell, and can be used to filter out false positives.
Drug side effects are one of the main health threats worldwide, and an important obstacle in drug development. Understanding how adverse reactions occur requires knowledge on drug mechanisms at the molecular level. Despite recent advances, the need for tools and methods that facilitate side effect anticipation still remains. IntSide is a web server to elucidate the molecular processes involved in drug side effects through the integration of chemistry and biology. IntSide currently catalogues 1,175 side effects caused by 996 drugs, associated with drug features divided into eight categories, belonging to either biology or chemistry. On the biological side, IntSide reports drug targets and off-targets, pathways, molecular functions and biological processes. From a chemical viewpoint, it includes molecular fingerprints, scaffolds and chemical entities.
This software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.
Tool to predict a splicing consequence of an SNV at intron positions -50 to -3 close the 3’ end of an intron of the human genome.
This web-server was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster.
Given nucleosome genomic coordinates, ligation junctions (in pairs format) produced by the Pairtools program, the inucs command line tool identifies interactions falling into different nucleosomes and counts them.
Analysing global economic costs of invasive alien species with the invacost R package. The invacost R Package: Global Costs of Biological Invasions. Leroy B, Kramer A, Courchamp C, Vaissière AC & Diagne C 03/12/2020. This approach is generalisable to any subset of the InvaCost database, regardless of data quantity. However, it does not account for the temporal dynamics of costs, and may thus underestimate the costs of invasions, especially for recent years for which we likely have incomplete data.
Finding genomic inversions from high-throughput sequence data based on feature mining. We released three programs, InvBFM, fixRealData, and fixSimuData. Both fixRealData and fixSimuData are written in Shell for data preprocessing. InvBFM is written in Python which proposed in our paper.All three programs are packaged as executables, downloading from their source code and changed their permissions to executable for using as a tool.
invClust is a method to detect inversion-related haplotypes in SNP data
Package to find genetic inversions in genotype (SNP array) data.
An expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms.
Bayesian inversion genotyping with Strand-seq data.
These scripts provide functions to analyse splice sites based on a genome sequence (FASTA) and a corresponding annotation (GFF3) provided by the NCBI. Next, RNA-Seq reads can be mapped via STAR and the resulting BAM files can be converted into customized coverage files (COV) which are required for the validation of splice sites. The usage of individual splice sites can be quantified based on the number of mapped and propperly splitted RNA-Seq reads. These scripts generate report files and figures for the documentation of the analysis process.
investigation of (non canonical) splice sites
Database that stores inversion predictions from healthy individuals and enables to search inversions by gene symbol, genomic position and inversion name.
An interactive tool for statistical analysis of omics data and clinical data.
Real-time Genomic Analysis iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive
IOBR is an R package and accompanying documentation designed to facilitate multi-omics immuno-oncology biological research, specifically focusing on deciphering tumor microenvironment and identifying clinical translation signatures. The package offers a user-friendly pipeline with comprehensive guides for data preprocessing, TME estimation, and interaction analysis.
IOBR is an R package and associated documentation designed for multi-omics immuno-oncology biological research, enabling users to decipher tumor microenvironment and signatures for clinical translation. It offers a comprehensive analysis pipeline and visualization capabilities.
This project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.
An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. iODA, short for integrative Omics Data Analysis, is an evidence-based bioinformatics model and software tool for omics data analysis. iODA is a graphical user interface (GUI) local tool with the aim of integrating and analyzing data sets including mRNA, microRNA (miRNA), and protein–DNA interaction (chromatin immunoprecipitation followed by high-throughput sequencing, ChIP-Seq) for pathway consistency (Figure 1).
A python library for reading, writing, and converting computational chemistry file formats and generating input files. IOData is a HORTON 3 module for input/output of quantum chemistry file formats. Documentation is here: https://iodata.readthedocs.io/en/latest/index.html.
USDA, NIH and FDA Iodine Database of U.S. Foods for Estimating Iodine Intakes.
An interactive online feature selection tool for survival analysis.
Dedicated for MS data measured in high resolution mode and their interpretation. Primarily oriented on devices developed by the Thermo-Fisher Scientific company.
University of South Bohemia, Czech Republic
Cloud based workflow analysis framework for managing, analyzing and visualizing NGS data.
Mass Spectrometry Imaging Data Analysis Platform for Continuous Ionization Techniques.
bioinformatics plugins toward genomics-assisted breeding. Genotyping and genomic selection plugins for Ion Torrent NGS platform. version: 1.01 (March 12 2020 update). IonBreeders: automated bioinformatics plugins toward genomics-assisted breeding. The National Agriculture and Food Research Organization (hereinafter referred to as NARO) does not guarantee that defects, errors or malfunction will not occur with respect to IonBreeders.
A reference-based compression tool for ion torrent sequence files. IonCram is the first compression tool that efficiently compresses the Ion Torrent BAM files. IonCram extends the popular CRAM program by improving the compression of the flow signals. IonCram could improve the compression of CRAM by 13% achieving an overall space saving of about 45%.
Galaxy tool for processing and analysis of ionomics data , based on the modification of R package IonFlow.
Publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. Both its components and their configuration are based on a research process aimed to discover the optimal combination of tools for obtaining good results from single-end reads generated by the Ion Torrent PGM sequencer.
IONISE is a Bayesian inference method for estimating epidemiological parameters, addressing biases arising from unrealistic assumptions in conventional models. The tool, implemented as a user-friendly package, accurately estimates the reproduction number and reveals changes in the infectious period distribution, as demonstrated in the COVID-19 pandemic.
Tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.
Integrative approach to model and predict multiple data sources based on orthogonal matrix factorization.
University of Ljubljana Faculty of Computer and Information Science
Python package for prediction of peptide collisional cross-section (CCS) values.
A Framework for the Agile Development of Bioethics Ontologies in Pandemics, Applied to COVID-19.
This package provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry.
A database for the prediction of the structures and functions of insect olfactory receptors.
iORI-ENST is a tool for identifying origin of replication sites based on elastic net and stacking learning.
A computational platform to identify origins of replication sites in eukaryotes. Home About us Web-Server Contact us Download Citation. DNA replication is a key step in maintaining the stable transmission of genetic information from parent to child and it is the basis of biological inheritance.
An Open-source Framework for IoT Traffic Generation. IoT-Flock is an open-source tool for IoT traffic generation which supports the two widely used IoT application layer protocols, i.e., MQTT and CoAP. IoT-Flock allows a user to create an IoT use case, add customized IoT devices into it and generate normal and malicious IoT traffic over a real-time network.
Platform for genomic selection, performing streamlined GS analysis.
An integrated platform for mass spectrometry-based metabolomics data mining. BACKGROUND:Metabolomics data analyses rely on the use of bioinformatics tools. Many integrated multi-functional tools have been developed for untargeted metabolomics data processing and have been widely used. More alternative platforms are expected for both basic and advanced users. RESULTS:Integrated mass spectrometry-based untargeted metabolomics data mining (IP4M) software was designed and developed
Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies
The IPA platform provides probabilistic annotation of intrinsically disordered regions (IDRs). It standardizes computational feature prediction using a reverse Bayes approach to transform logistic regression outputs into true probabilities, effectively removing the influence of training data priors. Preprint: https://www.biorxiv.org/content/10.1101/2024.12.18.629275.full
Novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.
Powerful package which in conjunction with FIRE provides a complete meta-analysis of whole-genome datasets.
Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles. IPANEMAP is a software for predicting stable RNA secondary structures compatible from multiple chemical probing (SHAPE, DMS, Enzymatic...) reactivities profiles. From one or several input sequences, along with several reactivity profiles, it computes and outputs one or several secondary structures, corresponding to the conformers best supported by experimental data and thermodynamics.
Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data.
An atlas of intronic polyadenylation quantitative trait loci across human tissues.
An improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach.
Identification of Permissive Amber Sites for Suppression (iPASS) is a tool for the identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.
Intelligent prediction and association tool for genomic research.
iPath is a web-based tool for the visualization and analysis of cellular pathways. Based on functional annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, iPATH allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets.
iPath is a tool developed by IMIM which provides mechanistic hypotheses for drug adverse events. iPath aims at identifying pathways in functional networks that connect drug targets, off-targets, ADME proteins and proteins associated to the toxicity phenotype elicited by a drug. It leverages information from diverse omics datasets, namely protein interaction networks, toxicogenomics data, gene and protein expression data, genotype-phenotype associations and chemical biology information. iPath uses as input tissue/organ-specific protein interaction networks and a list of genes of interest (seed genes), and after mapping the seeds to the network it applies network optimisation algorithms to identify the subnetwork. It can be used to identify molecular pathways related to drug toxicity.
iPathwayGuide is a tool for disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases.
integrated Pathway Resources, Analysis and Visualization System: provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate,filter, browse, search, analyze, visualize and compare the integrated pathway resources.
This tool uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.
Using current public available microarray data, this tool investigates the feasibility and effectiveness of deriving informative priors from historical data and using them in the problem of detecting differentially expressed genes.
Web service and standalone program for the estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including computationally optimized pKa sets. According to the benchmarks, the newly developed pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation of 0.87 and 0.25 pH units, respectively.
IPCARF is a tools for improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier.
An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network. Python package to interactively simulate genealogies and sequence data under the multispecies coalescent. Full documentation here: https://ipcoal.readthedocs.io. Welcome to ipcoal’s documentation! — ipcoal documentation. Free document hosting provided by Read the Docs.
An R package for inverse probability of censoring weighting with an application to switches in clinical trials | In randomized clinical trials (RCT), the analysis is based on the intent-to-treat principle to avoid any selection bias in the constitution of groups. However, estimates of overall survival can be biased when significant crossover occurs because the separation of randomized groups is lost. To handle these switches, the inverse probability of censoring weighting (IPCW) method has been proposed; however, it is still poorly used in RCT, notably because of its complex implementation. In particular, for time-to-event outcomes, it can be difficult to format data, especially when time-dependent covariates have to be managed, with different measurement times between patients
Set of specialist databases related to the study of polymorphic genes in the immune system. The project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted for online publication. It consists of four databases: KIR, MHC, human platelet antigens and ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines.
Database that provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.
The IPD-MHC Database is a comprehensive and curated repository for Major Histocompatibility Complex (MHC) sequences from non-human species, providing data and tools for researchers studying MHC function and evolution.
Infectious Pathogen Detector (IPD) is an automated pathogen analysis pipeline for seamless analysis of single and paired-end data from heterogenous NGS platforms.
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Infectious Pathogen Detector (IPD). IPD is an automated pathogen analysis pipeline for seamless analysis of single and paired-end data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation. IPD is an in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS- CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation.
iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
A PIWI-bound piRNAs database to mining NGS sncRNA data and beyond.
Reconstruct Individual Patient Data from Published Kaplan-Meier Survival Curves. Map Digitized Survival Curves Back to Individual Patient Data. Trial Design – Innovative Methodologies. An implementation to reconstruct individual patient data from Kaplan-Meier (K-M) survival curves, visualize and assess the accuracy of the reconstruction, then perform secondary analysis on the reconstructed data.
An R Shiny tool for analyzing and visualizing individual patient data meta-analyses of diagnostic test accuracy.
Identification of differentially methylated regions with interval p-values. Quality control and analysis tools for Illumina DNA methylation BeadChip. Tool kits for quanlity control, analysis and visulization of Illumina DNA methylation arrays.
IPECAD is an open-source model framework for the health-economic evaluation of early Alzheimer's disease treatment, designed to support transparency and cross-validation. The framework is available as R code, a spreadsheet, and a web-based version.
Integrated pipeline for rational quality control and association analysis of genome-wide genetic studies.
An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences.
iPhylo is a platform for building and annotating biological and chemical taxonomic trees. It includes a CLI for local use and a web-based visualization module, supporting diverse data formats and customizable hierarchical databases.
An Open Non-Contact Imaging-Based Physiological Measurement Toolbox. In the past few years a lot of attention has been given to methods for remotely measuring physiological signals using low-cost cameras. Imaging PPG (iPPG) focuses on the measurement of volumetric changes in blood flow at distance from the body using imaging devices to capture changes in transmitted or reflected light. Imaging ballistocardiography (iBCG) typically leverages optical flow estimation to track the vertical motion of the head or body from a video sequence. Both iPPG and iBCG methods can be used to recover human vital signals.
Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. It effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences.
The iPick program is available as a module for the POKY and NMRFAM-SPARKY. It is highly recommended that you use the module instead of the command line tool. The main reasons are the ease of work and the extended capabilities provided in the module.
Identification of piRNA-disease associations based on Graph Convolutional Network.
Identifying piwi-interacting RNA-disease associations based on Learning to Rank.
Targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser
Importance-Penalized Joint Graphical Lasso (IPJGL).
A combination of several software tools for sequence analysis developed at the IPK Gatersleben. The BLAST server utilizes a homology search against the cereal genome resources (barley, rye and bread wheat). Kmasker plants is able to mask sequences originating from ten agronomically important plants based on mathematical defined repeats, furthermore, selection of sequences applicable for guideRNA construction for genome editing (CRISPR) or for fluorescence in situ hybridization is also possible. MISA web searches a sequence for microsatellites and is able generate molecular markers or primer. Using BRIDGE the complete barley collection of the IPK genebank can be visually explored in an interactive manner through diversity, certain phenotyped traits, and based on sequence polymorphisms. The barley genome explorer (BARLEX) is a system to visually inspect the reference genome sequence of barley, enriched with expression data, repeat and gene annotation and molecular marker data.
A homology search against the current barley sequences resources is provided. The complete sequences data set comprises the whole genome shotgun assemblies of the cultivars Morex, Barke and Bowman as well as the high and low confidence gene sets. The newest POPSEQ anchoring data is integrated. Furthermore, the barley exome capture targets are provided. Additionally, resources like bacterial artificial chromosome assemblies, BAC end sequences and full length cDNAs are included.
IPknot provides services for predicting RNA secondary structures including a wide class of pseudoknots. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.
A knowledge-based approach for identifying protein-nucleic acid interaction hot spots. A webserver for identifying protein-nucleic acid interfaces hotspot residues. iPNHOT was developed by using support vector machine based on three different kinds of features including atom number of the residue, depth and protrusion index, solvent accessible surface area, electrostatic potential and secondary structure. It needs one input file: pdbfile which contains the coordinates of a protein-nucleic acid complex. More details can be found in the tutorial.
The outcome of XCMS data processing strongly depends on the parameter settings. Isotopologue Parameter Optimization is a parameter optimization tool that is applicable for samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. It uses natural, stable 13C isotopes to calculate peak picking score. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.
Efficient enumerative algorithm for incomplete Perfect Phylogeny Haplotyping.
This web-server used to predict the Protein-Protein Binding Sites(PPBS).
This web-server is used to predict the Protein-Protein Binding Sites(PPBS).
The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.
An integrated peptide and protein function prediction framework based on fused features and ensemble models.
IPPI is a web server of inferring protein-protein interactions
IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.
Ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC.
PREDICT is a web tool that utilizes a k-mer pipeline to predict gene expression and identify transcription factor binding motifs in plants under stress conditions. It improves gene expression prediction models and facilitates understanding of the cis-regulatory code in plant adaptation.
iPRESTO (integrated Prediction and Rigorous Exploration of biosynthetic Sub-clusters Tool) is a command line tool for the detection of gene sub-clusters in a set of Biosynthetic Gene Clusters (BGCs) in GenBank format.
A novel model based on generative adversarial learning for identifying promoters and their strength
A framework for identifying promoters in multiple species.
Sequence-based predictor for identifying σ54 promoters with pseudo k-tuple nucleotide composition.
A machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences.
CNN base prediction tool for σ54 Promoters.
A two-layer model to identify plant promoters and their types using convolutional neural network.
A two-layer model to identify phage promoters and their types using a convolutional neural network.
Two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.
A Novel Fusion Decision Predictor for the Identification of 5-Methylcytosine Sites in Genome-Wide DNA Promoters. This prediction tool was built on the basis of known promoter methylation of human small cell lung cancer cell coefficients. The primary goal was to predict all promoter 5mC sites in human small cell lung cancer cell lines. This prediction website is based on known human small cell lung cancer cell coefficients based on sites with significant promoter methylation levels. The main goal is to achieve the prediction of all 5mC promoters in human small cell lung cancer cell lines.Experimental data download.
Identifying promoters using bidirectional long short-term memory and sequence-embedded features.
Web-based interactive platform for integrated proteome and phosphoproteome analysis.
A Tool to Accurately Predict Protein Glycation Site Using Structural-Based Features.
iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics. iProX is composed of a data submission system and a proteome database.
Tool for prognostic prediction of AML patients based on immunity and pyroptosis gene-pair signature (IPRP)
A tool for the visualization of Interproscan results. Interproscan results are parsed from the Interproscan XML or EBIXML file into an SQLite or MySQL database. The results for each signature database scan are read and displayed as pie-charts or bar charts as summary statistics.
An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection.
The integrative pipeline for splicing analyses: 1) Quantifies splice junctions and splice boundaries; 2) Calculates splicing indices, exon- and intron-centric; 3) Analyzes micro-exons and local splice-graph structure.
Identifying RNA pseudouridine sites using random forest and NCP-encoded features. Pseudouridine modification is most commonly found among various kinds of RNA modification occurred in both prokaryotes and eukaryotes.
Database of Italian present-day stress indicators, IPSI 1.4. The database IPSI is licensed under a. Creative Commons Attribution 4.0. IPSI database, "Italian Present-day Stress Indicators", is a georeferenced repository of information on the crustal present-day stress field maintained at INGV. It consists of horizontal stress orientations analysed and compiled in a standardized format and quality-ranked for reliability and comparability on a global scale. Nowadays the database contains 928 data records updated to January 2020. The next update will be until December 2020 and is scheduled to be released within the first months of 2021.
IPTDFold is a de novo protein structure prediction by iterative partition sampling, topology adjustment, and residue-level distance deviation optimization.
IPTK is a Python library specialized in the analysis of HLA-peptidomes identified through an Immunopeptidomic(IP) pipeline. The library provides a high level API for analyzing and visualizing the identified peptides, integrating transcritomics and protein structure information for a rich analysis of the identified immunopeptidomes. It also provides a toolbox for integrating and comparing different experiments and/or different runs.
Identification of plant vacuole proteins by exploiting deep representation learning features.
pyBioPortal is a Python package designed to simplify data access from cBioPortal, leveraging its REST API and providing data in Pandas DataFrame format for further analysis.
Python toolbox for assessing microbial growth and cell viability in high-throughput colony screens. A python toolbox for phenotype analysis of arrayed microbial colonies written by Stephan Kamrad (stephan.kamrad at crick.ac.uk). Python toolbox for phenotype analysis of arrayed microbial colonies.
Interactive assembly and analysis of RADseq datasets. ipyrad: interactive assembly and analysis of RAD-seq data sets. Welcome to ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. Welcome to ipyrad — ipyrad documentation.
Recovering Historical Signal from Heterotachously-evolved Sequence Alignments | Molecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce the General Heterogeneous evolution On a Single Topology (GHOST) model of sequence evolution, implemented under a maximum-likelihood framework in the phylogenetic program IQ-TREE (http: www.iqtree.org).
An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. This is an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.
Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.
The purpose of the tool is to provide a complete framework for automatic detection of image quality for Breast DCE MR images. The assessment is performed on the first post-contrast dynamic phase in order to assess the most clinically relevant sequence among a number of identical acquisitions. Two categories are available for image classification, i.e. high and low quality, depending on the level of noise, degree of blurring and presence of artifacts.
iQcell is a platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.
Integrated web server for protein scoring using multiscale deep learning models.
Integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework
R code for mapping imprinted quantitative trait loci (iQTL) in F2 experimental cross.
R code for iQTL mapping with Variance Component model in experimental cross.
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time
Automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification.
A multi-method network gene set analysis leveraging the Network Data Exchange.
An Open Source Data Integration Tool for Big Data Transcriptomics Designed for the Malaria Vector Anopheles gambiae. IR-TEx allows selection of datasets dependent on the user’s criteria. Download the .zip file containing the following: IR-TEx. Download the latest version of R software, available at https://cran.r-project.org/mirrors.html.
This is a hybrid fusion method for infrared and visual image by the combination of DSWT, DCT and SF
A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns.
irAExplorer is a database that explores the landscape of immune checkpoint inhibitor-induced adverse events. It aggregates clinical trial data from ClinicalTrials.gov to provide insights into the incidence of serious adverse events across cancer types, treatment agents, and regimens.
RamanSPy is an open-source Python package designed for integrative Raman spectroscopy data analysis. It offers tools for data processing, analysis, and visualization, supporting various spectroscopic techniques and data formats.
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
A computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences.
Improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations.
A tool for intron retention detection from RNA-seq data. iREAD (intron REtention Analysis and Detector)is a tool to detect intron retention(IR) events from RNA-seq datasets. Independent introns, referring to those introns that do not overlap with any exons of any splice isoforms, are used for detecting IRs. iREAD takes two input files: (1) a BAM file representing transcritome, and a bed-like text file containing independent intron coordinates, and output intron retention events based on a set of criteria that filter for reliable IR events. These criteria involves the number of reads/fragments in intronic regions, FPKM, junction reads, read distribution patterns within an intron.
iReceptor is a data discovery platform that facilitates the curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires (Adaptive Immune Receptor Repertoire or AIRR-seq data) and related subject and sample metadata from multiple studies across many labs and institutions.
Structure-based design of small imine reductase panels for target substrates.
Provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB and MPPI.
This tool allows the user to load any version of the consolidated protein interaction database "iRefIndex" and perform tasks such as: selecting databases, pmids, experimental methods, searching for specific proteins, separate binary interactions from complexes and polymers, generate complexes according to an algorithm that looks after possible binary-represented complexes, make general database statistics and create network graphs, among others.
Plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network.
Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb. Discovered a protein or a gene likely to be involved in a disease, and you want to find out what is known about its interactions with other proteins. Identified a group of co-expressed genes, and would like to check if the proteins they code for interact physically.
An integrative Regulatory Network analysis tool for Arabidopsis thaliana.
IReNA (Integrated Regulatory Network Analysis) is an R package to perform regulatory network analysis. IReNA contains two methods to reconstruct gene regulatory networks. The first is using single-cell RNA sequencing (scRNA-seq) data alone. The second is integrating scRNA-seq data and chromatin accessibility profiles from Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq). IReNA performs modular regulatory network to reveal key transcription factors and significant regulatory relationships among modules, providing biological insights on regulatory mechanisms.
A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. IRESbase-A Comprehensive Database of Experimentally Verified Internal Ribosome Entry Site (IRES). A Comprehensive Database of Experimentally Verified Internal Ribosome Entry Sites (IRESs).
Uncertainty-aware quantification of transposable elements expression in scRNA-seq
Our database presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions.
Support Vector Machine (SVM) based computational tool to predict the presence of Internal Ribosome Entry Site (IRES) in viral and cellular sequences.
A national web-based platform for operationalizing single IRB review.
GUI for segmentation of in-resin fluorescence (IRF) for cells in ultrathin slices.
A comprehensive suite to discover and explore intron retention.
irg is an R Package for Granger-Causal Analysis of irregularly sampled signals.
Iranian traditional medicine General Ontology (IrGO) and knowledge base. Iranian traditional medicine (also called Persian Medicine), is an elaborate holistic system of healing grounded in a philosophical basis.
irGSEA is an R package designed to assess outcomes of gene set scoring methods when applied to single-cell RNA sequencing data. It integrates six scoring methods and provides visualization tools for result analysis.
A Robust in silico Method for Optimal Reference Gene Validation.
iRibo is a software program for integrating ribosome profiling samples to infer annotated or unannotated translated open reading frames. It can be used to generate a species' translatome from a set of ribosome profiling samples, as demonstrated using *S. cerevisiae*.
An integrated XGBoost model for detecting multitype post-translational modification sites in rice.
Open source software for processing images from infrared thermal cameras.
Image processing software that automatically quantifies several features of microbial colonies in high throughput.
An integrative single-cell RNA-Seq interpretation system for functional gene module analysis. ---Integrative scRNA-Seq Interpretation System for Functional Gene Module analysis. Single-cell RNA-Seq data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases.
An accurate and efficient barcode calling tool for in situ sequencing. Information Refining for In situ Sequencing. See 'README.1.pyIRIS.md' for detail.
Integrated cell-type-specific regulon inference server from single-cell RNA-Seq. The underlying regulatory mechanisms that induce the identity of cell types or physiological states are normally uncovered in the single-cell RNA-Sequencing (scRNA-Seq) analyses. Here we propose IRIS3 (Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq) as the first-of-its-kind web server for CTS-R inference in human and mouse. integrated cell type specific Regulon inference from single-cell rna seq.
IrisSpatialFeatures reads the output of the PerkinElmer inForm software and calculates a variety of spatial statistics. In addition to simple counts, it can derive average nearest neighbors for each cell-type and interaction summary profiles for each celltype. These statistics are derived across images, both overall and regions of interest as defined by user defined masks.
IRMa ( Interprétation des Résultats Mascot) toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches.
Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data
A novel computational method for effectively detecting N4-acetylcytidine sites in human mRNA.
Computational identification of N6-methyladenosine sites in multiple tissues of mammals. Home About us Web-Server Contact us Download Citation. N6-methyladenosine (m6A) is the methylation of the adenosine at the nitrogen-6 position, which is the most abundant RNA methylation modification and involves a series of important biological processes. Type or copy paste the query RNA sequences into the input box at the center,or upload a FASTA file. Choose Species: Human Mouse Rat and Tissues: Brain Liver Kidney.
This web-server was developed to identify the N6-methyladenosine (m6A). It was observed by the rigorous cross-validation test on the benchmark dataset that the accuracy achieved by the predictor in identifying m6A was 65.59%.
The First Predictor to Identify RNA 5-Hydroxymethylcytosine Modifications Using Machine Learning. A generic webserver for predicting RNA 5hmC sites.
Accurate prediction of RNA 5-hydroxymethylcytosine modification by utilizing novel position-specific gapped k-mer descriptors. iRNA5hmC-PS: Accurate prediction of RNA 5-Hydroxymethylcytosine Modification by Utilizing Position-Specific k-mer and Position-Specific Gapped k-mer. Authors: Sajid Ahmed†, Zahid Hossain†, Mahtab Uddin, Ghazaleh Taherzadeh, Alok Sharma Swakkhar Shatabda*, Abdollah Dehzangi*.
Identify DNA replication origins by three-window-based PseKNC.
iROAR (Immune Repertoire Over Amplification) is a tool for multiplex PCR-specific bias evaluation and correction to adjust clonal count of VDJtool output table.
Open-source project dedicated to providing a MATLAB framework for vibrational spectroscopy. The goal of the project is to provide a comprehensive and user-friendly environment for analysis, whilst facilitating development and validation of algorithms for computational biology using vibrational spectroscopy.
Augmented tool to detect inverted repeats in plastid genomes.
High throughput immune receptor profiling.
Visualize the junction sites of chloroplast genomes.
Identify recombination spots with pseudo dinucleotide composition.
Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components.
A Web Server for Artificial Intelligence Based Prediction of Major Basmati Paddy Seed Varieties. “Basmati” derives its roots in two Sanskrit words “Vas”(vasay) meaning “aroma” and “Mati” (mayup) meaning ingrained from the origin, common usage could have resulted in change of vas to bas resulting in Basmati. According to a survey conducted by MoEF&CC, published in report ”Report on Identity Preservation of Basmati Rice at Various Stages in the Rice Supply Chain”, in Haryana, 80-85% farmers were able to identify the seed variety whereas, a large number of farmers (almost 20%) were still depending on the tag on seed bag they purchased whereas in Aligarh market area of Uttar Pradesh 100% farmers were depending on the tag on seed bag. Primary Basmati Quality Characteristics.
An R Package for Estimating IRT Models With Guessing or Slipping Parameters.
Tool designed to reduce the complexity of very large sets of data by decomposing it into so-called “modules”. In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments.
A scalable Java library for creating ISA-Tab metadata. isa4j is a comprehensive and scalable Java Library for the programmatic generation of experimental metadata descriptions using the ISATab container format. We're assuming you're familiar with the ISA-Tab framework in the remainder of the manual; if you're not, please read up about it first. This is an XML namespace defined in the XML Linking Language (XLink) specification.
An open platform for interoperable life science experimental metadata. Built around the ‘Investigation’ (the project context), Study’ (a unit of research) and ‘Assay’ (analytical measurement) general-purpose Tabular format, the ISA tools helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable. The ISA API aims to provide you, the developer, with a set of tools to help you easily and quickly build your own ISA objects, validate, and convert between serializations of ISA-formatted datasets and other formats/schemas (e.g. SRA schemas). The ISA API is published on PyPI as the isatools package.
Framework and tools that help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies.
ISAAC comprises of genome aligner and variant caller, by Illumina.
Accelerated 2D Classification With ISAC Using GPUs.
Tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. It is included in the GEPAS package.
A program for identifying a favored mutation in positive selective sweep. It enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals.
Intelligent System for Analysis, Model Building And Rational Design.
iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.
Fast aligner for color and base space short read data.
An R package for multi-sample spatial clustering analysis of spatial transcriptomics data.
A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.
iscDNase-seq is scripts for a multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.
A framework for clustering (CORE) and estimation of relationship between pairs of clusters (scGPS) from single cell data
Novel ChIP-seq simulating program with superior versatility. In Silico ChIP-seq is a fast realistic ChIP-seq simulator. The modelling of the chromatin immunoprecipitaion followed by next generation sequencing process is based primarily on Illumina protocol. In addition, extra flexibility is implemented for the isChIP’s options to be straightforwardly re-formulated in other formats, such as Ion Torrent, Roche454, etc.
Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare. ISCompare: a new tool for the identification of differentially located insertion sequences on bacteria. Bacterial genomes are composed by a core and an accessory genome.
Developed to predict ISD of retroviruses, including HERV, HTLV-1, HIV-1, STLV and SIV.
Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.
This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with and without controls and replicates.
Automated identification of insertion sequence elements in prokaryotic genomes.
It is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repositaory including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information and classified into a group or family to provide some insight into its phylogeny.
De Novo Recognition of In-Source Fragments for Liquid Chromatography-Mass Spectrometry Data.
An R package for integrative dimension reduction analysis.
Identification of Sub-Golgi protein localization by use of deep representation learning features. if computing on a GPU, it would be fasster.
Tools for predicting interferon stimulated human genes
An R package for visualizing and analyzing a spatial model of intratumor heterogeneity.
Open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks.
This tool aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic regions of potential horizontal origin.
Prediction and analysis of genomic islands in bacterial and archael genomes. It integrates four different genomic island prediction methods: IslandPick, IslandPath-DIMOB, SIGI-HMM, and Islander.
slendr is an R package that provides a framework for simulating spatially-explicit genomic data, leveraging real cartographic information for spatiotemporal population dynamics. It allows users to programmatically and visually encode spatial population ranges and their temporal dynamics, and schedule splits and gene-flow events.
Individual-specific reference panel recovery improves cell-type-specific inference. ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.
Genetic Grouping of SARS-CoV-2 Coronavirus Sequences using Informative Subtype Markers for Pandemic Spread Visualization. Informative Subtype Markers (ISM) is an efficient framework for genetic subtyping of a pandemic virus and implement it for SARS-CoV-2, the novel coronavirus that causes COVID-19. Web site created using create-react-app.
Index-based Subgraph Matching Algorithm. Fast subgraph enumeration in large networks using optimized search trees.
A Cytoscape app for motif enumeration with ISMAGS. Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries. This page contains an implementation of the Index-Based Subgraph Matching Algorithm with General Symmetries. This app serves as the GUI for the [ISMAGS][] algorithm, which can **enumerate all instances of a motif in a graph**, making optimal use of the motif’s symmetries to make the search more efficient. Cytoscape App for the ISMAGS motif detection algorithm.
Models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Integrated System for Motif Activity Response Analysis client . Locally pre-process expression or ChIP-seq data before upload it to the ISMARA web server.
Browser for image-based single-cell multi-omics data.
The web-server iSMP-Grey was establish for identifying uncharacterized proteins as secretory proteins of malaria parasite or not according to their evolutionary information in form of position specific scoring matrix (PSSM).
ISN-tractor is a Python library designed for the fast and scalable computation of individual-specific networks (ISNs) from omics data. It enables the analysis of individual-specific relationships between biological entities and supports various data types, including transcriptomics, proteomics, and genotype arrays.
The injured sciatic nerve atlas (iSNAT), insights into the cellular and molecular basis of neural tissue degeneration and regeneration.
New predictor which was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains.
New predictor which was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP) into the general form of pseudo amino acid composition (PseAAC).
identifying snoRNA-disease associations based on local similarity constraint and global topological constraint.
Identifying snoRNA-disease associations based on multiple biological data by ranking framework.
Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker.
Software for steady-state 13C Metabolic Flux Analysis.
Calculates the isotopic distribution of a chemical formula or a amino acid chain.
IsoBank is a community-driven open-access repository for stable isotope data, designed to improve accessibility and promote collaborative engagement in interdisciplinary research. It provides a web-accessible database supporting a wide range of stable isotope research areas.
isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.
IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides.
IsoBase is a database identifying functionally related proteins across five major eukaryotic model organisms: yeast, fly, worm, mouse, and human. Clusters were computed using the IsoRankN algorithm, which uses spectral methods, to combine sequence and PPI data to produce clusters of functionally related proteins. IsoBase may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword.
Use transcripts to assess a de novo assembly.
An R package to streamline and standardize stable isotope calculations in ecological research.
Interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control.
In silico optimization of copy number variant detection from targeted or exome sequencing data.
This repository contains an open source Python library that focuses on user defined (such as meteorological, spatial, etc.) and isotopic composition variables analysis and generating the regression – statistical estimation models. data_preparation.preprocess class. pip can be used for the installation:. Hassanzadeh, A., Valdivielso, S., Vázquez-Suñé, E., Criollo, R., Corbella, M., 2023.
IsoDA is a tool for Isoform-Disease Association Prediction by Multiomics Data Fusion. A gene can be spliced into different isoforms by alternative splicing, which contributes to the functional diversity of protein species. Computational prediction of gene-disease associations (GDAs) has been studied for decades. However, the process of identifying the isoform-disease associations (IDAs) at a large scale is rarely explored, which can decipher the pathology at a more granular level. The main bottleneck is the lack of IDAs in current databases and the multilevel omics data fusion. To bridge this gap, we propose a computational approach called Isoform-Disease Association prediction by multiomics data fusion (IsoDA) to predict IDAs
Expectation maximization algorithm for estimating alternative splicing isoform frequencies
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data.
Web-based platform for isoform-level expression analysis in human cancer.
IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.
A peptide-centric algorithm for protein inference.
Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.
IsofunGO, a tool, to differentiate massive functions of isoforms by GO embedding.
This interface of the IsoGene package identifies genes with a monotonic trend in the expression levels with respect to the increasing doses through several test statistics.
De novo prediction of isoform specific mucin-type O-glycosylation. Isoform Specific mucin-type o-glycosylation prediction. Isoform Specific O-Glycosylation Prediction (ISOGlyP).
Functional annotation of protein-coding splice variants. The advent of RNA-seq technologies has switched the paradigm of genetic analysis from a genome to a transcriptome-based perspective. Alternative splicing generates functional diversity in genes, but the precise functions of many individual isoforms are yet to be elucidated. Gene Ontology was developed to annotate gene products according to their biological processes, molecular functions and cellular components. Despite a single gene may have several gene products, most annotations are not isoform-specific and do not distinguish the functions of the different proteins originated from a single gene. Several approaches have tried to automatically annotate ontologies at the isoform level, but this has shown to be a daunting task
Algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
isolateR is an R package designed for generating microbial libraries from Sanger sequencing data. It automates processing, performs taxonomic classification, and facilitates strain library creation with customizable dereplication thresholds.
This package provides a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies.
An integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps. To replicate the algorithm use the following steps:.
A system for analyzing small-RNA-seq data in an integrative and user-friendly manner. The IsomiR Window project is a user-friendly tool that enables biologists to perform the analysis of small-RNA-seq data, uncovering the complexity of miRNA biogenesis.
The first tool implemented in order to perform reads alignment on miRNAs databases by considering the miRNA:mRNA interaction pairing aspects.
A miRNA expression database with isoform resolution. isomiRdb stores miRNA and isomiR expression values for 42499 miRNA-seq samples collected from miRMaster, The Cancer Genome Atlas and Sequence Read Archive and uniformly processed from raw reads using sRNAbench .
IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. IsoMiRmap is an open source python application for the fast, deterministic, and exhaustive mining of isomiRs. The tool produces output in HTML, miRGFF3, and in tab-delimited formats. isoMiRmap is a miRNA and isomiRs mining tool that let's you quickly, exhaustively and deterministically map your dataset.
Characterization of miRNAs and isomiRs, clustering and differential expression.
A comprehensive portal of pan-cancer 5'-isomiR targeting.
Isotropic Reconstruction of Electron Tomograms with Deep Learning.
Reference-free transcriptome reconstruction from Oxford Nanopore data.
Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation. IsoResolve is a computational approach for isoform function prediction by leveraging the information of gene function prediction models with domain adaptation (DA). IsoResolve treats gene- level and isoform-level features as source and target domain, respectively. It employs DA to project the two domains to a latent variable (LV) space in such a way that the LVs projected from the gene and isoform domain features are of approximately the same distribution, enabling that the gene domain information can be leveraged for predicting isoform functions.
Proteomics software to quantify peptides based on the total ion intensity of the MS/MS spectra. The software provides also relative quantification of isobaric peptides co-fragmented in MS/MS spectra which share the same sequence but have distinct localizations of post-translational modifications (PTMs).
New method for transcript assembly that incorporates change-point analysis to improve the 3′ UTR annotation process.
IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.
IsoSolve an integrative framework to improve isotopic coverage and consolidate isotopic measurements by MS and/or NMR. IsoSolve is a Python module realizing an integrative framework for isotope labeling measurements. It can provide both symbolic and numeric solutions for integrating and consolidating heterogeneous measurements, e.g. NMR and MS measuring ¹³C labeling, to cite the most wide spread ones.
IsoSplitter is a de novo identification tool of alternative splicing sites using long-reads transcriptome without a reference genome.
IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.
MATLAB and R code for calculating the isotopic distribution of a molecule (e.g. insulin).
MATLAB code for calculating isotopic fine structure.
ISOform-guided prediction of epiTOPEs in cancer. The following pipeline have been developed for the identification of cancer-specific splicing-derived epitopes from RNA-seq. The pipeline is divided in 4 parts, depending the event type the user wants to obtain:. For the obtention of exonizations, neoskipping and A5_A3 events, the first input are the read counts mapped to all posible junctions in the genome. This file (readCounts.tab) is created through Junckey (https://github.com/comprna/Junckey#1-format-star-output). From these junctions, ISOTOPE will obtain all splicing events expressed significantly.
Console application for calculating isotope distributions based on Yergey's method.
Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.
Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.
Isotope tracer addition experiments are used to answer a wide variety of biological, ecological and evolutionary questions. In these experiments, a labeled element is injected into a biological system and its fate is traced throughout the system to estimate the flux of matter across compartments. Tracer additions can be used across all levels of biological organization from cells and tissues, to organisms and ecosystems. The isotracer package provides tools to analyze data from such experiments.
Processing and visualizing functional features of translated transcript isoforms. IsoTV is Snakemake pipeline to analyze and visualize functional features of translated transcript isoforms. IsoTV incorporates various tools to predict protein domains, secondary structure, disordered regions, and post-translational modification sites. The visualization facilitates comparison of the set of transcript isoforms expressed across conditions and explored the functional consequences of isoform differences. IsoTV supports a range of transcriptome sequencing technologies, including short-reads, Oxford Nanopore (ONT) long-reads, Pacific Bio-sciences (PacBio) long-reads. It also supports other inputs, including single or multiple gene sequences.
A webserver for visualization and annotation of alternative RNA isoforms
Accurate somatic mutation identification in the absence of normal tissue controls.
A approach to inferring gene-gene net-works using SPACE model with log penalty.
A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software. We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule
Provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.
Integrated structure-based protein interface prediction.
iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.
Prediction of interaction sites in proteins.
Deep neural networks and embeddings for predicting interaction sites in protein sequences.
A Machine Learning Model to Predict the Immune Subtype of Kidney Cancer Samples by Four Genes. The code and dataset used in the construction of ISPRF.
Short Sequence Assembly by K-mer search and 3' read Extension, Immunology version (iSSAKE)
Inferring contacts among protein secondary structure elements using deep object detection. ISSEC adopts deep learning to learn specific patterns within predicted inter-residue contacts and subsequently identifies the objects having these patterns as inter-SSE contacts.
This server is an attempt to help biologist identify Inteins hiding in their protein sequences.
An integrated predictor constructed by using sequence information and prediction results from different element predictors.
ISTDECO (In Situ Transcriptomics Decoding by Deconvolution) is a simple tool for deconvolving combinatorial image data generated by FISH techniques into series of non-combinatorial images.
Tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required, some browser requirements and set-up necessary.
Development and implementation of common data elements for venous thromboembolism research. Data Standards for Clinical Research. The International Society on Thrombosis and Haemostasis' Common Data Elements (CDE) provides pre-defined data standards for clinical research in venous thromboembolism (VTE). Researchers can review and download structured data elements that expedite the development of research datasets and case report forms (CRFs), and enable meta-analyses across studies using common definitions and coding. ISTH’s Common Data Elements (CDE) project provides investigators with pre-defined clinical data elements to reduce study design time and enable meta-analyses across studies.
This web-server is established for predicting the lysine succinylation sites in proteins.
This web-server used to predict the lysine succinylation in protein.
Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids.
Prediction of lysine sumoylation sites using statistical moments and Chou's PseAAC.
IsUnstruct is a new method based on the Ising model used for the prediction of disordered residues from protein sequence alone.
Identification of sequence variant associated with splicing event using RNA-seq data.
Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. Swarm-CG is designed for automatically optimizing the bonded terms of a MARTINI-based coarse-grained (CG) molecular model, in explicit or implicit solvent, with respect to a reference all-atom (AA) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:. Evaluating the bonded parametrization of a CG model. Optimizing bonded terms of a CG model.
Identification of Bacterial Type III Secreted Effectors Using PSSM Profiles and XGBoost Feature Selection.
Tool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data.
Interactive Tree Of Life is an online tool for displaying, annotating, and managing phylogenetic trees. It allows users to manage and visualize trees directly in the browser, and annotate them with various datasets.
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.
A web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.
Toolkit to create comprehensive CO1 reference databases.
iTaxoTools is a tool suite for integrative taxonomy. The suite contains tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests.
Deep learning framework for identification of T cell epitopes by harnessing fusion features.
Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM.
A method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application.
The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples.
Variable selection method for applying survival analysis to microarray data.
A framework for performing clustering analysis iteratively.
A barcode clustering algorithm for long fragment read analysis. The IterCluster is a barcode clustering algorithm fragment read analysis. There is pipeline for stLFR raw reads using the IterCluster.
The package provides a flexible algorithm to screen features of two distinct groups in consideration of overfitting and overall performance. It was originally tailored for methylation locus screening of NGS data, and it can also be used as a generic method for feature selection. Each step of the algorithm provides a default method for simple implemention, and the method can be replaced by a user defined function.
iThermo: Thermophilic Protein Prediction uses the protein sequence information to predict the thermophilic proteins. It is based on Multi-layer Perceptron classifier trained model.
Ithildin is an open-source C++ library for efficient, parallelized simulations of anisotropic reaction-diffusion problems in excitable media, utilizing MPI for multi-core CPU processing. It's demonstrated through simulations of cardiac electrophysiology, providing tools for analyzing wave patterns and cardiac tissue behavior.
ITI project [Interactome-Transcriptome Integration] is a network-based robust classification of transcription profiles in cancer by large scale data integration of protein-protein interaction with DNA microarray data.
tidysbml is an R/Bioconductor package that extracts data from Systems Biology Markup Language (SBML) documents into dataframes, facilitating analysis and network construction. The package is distributed under a CC BY 4.0 License and is available on Bioconductor and GitHub.
Tihi Toolkit is an open-source, multiplatform software for peak detection and signal decomposition, designed to provide accessible tools for spectral data analysis. It offers a user-friendly GUI and supports various spectroscopic techniques, aiming to replace costly commercial alternatives.
iTIME (interactive Tumor Immune MicroEnvironment) is a shiny application that creates interactive figures for examining spatial organization of individual tumors and provide basic spatial and summary information. https://fridleylab.shinyapps.io/iTIME/
This web-server was developed to identify Translation initiation site (TIS) by using the physicochemical properties of the pseudo trinucleotide composition.
A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks.
Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. It provides a large variety of tree layouts, drawing and annotation features including circular tree layout. iTOL is well-suited for a wide range of tree sizes up to several thousand leaves. Tree displays can be exported in several graphical formats, both bitmap and vector based.
TopicVelo is a tool that disentangles simultaneous, yet distinct, bursty transcriptional dynamics using a probabilistic topic model for RNA velocity estimation in single-cell RNA-sequencing data. It enables more accurate velocity estimation by integrating process-specific signals.
An Algorithm for Generating Individualized Treatment Decision Trees and Random Forests. ITR-Forest is used to generate individualized treatment rule (ITR) for both randomized clinical trail data and observational study.
Trackplot is an R script designed for rapid generation of integrative genomics viewer (IGV) style track plots, profile plots, and heatmaps from bigWig files, offering significant performance gains and minimal dependencies.
Interactive exploration of mono- and combination therapy dose response profiling data.
A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.
The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.
Open-source package to reliably segment and measure sounds by frequency modulation. Identify, Track and Segment sound (by) Frequency (and its) Modulation — itsFM 0.0.1 documentation.
A comprehensive collection of the fungal ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental communities.
ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.
TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.
ITSxpress: Software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files
Improved and robust identification of tumor T cell antigens by utilizing hybrid feature representation. This is the website for predicting T-Cell peptides from the publication called ... iTTCA-Hybrid: Improved and robust identification of tumor T cell antigens by hybridizing multiple feature representations.
A random forest predictor for tumor T cell antigens.
This web-server is a web server that could predict ubiquitination sites in proteins. With the assistance of SVM, the highlight is to employ amino acid sequence features extracted from the sequence evolution information via grey system model (Grey-PSSM).
Train neural networks based on geographic species occurrences, environmental data and existing IUCN Red List assessments to predict the conservation status of "Not Evaluated" or "Data Deficient" species, for any taxon or geographic region of interest.
A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides. The UMP-TR dataset consisted of 112 umami and 241 non-umami peptides while the UMP-IND dataset consisted of 28 umami and 61 non-umami peptides. This is the website for predicting Umami Peptides from the publication called .
iUP-BERT is a user-friendly web server. It can directly identify whether a polypeptide is an umami peptide only from the sequence.
Efficient identification of inverted repeats in IUPAC-encoded DNA sequences. An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. IUPACpal is an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences as substrings of a large text, allowing also for potential mismatches and gaps.
An online reference resource for classes of human drug targets and related proteins. As well as providing recommended nomenclature, the database integrates information on the chemical, genetic, functional and pathophysiological properties of receptors and ion channels, curated and peer-reviewed from the biomedical literature by a network of experts.
IUPred3 is a tool for prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation.
Recognizes unstructured/disordered regions from the amino acid sequence based on the estimated pairwise energy content.
Intersection-union survival mixture-adjusted mediation test (IUSMMT) is a R procedure for examining whether a set of gene-based methylation loci affects cancer survival through gene expression under the framework of mixed models.
Effectively detecting differential isoform usage from RNA-Seq data.
IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
Interpretation-oriented tool to manage the update and revision of variant annotation and classification. iVar - DataBase of Genomics Variants.
Identification of genetic variants affecting alternative splicing.
An Open-Source Toolbox for Visualization and Analysis of Crowd-Sourced Sensor Data.
IVEA is a computational method that predicts enhancer-gene regulatory interactions by estimating promoter and enhancer activities using variational Bayesian inference. The code is available on GitHub and used publicly available datasets.
Interactive HTML5 visualizer of protein-ligand complex.
Cyberinfrastructure-supported tools and data to power DNA virus ecology.
Processing utilities for high-resolution images for spatially resolved transcriptomics data.
This web-server was developed to predict the subfamilies of votaged-gated potassium channel using tripeptide compositions.
volcalc is a package that automates the calculation of estimated relative volatility index values for organic compounds, leveraging functional group contributions based on the SIMPOL.1 method. It utilizes chemoinformatic tools to predict volatility for metabolites within the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
IVS Caffe is a deep learning framework made with expression, speed, and modularity in mind.
R package for interactive visualization of functional analysis results of meta-omics data.
Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.
iwa-miRNA is a web-based platform for interactive annotation of plant miRNAs
A computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data. Dockerized Whole Exome Sequencing (WES) pipeline. A pipeline for Whole Exome Sequencing (WES) variants identification in mathced tumor-normal samples. It runs into a Docker container, ready to be downloaded and used on any operating system supported by Docker. All the steps of the pipeline and their dependencies are controlled by SCons so that in case of any stop, like killing by error or even shutting down the computer, it will automatically resume the analysis from the last run process.
Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.
IxPopDyMod is an R package providing a framework for writing, running, and analyzing tick population and infection dynamics models. It facilitates the creation and sharing of reproducible models, aiding in public health research and understanding tick-borne diseases.
3D X-ray diffraction simulation software supporting 3D polycrystalline microstructure morphology descriptions.
This resource provides a cgMLST database and software for genomic surveillance of *Yersinia enterocolitica* infections in France, enabling detection and investigation of outbreaks. The cgMLST utilizes a 1,727-gene core genome and allows for isolate clustering.
Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.
Circos plot tool that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions.
It is a comprehensive portable software package for analysis and visualization of microarray data. It gives access to methods for unsupervised analysis, supervised analysis and visualisation in an integrated and flexible way. Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers. Supervised analysis can be performed on samples by simple sample annotation or on genes through tools for metabolic pathway analysis and Gene Ontology mapping.
Joint Model-Based Deep Learning for Optimized Sampling and Reconstruction. Joint model-based deep learning for parallel imaging.
A Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.
Collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence It is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance.
Swift, versatile phylogenomic and high-throughput sequencing simulator.
Fast enumeration of single- and multi-copy CRISPR binding sites. JACKIE pipeline & database – Albert Cheng Lab. JACKIE (Jackie and Albert’s CRISPR K-mer Instances Enumerator) scans the genome and enumerate all potential SpCas9 binding sequences and output their copy number and locations. A example use is for finding clusters of repetitive sequences for genomic imaging.
New approach that allows one to accurately identify genomic variables that are statistically significantly associated with any subset or linear combination of principal components (PCs).
JAVA framework for accurate Variant assessment (JACUSA2) is a one-stop solution to detect single nucleotide variants (SNVs) and reverse transcriptase induced arrest events in Next-generation sequencing (NGS) data.
Program for computing distances between nucleic acid sequences. It allows specific comparison of coding sequences, of non-coding sequences, or of coding and non-coding sequences.
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions. It will output the names and locations of candidate gene fusions along with the cDNA sequence of their breakpoints. JAFFA is based on the idea of comparing a transcriptome (e.g. in a cancer sample) against a reference transcriptome. In this way, it is a transcript-centric approach rather than a genome-centric approach like other fusion finders. In validation studies, JAFFA performed well over a range of read lengths - from 50bp to full-length transcripts and on single and paired-end reads. For more information please see one of the wiki pages below:
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
Alignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.
Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems.
JAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.
Just Annotate My Genome (JAMg) is focused on delivering a process for feature annotation for all the species that are not model species
Fast computation of conditional mutual information for ceRNA network analysis.
Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types.
Peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.
JAMMING is a software for prediction of critical residues for protein function based only on the 3D structure of proteins
JAMSalpha is a script for taxonomic and functional analysis of single metagenomic samples, utilizing contig assembly for improved accuracy. It's evaluated within a larger study assessing various shotgun metagenomics pipelines, demonstrating its utility in community taxonomic classification.
Fast, self-contained in silico simulator capable of generating simulated MS and LC- MS runs while providing meta information on the provenance of each generated signal.
Deep learning for genomics using Janggu. Janggu - Deep learning for Genomics. Janggu is a python package that facilitates deep learning in the context of genomics. The package is freely available under a GPL-3.0 license.
Stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis.
This is the Schizosaccharomyces japonicus genome database.
Scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.
Efficient lossless compression of genomic sequences using a competitive prediction between two different classes of models: weighted stochastic repeat models and weighted context models.
Computational scanning tunneling microscope image database. JARVIS-Tools: an open-source software package for data-driven atomistic materials design. NIST-JARVIS (Joint Automated Repository for Various Integrated Simulations) is an integrated framework for computational science using density functional theory, classical force-field molecular dynamics and machine-learning. The NIST Materials Data Curation System (MDCS) provides a means for capturing, sharing, and transforming materials data into a structured format that is XML based amenable to transformation to other formats.
JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges) is an automated pipeline for alignment and SV calling in long-read datasets. The tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
JASP is an open-source statistics program that is free, friendly, and flexible. Armed with an easy-to-use GUI, JASP allows both classical and Bayesian analyses.
JASPAR is a high-quality, open-access database that provides manually curated, non-redundant transcription factor (TF) binding profiles for six taxonomic groups (fungi, insecta, nematoda, plantae, urochordata, vertebrata). These profiles are stored as position frequency matrices (PFMs), which can be transformed into models to predict TF binding sites (TFBS) in DNA sequences. The database collects motifs both internally, analyzing sequences using a custom motif discovery pipeline, and externally from publications and other resources. All selected motifs are manually curated for quality and supporting evidence. JASPAR now offers a tool for TFBS enrichment analysis in user-provided genomic regions. Data is accessible through the JASPAR website, its RESTful API, Bioconductor, or the Python package pyJASPAR.
Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).
JASPAR is a widely used open-access database containing curated, non-redundant transcription factor binding profiles. The JASPAR RESTful API enhances accessibility by enabling users to programmatically access the database by most programming languages.The API uses the Representational State Transfer (REST) architecture to provide data in multiple formats (JSON, JSONP, JASPAR, MEME, PFM, TRANSFAC, BED, and YAML). The JASPAR API is user-friendly, offering a browsable interface designed for bioinformatics tool developers.
Previously, a web service interface to the JASPAR database containing profiles of transcription factor binding sites. The SOAP API has been replaced with the JASPAR RESTful API.
Jasper is a tool for visualizing profiles from 16S and whole-genome sequencing, and orders taxa along a space-filling Hilbert curve. The result is a Microbiome Map, where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order the taxa in two ways, and depending on the ordering, the maps can highlight "hot spots" of microbes that are either common to, or unique to, the biological conditions under study.
A fast genome polishing tool that improves accuracy of genome assemblies.
Scan DNA sequences for transcription factors.
software package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface.
Predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs.
Java TreeView is an enhanced, open source, cross-platform gene expression visualization tool. It interactivly display clustered gene expression data, similar to eisen’s TreeView.
A Java-based Deep Learning Tool to Predict Drug Responses. Intelligent Molecular Discovery Laboratory. JavaDL is a deep learning program based on Java, freely available for download here.
Out-of-core open-source toolkit for association mapping using high-throughput sequence data.
JAX-CNV: clinical-graded copy number variation detector.
A tool that leverages modern machine learning infrastructure to enable extremely fast optimization of ReaxFF parameters.
A new Java API for biclustering analysis in the context of gene expression data, allowing the use of 21 biclustering algorithms.
Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.
Modular genome browser with views of synteny and structural variation.
JBrowseR is an R package that provides a simple and clean interface to JBrowse 2 for R users
Tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.
A joint continual learning neural network for biomedical information extraction.
circRNA full-length sequence assembly through integrated junction contigs. It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage.
Joint covariate detection tool for survival analysis on tumor expression profiles.
Integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails.
Progressive multifocal leukoencephalopathy lesion and brain parenchymal segmentation from MRI using serial deep convolutional neural networks. This is a deep learning workflow for Progressive Multifocal Leukoencephalopathy (PML) lesion and brain segmentation from brain MRI using Python 3, Keras, and TensorFlow. The model generates segmentation masks of the brain parenchyma and lesions in PML patients. This work was conducted at the Neuroimmunology Clinic (NIC) and Translation Neuroradiology Section (TNS) of the National Institute of Neurological Disorders and Stroke (NINDS), in collaboration with colleagues at the National Institute of Mental Health, and the Henry Jackson Foundation at the National Institutes of Health.
An Explainable COVID-19 Diagnosis System by Joint Classification and Segmentation. Official repository of the paper: JCS: An explainable COVID-19 diagnosis system by joint classification and segmentation, IEEE Transactions on Image Processing (TIP) 2021.
A Java package that utilises a series of D2 statistics to extract k-mers (subsequences at defined k length) from a set of biological sequences, and generate pairwise distances for each possible pair. This distance can be used directly for phylogenetic inference using neighbour-joining.
JDC is a novel essential protein identification method based on protein-protein interaction networks (PPI) and gene expression data. Some proposed methods for identifying essential proteins have better results by using biological information. Gene expression data is generally used to identify essential proteins. However, gene expression data is prone to fluctuations, which may affect the accuracy of essential protein identification. Therefore, we propose an essential protein identification method to calculate the similarity of "active" and "inactive" state of gene expression in a cluster of the PPI network based on gene expression and the PPI network data. Our experiments show that our method can improve the accuracy in predicting essential proteins.
JDFTx is a fully-featured open-source electronic density-functional theory software designed specifically to facilitate rapid development of new theories, models and algorithms.
Joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data .
An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics.
Open-source software package for the analysis of large 2D TFM data within ImageJ.
The JECFA Data Retriever is an R package and associated workflow that automates the retrieval of key identifiers and toxicological data from the Joint FAO/WHO Expert Committee on Food Additives (JECFA) database via web scraping. It provides a reproducible pipeline for accessing and processing JECFA data, facilitating more efficient research.
Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Circular RNA Prediction based on Junction Encoders and Deep Interaction among Splice Sites. Abstract Circular RNA is a novel class of endogenous non-coding RNAs that have been largely discovered in eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backsplices to an upstream acceptor site. These circular form of RNAs are conserved across species, and often show tissue or cell-specific expression. Emerging evidences have suggested its vital roles in gene regulation, which are further associated with various types of diseases. As the fundamental effort to elucidate its function and mechanism, numerous efforts have been devoted to predicting circular RNA from its primary sequence
JEDi (Java Essential Dynamics Inspector) is a powerful tool for inspecting the dynamics of proteins from trajectories derived from MD or Geometric simulation.
A command-line algorithm for counting k-mers in DNA sequence.
The GFP mRNA will express a green fluorescent protein, originally isolated from the jellyfish, Aequorea victoria. GFP could be used in a wide range of applications where they have functioned as a cell lineage tracer, reporter of gene expression, or as a measure of protein-protein interactions.
Jenever is a command-line tool for haplotype prediction that utilizes a deep generative model to improve variant detection in next-generation sequencing data, particularly for small variants, demonstrating superior accuracy compared to existing methods.
Provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources.
Novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype.
Jerman Enhancement Filter is a MATLAB tool for enhancement of vessel/tube and blob/sphere like structures in 2D/3D images using hessian eigenvalues.
Software components to create and publish EST alignments and clusters.
Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.
JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and monitor workflows.
A Multistaged Hyperparallel Optimization of the Fuzzy-Logic Mechanistic Model of Molecular Regulation. Elucidating mechanistic relationships among intracellular macromolecules is fundamental to understanding the molecular basis of normal and diseased processes. The classical fuzzy logic approach employs varying degrees of truth to describe relationships between interacting molecules. jFuzzyMachine implements the fuzzy logic approach to elucidate mechanistic relationships among biological molecules and makes more readily available the fuzzy logic inference approach in a freely available tool.
Updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Custom scripts used in the analysis for JGI Plant Gene Atlas resource are available.
The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms.
A clinically and genomically annotated nerve sheath tumor biospecimen repository. Data and code required to analyze JHU Biobank Data. This repository contains the information about the RNA-seq processing and figure generation for the Scientific Data Biobank Manuscript. These instructions assume that you:.
Specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided.
Tool for managing large sets of biochemical model parametrizations.
JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models. The program provides an automated way to take advantage of the many succsessful methods for computational gene prediction and can provide substantial improvements in accuracy over an individual gene prediction program.
Joint Integration and Discrimination for Automated Single-Cell Annotation. JIND is a framework for automated cell-type identification based on neural networks. It directly learns a low-dimensional representation (latent code) inwhich cell-types can be reliably determined. To account for batch effects, JIND performs a novel asymmetric alignment in which the transcriptomic profileof unseen cells is mapped onto the previously learned latent space, hence avoiding the need of retraining the model whenever a new dataset becomes available. JIND also learns cell-type-specific confidence thresholds to identify and reject cells that cannot be reliably classified. We show on datasets with and without batch effects that JIND classifies cells more accurately than previously proposed methods while rejecting only a small proportion of cells. Moreover, JIND batch alignment is parallelizable, being more than five or six times faster than Seurat integration.
A unified multi-view-based joint representation learning for CircRNA binding sites prediction.
A toolkit to infer and analyse loss of heterozygosity (LOH) blocks starting from a reference genome (FASTA), mapped reads (BAM) and called variants (VCF).
Large enhancement of multi-omics data resources on the general Japanese population. jMorp: Japanese Multi Omics Reference Panel - Tohoku Medical Megabank Organization, Tohoku University.
Software package for advanced time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. Through a user-friendly graphical interface biomedical researchers and clinical radiologists can use state-of-the-art signal processing algorithms to analyse and quantify spectroscopic data: from a single spectrum to a full multidimensional MRSI dataset.
Interactively visualize the spectra and chromatograms in an mzML file.
A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Provides reading and writing capabilities, as well as supporting the validation of mzTab and the conversion of PRIDE XML and mzIdentML files to mzTab.
Reference implementation for mzTab 2.0 for metabolomics
Package which implemented the joint matrix factorization technique to integrating multi-dimensional genomics data for the discovery of combinatorial patterns.
Meta-analysis method for identification of DEGs based on joint non-negative matrix factorization.
R package to visualize outputs from the Johnson-Neyman technique for categorical and continuous moderators, including options for phylogenetic regressions.
This package implements three steps of an algorithm called JODA, which computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model).
This functions load, process and plot the data from the John Hopkins COVID-19 database.
Online interactive dashboard for the Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU).
Johns Hopkins Coronavirus Resource Center
Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes.
Multivariate elastic net regression through stacked generalisation
Joint-SNF method uses SNF to integrate the joint structure extracted by JIVE method to obtain the fusion matrix. The fused network enhances strong similarities and weakens spurious associations between samples while reducing the noise. The realization of Joint-SNF method relies on the following two important algorithms. Extraction of joint structures by JIVE; Similarity Network Fusion
Copy number estimation from read depth information.
A desktop client able to efficiently integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools.
Jorg is a method for achieving complete microbial genomes and improving bins from metagenomics data. This is a method to help circularize genomes from shotgun metagenomics data. It is MAG circularization method.
Jovian is an open-source, virus-focused metagenomic analysis workflow for Illumina data designed to address limitations in clinical diagnostics and surveillance. It generates annotated scaffolds, quality metrics, and interactive reports, demonstrating portability and reproducibility across various IT architectures.
JOY is a program for displaying 3D structural information in a multiple sequence alignment.
JPA (short for Joint Metabolomics Data Processing and Annotation), an R package that offers comprehensive and streamlined metabolic feature extraction and annotation.
A java application based on FastPCR software and provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, unique, group-specific, bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR); and microarray design;
EIDORS image is generated based on jpg image pixels.
JPG image to EIDORS finite element model data via linear interpolation
Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 or HBV genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 or HBV subtypes to predict the phylogenetic breakpoints and HIV/HBV subtype of the submitted sequence.
An open source Java library for reading and writing various tree and alignment formats. Application developers are able to implement format-independent data processing by including event based readers via the abstract strategy pattern. All readers are designed to deal with large amounts of data (alignments with many and/or very long sequences, large trees) without using a great amount of resources (CPU or RAM).
Aset java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome: 1) COG (cluster of orthologs) assignments; 2) Phylogenetic profiles of genes; 3) Intergenic distances between gene pairs.
Improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search databases.
The Jnet algorithm provides a three-state (α-helix, β-strand and coil) prediction of secondary structure. Given either a single protein sequence or a multiple sequence alignment, this tool derives alignment profiles from which predictions of secondary structure and solvent accessibility are made.
Cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.
Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. ProfileGrids are a new paradigm for visualizing and analyzing MSAs in a concise representation. For a protein sequence, a ProfileGrid matrix contains positional amino acid counts highlighted according to the frequency of the characters in the alignment.
Tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
Joint and Progressive Subspace Analysis (JPSA) is a linearized subspace analysis technique with spatial-spectral manifold alignment is developed for a semisupervised hyperspectral dimensionality reduction (HDR).
Predict whether a protein is disordered, given its amino acid sequence.
A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data. JavaScript Mass Spectrometry, a visualization GUI for Mass Spectrometry signal data. Presents a robust, 3-dimensional graph view that allows the creation, editing, and saving of XIC and envelope annotations in addition to panning, rotating, and zooming actions. Interfaces via HTTP to the MsDataServer API for access to MS data stored in the MzTree format.
Free, open-source, pure-Java library for working with SBML. It emulates libSBML’s API, with more Java idioms and without native object code.
JSOM (Jointly Evolving Self-organzing Maps) is an algorithm aims to align two related datasets that contain similar clusters by constructing two maps—low dimensional discretized representation of datasets–that jointly evolve according to both datasets. Below, it shows how two maps evolve over time when traiend with two independent MNIST datasets.
Static website generator for protein bioinformatics research. It is a JS application that creates a website based on the JSON data.
Makes it straightforward to visualize numbers in Java tables by the use of sparklines.
An easy to use, biologist-centric software designed to measure the probability if two genomes belonging to the same species or not.
Open-source javascript library specifically built for rendering highly-extensible, customizable phylogenetic trees. It can render complex trees, yet offers a simple method to do so. It leverages the recent XML schema definition specified for phylogenetic trees, phyloXML.
A new jsPsych plugin for psychophysics, providing accurate display duration and stimulus onset asynchrony. A jsPsych plugin for psychophysics. The jspsych-psychophysics plugin is developed for the purpose of conducting online/Web-based psychophysical experiments using jsPsych (de Leeuw, 2015). This plugin can be used free of charge under the MIT license.
A JavaScript implementation of the QUEST+ method for estimating psychometric function parameters in online experiments.
A java tool to visualize networks and edge scores.
A flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data. Clustering scRNA-seq by joint sparse representation clustering (jSRC) Overview:.
Java implementation of the PSI-MS Transitions Markup Language (TraML) specification.
JUCHMME, an acronym for Java Utility for Class Hidden Markov Models and Extensions is a tool developed for biological sequence analysis. The JUCHMME framework is ease of use and customization for various biological problems without requiring programming capabilities (settings will be made through a configuration file). It offers a large collection of training algorithms for HMM for labeled sequences. It integrates a wide range of decoding algorithms such as Viterbi, N–Best, posterior–Viterbi and Optimal Accuracy Posterior Decoder. It contains built-in evaluation procedures, such as options for independent test (self-consistency, jacknife, k–fold cross-validation). All the prediction algorithms also incorporate the corresponding reliability measures. To overcome HMM limitations, a number of extensions have been developed such as Hidden Neural Networks, models that condition on previous observations and a method for semi-supervised learning.
Juicebox is visualization software for Hi-C data.
Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.
Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models.
The `julia_mzML_imzML` library provides tools for reading mzML and imzML mass spectrometry data in Julia, offering significantly faster processing speeds compared to R. It supports various MS data types and platforms.
Based on a formal on/off model of gene expression, but uses a non-parametric procedure based on decision trees (called “jump trees”) to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes.
The free energy difference ΔG0 between two states can be calculated by a molecular dynamics simulation from time spent in both states. Here we provide an online tool to calculate errorbars of ΔG0 by the JumpCount method solely from numbers of transitions and temperature.
Discontinuous Transcript Assembly in Nidovirales
A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics. JUMPm is a software program for mass spectrometry-based metabolite identification.
Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study.
JUMPt (JUMP-turnover) software determines the protein turnover rates in pulse SILAC labeled animals using mass spectrometry (MS) data. JUMPt uses a novel differential equation-based mathematical model to calculate the reliable and accurate protein turnover rates. The proposed method calculates the half-life of individual proteins by fitting the dynamic data of unlabeled free Lys and protein-bound Lys from individual proteins simultaneously.
A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.
Open-source individual-based epidemiology simulation. This is the offical repository of JUNE, named after June Almeida, who was the female Scottish virologist that first identified the coronavirus group of viruses. checkout the release paper for a physical description of the model. A framework for high resolution Agent Based Modelling.
Jupyter Book is an open-source tool for building publication-quality books and documents from computational material.
Computational extraction of structural properties of viral epitopes.
Software tool with graphical and character user interfaces for deep learning-based object detection and segmentation in image analysis. Deep learning has been applied to solve various problems, especially in image recognition, across many fields including the life sciences and agriculture.
Database of plant long noncoding RNA expression profiles and functional network.
Jutils is a visualization toolkit for differential alternative splicing events. Jutils directly supports visualizing results generated by the differential splicing (DS) detection tools MntJULiP, LeafCutter, MAJIQ and rMATS, and can be easily adapted to use with other DS software.
Juxtapose is a Python tool that can be used to compare gene co-expression networks (GCNs). Juxtapose, together with different similarity measures, can be utilized for comparative transcriptomics between a set of organisms.
Split bed file into several bed files where each region is separated of any other by N bases.
Plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams.
Creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.
A pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping.
The K-Alpha Calculator is a user-friendly online web application designed to calculate Krippendorff's Alpha inter-rater reliability coefficient, simplifying a complex statistical calculation for researchers.
Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories.
Model-based branching point detection in single-cell data by K-branches clustering.
Predictor of the Protein Folding Mechanism and Rate.
An EST clustering algorithm which mitigates the effect of chimeric sequences by using a variable linkage merging algorithm.
Novel and user-friendly web-based program that systematically connects a set of query kinases to kinase inhibitors based on quantitative profiles of the kinase inhibitor activities. Users can find kinase inhibitors for a set of query kinases (obtained from high-throughput “omics” experiments) or to reveal new interactions between kinases and kinase inhibitors for rational drug combination studies.
A unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains. Klebsiella species serotype predictor and surface antigens modeler. K-PAM (Klebsiella species serotype predictor and surface antigens modeler) is an in silico diagnostic tool that can predict the serotype of Klebsiella spp. (K- and O-types) using the gene protein sequences of proteins involved in biosynthesis and transportations of CPS and LPS. The following documentation is to help the user in usage of K-PAM web server.
K-Pax contains an implementation of a Bayesian model-based method for simultaneously classifying aligned proteins into functionally divergent subgroups and identifying their function specific residues
Database of kinetics data on proteins and mutants.
k-seq (Kinetic sequencing) is an analytic toolbox for data from kinetic assay with DNA sequencing.
Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification.
Web service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.
Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data. K2Taxonomer is an R package built around a "top-down" recursive partitioning framework to perform unsupervised learning of nested “taxonomy-like” subgroups from high-throughput -omics data. This framework was devised to be flexible to different data structures, enabling its applicability to analyze both bulk and single-cell data sets. In addition to implementing the algorithm, this package includes functionality to annotate estimated subgroups using gene- and pathway-level analyses.
The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.
a novel software calculator program of the Objective Breast Cosmesis Scale (OBCS) | kOBCS© the digital calculator
Knowledgeable biomedical relation extraction system.
Known Antibody Search (KA-Search) is designed to facilitate the rapid and exhaustive search of antibody variable domains. It addresses a key challenge in immunology and biotechnology: the need to analyze and compare vast numbers of antibody sequences efficiently.
Tool for ortholog assignment and pathway mapping. It provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
Helps you create interactive visualizations of BLAST results from your web browser. Find your most interesting alignments, list detailed parameters for each, and export a publication-ready vector image, all without installing any software.
Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA).
KAGE is a tool for efficiently genotyping short SNPs and indels from short genomic reads.
KaIDA - Karlsruhe Image Data Annotation Tool. A modular tool for assisting image annotation in deep learning.
Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses.
Section for Bioinformatics, Department of Biology, University of Copenhagen
KAIKObase is a silkworm genome database.
Open-Source Software for the Analysis of Cardiac Optical Data Collected From Multiple Species.
Adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator.
A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures.
Fast and accurate multiple sequence alignment which handles large sequences.
Fast and accurate multiple sequence alignment algorithm for DNA and protein sequences.
Kalign is a fast and accurate multiple sequence alignment algorithm.
kalis is an R package providing a high-performance implementation of the Li & Stephens model for local ancestry inference, enabling rapid resolution of ancestry at loci of interest.
A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Improving genomic prediction accuracy of complex traits using machine learning determined parameters. Kinship Adjusted Multiple Loci Best Linear Unbiased Prediction.
KaMRaT is a C++ toolkit designed for k-mer count matrix dimension reduction, particularly useful for analyzing large RNA-seq datasets to identify condition-specific sequences without relying on gene or transcript annotation.
Java toolkit designed to convert DNA and RNA sequences into k-mers.
A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain.
Kraken metagenomics adjudication bioinformatics pipeline
Allows to infer regulatory sequence motifs implicated in 3’ end processing changes.
Sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
It is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version.
Karawun converts the results of a diffusion MRI tractography study, as might be used for surgical planning, to a form that is readable by the Brainlab software suite.
Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data
Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing
K-mer Antibiotic Resistance Gene Variant Analyzer.
Allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.
Karyon is a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies. Karyon is a pipeline for the assembly and analysis of highly heterozygous genomes. It uses redundans (Pryszcz & Gabaldón, 2016) to reduce heterozygosity during the assembly process, and then maps the original libraries against the reduced assembly to analyze the distribution of heterozygous regions. With this information, it generates a series of plots that can aid researchers to generate informed hypotheses with regard of the architecture of their genomes.
Plot customizable linear genomes displaying arbitrary data.
Novel computational framework for exploring kas-seq data.
KASP Assay Search is a tool for designing and searching for trait-specific KASP markers for rice genotyping applications. It allows users to access a database of validated KASP markers and design new markers based on genomic comparisons.
Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes. main.nf assembles KIR haplotypes from PacBio HiFi reads.
A web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exonomes.
Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files
An R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing. The Kataegis program provide a convenient tool to define the Kataegis region in.
An R package for detection, charcterisation and visualisation of kataegis.
Fast genotyping of rare variants directly from unmapped sequencing reads. A toolkit for performing set operations - union, intersection and complement - on k-mer lists. Detect genotypes from raw sequence data.
KAUSTNMF is a maximum correntropy criterion-based non-negative matrix factorization package.
Compilation of human SNVs collected from many and diverse sources, stressing accessibility and ease of use. Kaviar (~Known VARiants) is a very simple tool for answering a very specific question: What variants have been reported already for a given specific genomic location?
Search tool takes a text input and retrieves relevant proteins structures. Example searches include diseases, drug names, and protein functions.
The first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.
Convenient analysis tool for genome-wide and candiate-region association mapping.
Toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models.
KBoost is a R package to infer gene regulatory networks from gene expression data. It has been benchmarked using three datasets. It builds several models unsing kernel principal components regression and boosting and from them estimates the probability that each transcription factor regulates a gene.
An EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services.
A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment. Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.
A tool to aid in the evaluation and classification of chemical carcinogens.
Takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.
Very fast multi-threaded k-mer counting algorithm. It uses cache efficient burst tries to store k-mers
Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks.
An ultra-fast k-mer counter for assembled genome analysis.
kCSD-python is an open-source Python package for estimating Kernel Current Source Density (kCSD) and related tools for analyzing experimental data and interpreting results. It allows CSD estimation for arbitrary electrode distributions and includes diagnostic aids, demonstrated in a Jupyter Notebook tutorial.
Multi sample aCGH analysis package using kernel convolution.
Identification of lncRNAs subcellular localization with multiple features and nonnegative matrix factorization. Long non-coding RNAs (lncRNAs) refer to functional RNA molecules with a length more than 200 nucleotides and have minimal or no function to encode proteins. In recent years, more studies show that lncRNAs subcellular localization has valuable clues for their biological functions. So it is count for much to identify lncRNAs subcellular localization. In this paper, a novel statistical model named KD-KLNMF is constructed to predict lncRNAs subcellular localization. Firstly, k-mer and dinucleotide-based spatial autocorrelation are incorporated as the feature vector. Then, Synthetic Minority Over-sampling Technique is used to deal with the imbalance dataset. Next, Kullback-Leibler divergence-based nonnegative matrix factorization is applied to select optimal features. And then we utilize support vector machine as the classifier after comparing with other classifiers
The Comprehensive Knowledge Discovery System for Missense Variant (KD4v) webserver allows users to characterize and predict the phenotypic effects of missense variants.
Cytoscape app to learn biological network topology and its changes using profiling data and domain knowledge. It takes input data and runs KDDN algorithm to construct the dependency network.
Non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.
Web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them.
A Novel Visualization Tool to Explore Biodiversity in Metagenomes. A tool for viewing the contents of metagenomic samples. format_input.py: takes a file that contains a single BLAST query and taxon ID per line and formats it correctly as input for Keanu. The following command is used to create the taxonomy.dat and merged_deleted.dat databases necessary for running Keanu. There are no optional parameters. The input files - names.dmb, nodes.dmp, delnodes.dmp, and merged.dmp - come from the taxdmp file located at the NCBI Taxonomy FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/.
This package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences.
KEC (short for K-mer exclusion by cross reference) is a searching tool for unique DNA RNA amino acid sequences in large datasets.
Command line tool for generating, for a given reference genome, a set of k-mers absent in that genome.
Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.
KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases.
Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. This tool comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). Its Atlas is a new tool for the global analysis of metabolic pathways.
Kyoto encyclopedia of genes and genomes (KEGG)
An Effective Extraction Tool for KEGG Orthologs.
A Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes.
Web-based tool for visualizing experimental data in the context of biological pathways. It produces animations or static images of KEGG pathways by overlaying public or user uploaded high-thourghput data over handdrawn KEGG pathway maps.
A tool for representing genomic potential and transcriptomic expression into KEGG pathways.
Interface between a KEGG pathway and a graph object, as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers other functionalities including parsing, graph operation, visualization, etc.
See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.
Graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.
MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.
Annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. It facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.
A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.
Easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats.
Kernel-reweighted logistic regression method for reverse engineering the dynamic interactions between genes based on their time series of expression values.
A python tool for KEGG Module evaluation and microbial genome annotation expansion.
Analysis Tool for Multi-Process, Multi-State Single-Molecule Data. KERA (Kinetic Event Resolving Algorithm) is a tool for analyzing data which consists of time-series of data at discrete states.
A Wrapper For Fast Implementation Of Deep Learning Models In Genomics. Keras_dna: simplifying deep genomics. Keras_dna is an API that helps quick experimentation in applying deep learning to genomics. It enables quickly feeding a keras model (tensorflow) with genomic data without the need of laborious file conversions or storing tremendous amount of converted data. It reads the most common bioinformatics files and creates generators adapted to the keras models.
library for cell detection in biological images using deep neural networks. keras-rcnn is the Keras package for region-based convolutional neural networks.
Supervised learning and model analysis with compositional data.
Provides the possibility to use Ketcher v1. editor with Rails and contains server actions implementations.
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Extracts all maximal connected sub-networks that contain the genes that are differentially expressed. The exact quantities are modeled with two easy-to-interpret parameters (K, L) that allows the user to control the number of outliers (not dysregulated genes/cases) in the solutions. We developed two slightly varying models (INES and GLONE) that fall into the class of NP-Hard optimization problems.
Keyboard is an R package suite for early phase dose-finding designs. Phase I and or I II oncology trials are conducted to find the maximum tolerated dose (MTD) and or optimal biological dose (OBD) of a new drug or treatment. In these trials, for cytotoxic agents, the primary aim of the single-agent or drug-combination is to find the MTD with a certain target toxicity rate, while for the cytostatic agents, a more appropriate target is the OBD, which is often defined by consideration of toxicity and efficacy simultaneously. However, there still lacks accessible software packages to achieve both yet.
Keypoint MoSeq is a machine learning platform for identifying behavioral modules ('syllables') from keypoint data. It utilizes a generative model to distinguish noise from behavior and is applicable across multiple species and timescales.
Web-based implementation of the Knowledge-based FADE and Contacts model. It predicts the subset of residues responsible for the majority of a protein interface&apos,s binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.
Framework for fitting and cleaning outliers in kinetic measurements.
A framework to produce customized knowledge graphs for COVID-19 response. Prebuilt versions of the KG-COVID-19 knowledge graph build from all available data are available in the following serialization formats:. The KG-COVID-19 project is the first instantiation of such a KG Hub. Thus, KG-COVID-19 is a framework, that follows design patterns of the KG Hub, to download and transform COVID-19/SARS-COV-2 related datasets and emit a knowledge graph that can then be used for machine learning or others uses, to produce actionable knowledge.
KG-Microbe is a standardized, interoperable framework for constructing modular microbial knowledge graphs that harmonize information about bacteria and archaea, e.g., organismal traits, environments and growth preferences, media, assays, and genome annotations. Starting from a core KG, the framework generates a hierarchy of related KGs ranging from millions to over 0.5 billion edges (KG-Microbe-Core, -Biomedical, -Function, -Biomedical-Function) structured according to the Biolink Model. KG-Microbe supports customizable taxa subsets and host organisms. The framework uses standard TSV formats but also outputs n-triples.
Knowledge graph neural network for synthetic lethality prediction in human cancers.
KG-Hub-building and exchanging biological knowledge graphs.
A Graph-Based Deep Learning Framework for Chemical Structures. kGCN: a graph-based deep learning framework for life science.
A Knowledge-Graph-Based Multimodal Deep Learning Framework for Identifying Drug-Drug Interactions.
kGEM (k-Genotype Expectation Maximization algorithm) tool finds haplotypes for Single-amplicon sequencing data. This tool requires aligned reads in special internal format and auxiliary program ERIF could help to convert reads in this format either from fasta (unaligned) format or from SAM (pairwise alignment) format.
Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV).
Perform knowledge-based analysis for genome-wide association studies(GWAS). At present, it has three major functions, 1) prioritizing SNPs through a knowledge-based weighting method; 2) efficiently conducting powerful gene-based association tests using SNP p-values from GWAS; 3) advanced biological module-level analysis (pathway and PPI network enrichment) of significant genes suggested by the analyses of 1) or 2).
Software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits.
khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.
Kibio is an architecture and R package for next-generation data querying and sharing in big biology. It is used for easy scientific data handling, searching and sharing with Elasticsearch. kibior is built for data science and data manipulation, so when any data-related action or need is involved, notably sharing data. It mainly targets bioinformaticians, and more broadly, data scientists.
FASTQ compressor based on a new integer-mapped k-mer indexing method.
User-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies.
KiDoQ, a web server has been developed to serve scientific community working in the field of designing inhibitors against Dihydrodipicolinate synthase (DHDPS), a potential drug target enzyme of a unique bacterial DAP/Lysine pathway.
Tridesclous is a software package for spike sorting in large-scale brainstem recordings, developed to address the challenges of processing data from high-density electrodes. The software has been evaluated in conjunction with other spike sorting packages to identify physiologically relevant cell types.
Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate. KIMI: R package based on Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate.
Flexible linear mixed effects modeling with kinship covariance for RNA-seq data.
This package allows to work with mixed omics data introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot methodology to project variables (gene expression) on the compromise.
Knowledge guided multi-level network inference. KiMONo is a network inference tool for multi-omics datasets. The multi-omics network is calculated by sparse-group-LASSO regression and can incorporate prior biological information using protein-protein Interactions.
A python Package for Kinetic Modeling of the Chemical Mechanism.
Web-based repository of experimental data for KInetic MOdels of biological SYStems.
Novel computational method for predicting activating mutations in kinases. It is a machine learning approach that relies on structural and sequence data of proteins, such as environment residue, stability changes predictions, atomic interactions, graph-based signatures and residue conservation.
KinaFrag is an integrated database to explore the kinase-ligand fragment interaction space. KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery.
KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions.
BLAST search against Kinase domains stored in Kinase SARfari.
Search against small molecules stored in Kinase SARfari database.
Kinase mutations and drug response database. Mutations in kinases are abundant and critical to study signaling pathways and regulatory roles in human disease, especially in cancer. Somatic mutations in kinase genes can affect drug treatment, both sensitivity and resistance, to clinically used kinase inhibitors.
Identify kinase-specific phosphorylation sites in protein sequences.
A Predictive Model for Estimating Ligand-Kinase Inhibitor Constant (pKi). Model to predict kinase-ligand pKi values. Kinases to predict Inhibitor constant in terms of pKI (where pKi is decadic logarithm of Ki). We used the data points that were specifically represent Ki values to train and test the models. Download the docker image docker pull sirimullalab/kinasepkipred:py2. Run the container docker run --rm sirimullalab/kinasepkipred:py2 <protein_sequence> <compound_smiles>. To run with a built-in sample, do docker run --rm sirimullalab/kinasepkipred:py2. Set up the conda environment and activate it.
KinasePredictor is a tool that predicts protein kinases likely to phosphorylate a given site based on amino acid sequence preferences derived from mass spectrometry data. It provides a ranked list of kinases and is accessible via a webpage and stand-alone application.
A global database of kinship terminology.
MATLAB software package for likelihood-based analysis of kin-cohort data.
A web resource for structural classification of protein kinases and their inhibitors. Use the following command to create a virtual enviroment and install the necessary packages.
Using graph-based signatures to predict small molecule CDK2 kinase inhibitors.
A kinase to cytokine explorer to identify molecular regulators and potential therapeutic opportunities.
A simple web tool for ranking pairwise associations in biomedical applications.
Functions, classes & app for simulating and estimating close-kin dispersal kernels
KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).
Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.
KiNext is a Nextflow pipeline for the identification and classification of protein kinases from predicted proteomes. It uses Hidden Markov Models to identify and categorize kinases, improving upon existing methods and facilitating reproducible analysis.
Generates a generalized mass action model from the chemical equations of reactions and an estimation of the structural parameters of these reactions
Reproducible PET Pharmacokinetic Modelling in R | ABSTRACT Quantification of Positron Emission Tomography (PET) data is performed using pharmacokinetic models. There exist many models for describing this data, each of which may describe the data better or worse depending on the specific application, and there are both theoretical, practical and empirical reasons to select any one model over another. As such, effective PET modelling requires a high degree of flexibility, while effective communication of all steps taken through scientific publications is not always feasible. Reproducible research practices address these concerns, in that researchers share analysis code, and data if possible, such that all steps are recorded, allowing an independent researcher to reproduce the results and assess their veracity. In this article, I present kinfitr : a software package for performing kinetic modelling using the open-source R language, in a reproducible manner
Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. KinFragLib: Kinase-focused fragment library. We present here KinFragLib, a data-driven kinase-focused fragment library based on the structural kinome data retrieved from the KLIFS database.
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
KinImmerse translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.
Fortran program that calculates the informativeness of markers in inferring pairwise relatedness or relationships.
Web-based tool for interactive navigation through human kinome data.
A random forest classifier of sequence variants in the human protein kinase superfamily.
KinOrtho is method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. It is a combination of full-length and domain-based orthology inference methods.
A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. Welcome to the Github repository for the KinPred v1.0 project, which seeks to create sustainable and usable formats of whole human proteome predictions of kinases with site-specific substrates. Details of code are available within the Code and Data directory readme files. For orientation, the likely workflows you may be interested in, include:. Users of KinPred-formatted Prediction Algorithm Resources.
Algorithm that performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure.
Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach.
KiPar is a standalone Java application for the retrieval of textual documents likely to contain information relevant for kinetic modelling of a given metabolic pathway.
Knowledge-based Identification of Pathway Enzymes (KIPEs) allows the identification of players in a pathway or gene families. The identification relies of sequence similarity and phylogenetic relationships. Additionally, it is possible to consider functionally relevant amino acids.
Knowledge-based Identification of Pathway Enzymes
The basic command-line file versioning solution is a key-value data store that keeps track of when particular items are inserted or deleted (updates are deletes followed by inserts).It can recall versions by date or version id. It can keep versions in one or more volume files.
Web-based tool for bisulfite sequencing analysis
Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.
KISSE is a species search engine that utilizes collagen sequences from eight different species to identify unknown samples.
Predicting Off-Targets from Structural Similarities in the Kinome.
Kinetochore Tracking (KiT) is an open-source software package for tracking kinetochores from live-cell fluorescent movies.
A Java application aiming to detect any combination of microbe genomes selected to be detected from metagenome data
A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. KITSUNE: K-mer-length Iterative Selection for UNbiased Ecophylogenomics. KITSUNE is a toolkit for evaluation of the length of k-mer in a given genome dataset for alignment-free phylogenimic analysis.
Overcomplete Convolutional Architectures for Biomedical Image and Volumetric Segmentation.
Integration and visualization of network topology and gene-set analysis.
A comprehensive resource for kiwifruit genomics.
Tool that implements two algorithms to quantify the starting template in a PCR reaction. The first is a modified Ct strategy that assumes an ideal efficiency and is calculated for reference. The second employs a parametric fitting approach to construct a non-linear approximation to the reaction efficiency that is regressed backwards to establish a peak efficiency.
This application will give you explanations for clusters or groupings of entities described by ontology classes. For example, groups of patient profiles described by HPO classes.
Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors. kLDM is designed to infer multiple association networks based on variation of environmental factors.
Genomic surveillance framework and global population structure for Klebsiella pneumoniae. Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:. A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).
A web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry.
Ultra-fast and sensitive structural variant detection tool for long-read sequencing data.
Multiple kernel learning for integrative consensus clustering of omic datasets. The code contained in this folder can be used to reproduce the pancancer analysis presented in Cabassi and Kirk (2020). The data used for the analysis are those of Hoadley et al. (2014), which can be downloaded from Synapse. The links to each dataset can be found at the beginning of the R scripts where needed.
KLIFS — Kinase–Ligand Interaction Fingerprints and Structures — is a structural kinase database focusing on how kinase inhibitors interact with their targets. The aim of KLIFS is to support (structure-based) kinase research through the systematic collection, annotation, and processing of kinase structures.
KluDo (Diffusion Kernel-based Graph Node Clustering for Protein Domain Assignment), is an automatic framework that incorporates diffusion kernels on protein graphs as affinity measures between residues to decompose protein structures into structural domains.
Optimization process of WGCNA hierarchical clustering with k-means.
KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
New approach to alignment-free sequence comparison. While most alignment-free methods rely on exact word matches, it uses a distance measure based on inexact substing matches.
KAUST Metagenomic Analysis Platform (KMAP), Enabling Access to Massive Analytics of Re-Annotated Metagenomic Data. Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com). Supplementary Table 1, Gene Catalogs, ENA Project Ids, Links to GITs and KMAP Annotations. KAUST Metagenomic Analysis Platform.
KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.
Memory-frugal and retrieval-efficient encoding of counted k-mers.
A curated database of reconstructed individual patient-level data from 153 oncology clinical trials.
kmdiff provides differential k-mers analysis between two populations (control and case). Each population is represented by a set of short-read sequencing. Outputs are differentially represented k-mers between controls and cases.
Comprehensive collection of single and multiple substrate enzyme reactions and regulatory mechanisms that extends Cellerator function for the mathematical modeling of enzyme reactions.
Fast, Accurate, and Complete SSR Detection in Genomic Sequences.
Web server uses a support vector machine with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of genomic assays.
Reference-free SNP calling from raw reads based on matching. Kmer2SNP is a fast and accurate variants calling tool for next-generation sequencing data. It's a reference-free and alignment free method.
Interactive visualization tool for nucleobase and k-mer frequencies.
An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.
Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome.
A database encompassing the set of genomic and proteomic sequence information for each species.
Prediction of bacterial species using a fast K-mer algorithm.
KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.
A Tool to Identify Group-Specific Sequences With k-mers. KmerGO is a user-friendly tool to identify the group-specific sequences on two groups of high throughput sequencing datasets. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered “group-specific” here. Furthermore, KmerGO can also be applied to capture trait-associated sequences for continuous-trait dataset.
KmerKeys is a web resource for searching indexed genome assemblies and variants. It provides performant, rapid query speeds for cloud computation on genome assemblies. It enable fuzzy as well as exact k-mer-based searches of assemblies. To enable robust and speedy performance, the website implements cache-friendly hash tables, memory mapping and massive parallel processing. Our method employs a scalable and efficient data structure that can be used to jointly index and search a large collection of human genome assembly information. One can include variant databases and their associated metadata such as the gnomAD population variant catalog. This feature enables the incorporation of future genomic information into sequencing analysis.
Streaming algorithm for estimating the number of distinct k-mers present in high throughput sequencing data.
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
Efficient construction of Bloom filters for large sequencing data collections. kmtricks is a modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
Count the occurrences of k-mers in biological sequences (Fastq or Fasta formatted). It can then perform various analyses on the generated indices. The counting is resource intensive, but this tool can divide the computation up, so that it can be run as sequential parts (to fit in memory), in parallel (to exploit multiple CPUs), or distributed (to use a cluster of computers).
Finds pairs of genes with similar behavior across a gene expression dataset. It is intended to be used as a comparative tool to compare the network size (number of output rows) between N datasets with the same numbers of biological samples (input columns) and measured genes (input rows).
New software for predicting the consensus secondary structure for a given alignment of RNA sequences. It uses an innovative classifier system (a hierarchical network of k-nearest neighbor classifiers) to compute for each pair of alignment positions a “base pair” or “no base pair” prediction.
A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.
NetworkX-based topologically relevant KEGG parser.
Open source graphical workbench for building workflows. Among others it provides various extensions for data analysis and life sciences.
This KNIME framework is a data mining platform including manifold libraries for image processing (based on Fiji/ImageJ) and data exploration. The platform provides access to workflows and pipelines for (large-scale) automated phenotype analysis.
custom nodes for the interpretation of Next Generation Sequencing data with KNIME.
Comprehensive toolbox for next generation sequencing analysis.
A comprehensive database of physicochemical properties for k-tuple nucleotides. A comprehensive database of k-nucleotide physicochemical property values. After your Node.js environment and MySQL are ready, find out the location of the source code of KNIndex that you unpack and enter this directory in command line program. Then execute the command npm install to install all the dependencies of the project.
Interactive gene networks with KNIT. Knock-in/knock-out Interaction Tools. Knock-In / Knock-Out Network Interaction Tools.
Implementation of the k-nearest neighbors algorithm for estimation of missing values in microarray data. In our comparative study of several different methods used for missing value estimation we determined that KNNimpute provides superior performance in a variety of situations.
KnockoffTrio, a statistical method to identify putative causal genetic variants for father-mother-child trio design built upon a recently developed knockoff framework in statistics.
KnotAli is an algorithm for predicting the pseudoknotted secondary structures of RNA using relaxed Hierarchical Folding.
Applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots.
A Toolkit for Designing Personalised Dementia Care.
A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments' toxicities.
KnowSeq is an R package for the automatic smart gene expression tool for retrieving relevant biological knowledge. KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis.
Webserver that computes protein structure refinement based on minimization of a knowledge-based potential of mean force. Stereochemistry may also be optimized using the MESHI software.
KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).
Knockoff Boosted Tree for Model-Free Variable Selection.
KODAMA is an R package of the novel learning algorithm for unsupervised feature extraction. It is specifically designed for analysing noisy and high-dimensional datasets. It has additional functions that allow improved interpretation of high-dimensional data.
KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.
A database search algorithm for solving cross-linked peptide mass spectra.
Transcript-informed, targeted de novo assembly of gene loci.
Multistep approach to classify and cluster Biological Sequences and Structures, via Compression.
Taxonomy-oblivious Characterization of Metagenome Dynamics via K-core Decomposition. Revealing repeats using K-core on unitig graphs.
Knowledgebase of Microbes’ Battling Agents for Therapeutics.
A semantic text mining framework. Komenti is a tool for semantic query, annotation, and analysis of text using ontologies.
Komet is a Kronecker Optimized Method for Drug-Target Interaction (DTI) prediction, designed for scalability and performance. It leverages a large-scale dataset (LCIdb) and a three-step framework for improved DTI prediction.
Software to detect significantly under- or over-represented groups of homologous genes (KO groups) in one taxon (named test taxon) when compared with another (named background taxon) in a given biochemical pathway.
Imputing summary statistics of missing phenotypes in high-throughput model organism data.
KOnezumi-AID is a command-line tool designed for gRNA design in Target-AID mediated genome editing, facilitating the creation of multiplex knockouts by inducing premature termination codons or exon skipping. It supports both mouse and human genomes and offers batch processing capabilities.
A web application to explore the protein properties in a functional protein-protein interaction network.
Konnektor is an open-source Python package for planning, modifying, and analyzing free energy calculation networks using graph theory. It assists in drug discovery by providing tools for network operations and visualization, and is documented with example code and documentation available online.
A kmer-based screening and filtering tool for next-gen sequencing reads.
A coarse-grained knowledge-based scoring function for protein-ligand interactions. KORP-PL is a novel sidechain-free coarse-grained knowledge-based scoring function for protein-ligand interactions developed together with Pablo Chacón from IQFR Madrid. Our Knowledge-base ORientational Potential (KORP-PL), developed in a joint-venture with Sergei Grudinin lab outperforms state-of-the-art statistical potentials using a 3D joint probability and a minimalist protein representation. Our side-chain independent potential is a fast and highly discriminative energy function for protein ligand docking, please have a try. Here you can find a mirror site of the methodology.
KOSMOS is a web server for analysis of harmonic and anharmonic macromolecular structures for DNA, RNA, and proteins. Users can request thermal fluctuation study or transient pathway generation by submitting PDB ID or uploading personal data files. All the simulation outputs have been deposited into NMA and ENI database where most of data are disclosed to the public unless users requested.
An automatic implementation of the K/θ method for species delimitation.
Constructs three-dimensional (3D) structures of antibody variable domains from sequence using canonical rules, new H3-rules and evolutionary information.
A reproducible KEGG orthologue abundance workflow.
A database of 5,305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population.
Reference-based compression software of short read data sets.
Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures.
Probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences.
Knowledge-primed neural networks developed in the Bock lab at CeMM. KPNNs are neural networks that are trained using a knowledge-based network structure, which enables interpretability after training. Networks used in KPNNs should consist of nodes with labels (for example proteins in biological networks) that are connected based on prior knolwedge. After training, KPNNs enable extraction of node weights (importance scores) that represent the importance of individual nodes for the prediction.
The KPP (Kmer Phylogenetic Profile) is a new algorithm for constructing phylogenetic profile by compressing sequences to contig and generating evolutionary information features. Using this feature or concatenating other features with the ML framework for the prediction of PHI (pathogen-host interaction).
Ultrafast tool for genome-wide survey of microsatellites and primer design.
System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
Create BIOM-format tables from Kraken output
view report of classification for multiple samples
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”)
This tool converts data from Kraken to a Galaxy taxonomy representation.
KrakenParser is a streamlined toolkit that transforms Kraken-2 taxonomic reports into tidy CSV files, automatically computes relative abundances, and exposes an intuitive API suite for effortless downstream visualization.
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
Evaluating drug resistance mutations in kinases by molecular docking.
The large-scale variant database of 1722 Koreans based on whole genome sequencing.
Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface.
Bioinformatics Software Applications and Online Databases and Tools.
Predict MLST directly from uncorrected long reads
Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).
Extract from krona xml file (obtained by rankoptimizer), list of reads and blast offset for a given taxonomic name.
A workflow assembler for cancer genome analytics and informatics.
A uniform framework for single-cell replication timing analysis.
An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data.
KIRC-specific Stemness Calculator and Visualization (KSCV) is a computational framework that quantitates the stemness level of samples from RNA-Seq data in KIRC. By modeling the expression matrix by which genes are produced significant abnormal alternative splicing in RNA-Seq, the KSCV model uses one-class logistic regression to estimate the stemness index of KIRC patients.
Knowledge graph model for link prediction of novel phosphorylated substrates of kinases. KSFinder changes based on major revision comments from PeerJ.
An integrated method for predicting catalyzing kinases of phosphorylation sites in proteins. KSP is a method for predicting kinase annotations for phosphorylation sites by effective integration of.
Application developed for predicting novel substrates of kinases of interest.
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
Generalized platform for computational drug repositioning.
Sequences Dimensionality-Reduction by K-mer Substring Space Sampling Enables Effective Resemblance- and Containment-Analysis for Large-Scale omics-data | K-mer substring space decomposition | Kssd: K-mer substring space sampling/shuffling Decomposition | Kssd is a command-line tool for large-scale sequences sketching and resemblance- and containment-analysis. It sketches sequences by k-mer substring space sampling/shuffling, please see Methods part of our preprint (https://www.biorxiv.org/content/10.1101/729665v1) for how it works. It handles DNA sequences of both fasta or fastq format, whether gzipped or not. Kssd run on linux system, currently not support for MacOS and Windows OS
Kssdtree is an interactive Python package for phylogenetic analysis based on sketching techniques, designed to address limitations in existing tools. It offers improved performance and unique features like intra-species phylogenomic analysis, and is freely accessible with detailed documentation and a video tutorial.
KTH-package provides a collection of tools designed to make the microarray data analysis easier.
Kidney Transplantation Outcome Predictions (KTOP) allows the prediction of certain outcomes after kidney transplantations from brain-dead deceased donors.
Computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees.
An extra-fast and accurate adapter- and quality-trimmer for sequencing data. There is a bug in multi-file handling in v1.2.0 and previous versions of Ktrim, therefore the author strongly recommend all users update to version 1.2.1 (or later versions).
Integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes. Users’ Manual of kTWAS (Version 1.0.0). The kTWAS program leverages TWAS-like feature selection (Elastic Net weights) followed by a SKAT-like kernel-based score test, to combine advantages from both approaches.
A machine learning-driven framework for kinase inhibitors repositioning.
R package for detailed development of Maxent Ecological Niche Models.
Enabling whole brain parcellation in the presence of large lesions. A workflow to allow Freesurfer recon-all to run on brain images with large lesions. VBG is a bash script tested in Mac OSX, Ubuntu 18.0 and CentOS.
Provides protein-protein interaction (PPI) data. It allows users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, from five primary databases.
A novel approach for validation and completeness of protein orthologous groups. A novel approach for validation and enrichment of protein orthologous groups. KusakiDB is a database of protein orthologous groups (OGs) that:.
Kuura is an automated workflow for analyzing whole exome and whole genome sequencing data. It utilizes Nextflow and Docker for streamlined deployment and reproducibility.
A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.
This program performs rapid in silico genotyping for selected loci (e.g. phylogenetic SNPs, drug resistance mutations) in bacterial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.
The KVFinder software, originally published in 2014, is DEPRECATED. We published more recent software: parKVFinder and pyKVFinder.
KVFinder-web is an open-source web-based application of an updated version of parKVFinder software (v1.2.0) for cavity detection and characterization of any type of biomolecular structure, including but not limited to proteins and nucleic acids. KVFinder-web employs a geometric grid-and-sphere-based method with a dual-probe system for efficient cavity detection. The web-based application provides comprehensive characterizations, including shape, volume, area, depth, constitutional, and hydropathy information.
A web-based application for detecting and characterizing biomolecular cavities.
Develope interactive data exploration applications in genomics and systems biology. Collection of packages in the Go programming language that help application developers i) interface with the R statistical programming language; ii) specify and run statistical analysis pipelines; and iii) interface with online databases such as MsigDB and KEGG.
Parsimonious Reconstruction of Ancestral Recombination Graphs with Recurrent Mutation. Software implementing a parsimony-based heuristic algorithm for reconstructing ancestral recombination graphs (ARGs) with recurrent mutation.
The k-mer weighted inner product (kWIP) is a method for a de novo estimator of genetic similarity without the need of reference genome.
KymoAnalyzer is an open-source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor-based transport.
Method for automated kinematic analysis of rod-shaped plant organs.
Authoring Scalable Scatterplot Visualizations of Big Data. Kyrix - democratizing details-on-demand data visualizations. Kyrix facilitates the creation of data visualizations with details-on-demand interactions (e.g. pan and zoom, see the demo gallery1 above). In visualizations of such, the underlying dataset is often large. To deal with large data, Kyrix is focused on optimizing two goals: 1) usable declarative API library for visualization developers and 2) 500ms response time to user interactions, which is required to enable interactive browsing.
Allows researchers to extract quantitative morphological measurements from neuronal reconstructions. Neuronal reconstructions are typically obtained from brightfield or fluorescence microscopy preparations using applications such as Neurolucida, Eutectic, or Neuron_Morpho, or can be synthesized via computational simulations.
A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data.
Second-Order Ultrasound Elastography With L1-Norm Spatial Regularization.
L1pred is a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier
L2L is a simple but powerful tool for discovering the hidden biological significance in microarray data. Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. A downloadable command-line version can run customized and batch analyses.
Harnessing Multi-View Perspective of Light Fields for Low-Light Imaging. Light Field (LF) offers unique advantages such as post-capture refocusing and depth estimation, but low-light conditions, especially during night, severely limit these capabilities.
Normalized L3-based link prediction in protein-protein interaction networks.
Open source application to generate 2D/3D bioimages of the elemental distribution of the elements present in a set from ICP-MS spectra.
Bioscope Group, University Nova of Lisbon
Data workflow management platform to streamline NGS analyses.
New computational approach for accurate prediction of the calpain substrate cleavage sites from amino acid sequences.
Label3DMaize was applied to achieve semi-automatic point cloud segmentation and annotation of maize shoots at different growth stages, through a series of operations, including stem segmentation, coarse segmentation, fine segmentation, and sample-based segmentation.
Labial temperature and self-reported sexual arousal for films processed
Labial thermistor and potentiometer processing
labManager is an open-source tool designed to provide infrastructure for shared lab facilities, particularly in behavioral sciences, ensuring data safety and compliance with regulations like GDPR. It provides bare metal environments for research projects, simplifying management and providing data isolation.
Lightweight Alignment-Based Reckoning of Alternative Three-prime ends or LABRAT is designed to quantify the usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions.
Versatile databases for genomic sequencing and lab management. LabxDB comes with ready-to-use databases. Data is stored in PostgreSQL. LabxDB provides web-browser GUI and a programmatic API for intregration into pipelines. LabxDB for high-throughput sequencing (HTS) annotation. LabxDB seq organizes sample annotations using a structure of nested levels: from the top-level projects to the bottom level sequencing runs. LabxDB provides forms to easily create sample structure, to annotate and view (as captured by the image on the left) all levels at the same time. LabxDB seq comes with scripts to import HTS data from local sequencing facilities or public resources.
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly.
A free web-based lac operon simulation that enhances student learning of gene regulation concepts.
LaCyTools is an open-source software for LC-MS data analysis, including retention time and m/z calibration, peak integration, and quality control.
Designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals, that covers the maximum number of alleles represented in the database, with all alleles represented only once.
Tools for genomic alignment. These include the MLAGAN multiple alignment tool, and Shuffle-LAGAN for alignment with rearrangements.. All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy.
Link-aware Graph Attention Network for Drug-Drug Interaction Prediction.
This is a plotting tool for Lagrange-NG, which is a tool for inferring ancestral biogeographies. It takes the results JSON file and plots the results as an SVG. The results are plotted as a phylogram with pie charts at the interior nodes displaying the likelihood weight ratio for the top distributions.
The LAGLIDADG Homing Endonuclease Database and Engineering Server (LAHEDES) is a database listing basic properties of LAGLIDADG homing endonucleases (LHEs) with validated biochemical activity and known target site specificity. It also supports web-based searches of DNA sequences (ranging from single or multiple genes to entire genomic reads) for potential target sites that might be recognized either by wild-type or by engineered variants of those endonucleases.
Structure analysis through local annotation of homology-matched amino acids. Local Annotation of Homology Matched Amino acids. Search LAHMA database by PDB identifier.
A search engine which provides an exploration of plant genomic data for forward genetic research and comprises millions of quarterly updated and indexed information from major life science databases as well as millions of evidence ranked gene annotations to associate these facts to plant genome loci.
LAILAPS Search Engine (transPLANT instance)
A machine learning approach for optimizing data searching and filtering from life-science databases. It is integrated in the LAILAPS search engine.
Search engine which provides an exploration of plant genomic data for forward genetic research and comprises millions of quarterly updated and indexed information from major life science databases as well as millions of evidence ranked gene annotations to associate these facts to plant genome loci. This instance serve for index of IPK hosted databases. It comprise search indexes for IPK plant genome databases, molecular databases and germplasm collections.
Tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.
Modelling lake trophic state. Hollister, J. W., W. B . Milstead, B. J. Kreakie. (2016). Modeling Lake Trophic State: A Random Forest Approach. Ecosphere 7:3 10.1002/ecs2.1321. This repository contains all the materials needed to reproduce Hollister et al. (2015) Modeling Lake Trophic State: A Random Forest Approach. These materials are presented as an R Package which contains code used for analyses, code used to develop figures, raw data used for all analysese, and a package vignette that contains the accepted, unformatted version of the manuscript.
Find internal duplications by calculating non-intersecting local sequence alignments.
Automated image analysis for developmental phenotyping of mouse embryos. LAMA (Lightweight Analysis of Morphological Abnormalities). Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images.
Model-based clustering for flow and mass cytometry data with clinical information. An R package of model based clustering for flow and mass cytometry data.
Lambda3 is a local alignment application enabling homology searches for protein, nucleotide, and bisulfite-converted sequences. It offers comparable performance to Diamond for protein alignment and outperforms established nucleotide aligners, offering a universal framework for various use-cases.
Fast and accessible protein-specific phenotype predictions.
Database focusing on the non-collagenous extracellular matrix protein family, the LMs.
A Database Linking Antimicrobial Peptides.
LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins. LAMPA, LArge Multidomain Protein Annotator. This repository contains R package LAMPA presented in LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins by Gulyaeva AA, Sigorskih AI, Ocheredko ES, Samborskiy DV, Gorbalenya AE. Sorry, something went wrong. Reload?. Sorry, we cannot display this file. Collection of Jupyter notebooks that were used for LAMPA paper. Sorry, this file is invalid so it cannot be displayed.
Detect statistically significant epistatic interactions of two or more SNPs from GWAS data. This software can be used in the same way as the widely used GWAS analysis software PLINK, but it has the additional options for the detection of epistatic interactions with LAMP, which is a multiple testing procedure for combinatorial effects discovery.
Manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens.
An analysis pipeline for sequence-specific ligation-mediated amplification reads. Sequence analysis pipeline for 2C-ChIP and 5C products. The 'Ligation-mediated Amplified, Multiplexed Primer-pair Sequence' or LAMPS is is a Linux/MacOS command line interface for analyzing Ligation-Mediated Amplification (LMA) sequences, which may or may not be multiplexed.
A deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq. LanceOtron is a machine learning, genomic data extraction and analysis tool trained for ATAC-seq, ChIP-seq, and DNase-seq peak calling. A freely available and fully-featured webtool version, utilising the graphical user interface MLV and hosted at the MRC WIMM Centre of Computational Biology, University of Oxford, can be found at LanceOtron.molbiol.ox.ac.uk.
Somatic variant analysis of linked-reads sequencing data with Lancet. Lancet is a somatic variant caller (SNVs and indels) for short read data. Lancet uses a localized micro-assembly strategy to detect somatic mutation with high sensitivity and accuracy on a tumor/normal pair. Lancet is based on the colored de Bruijn graph assembly paradigm where tumor and normal reads are jointly analyzed within the same graph. On-the-fly repeat composition analysis and self-tuning k-mer strategy are used together to increase specificity in regions characterized by low complexity sequences. Lancet requires the raw reads to be aligned with BWA (See BWA description for more info). Lancet is implemented in C++.
A deep learning language model for predicting DNase I hypersensitive sites in mouse genome.
Lantern is an integrative repository of functional annotations for lncRNAs in the human genome. It is a genome-scale lncRNA ontology annotation extractor and cellular network repository.
A tool for high-throughput automated cell counting | High-throughput image analysis for automatic cell counting | Inspired by the seer from ancient Greek/Roman mythology, Laocoön, this package synthesizes different packages and methods available in the field of computer vision to create an automatic and efficient means of counting the number of cells in fluorescently stained Fucci cells | The only way that we can get these quantitative analyses is by actually counting the cells | To put it briefly, Fucci cells are stained with certain fluorescent proteins where a certain color corresponds with a certain part of the cell cycle
Liability antibody profiler by sequence & structural mapping of natural and therapeutic antibodies.
Large-scale prediction of adverse drug reactions-related proteins with network embedding.
LAPIS is a fast web API for massive open virus sequencing data.
Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes.
Linear assignment particle tracking with tunable metrics.
“lagrangian relaxed structural alignment” is a tool for the sequence-structure alignment of RNA sequences.
Parallel and vectorized program for sequence-structure alignment of RNA sequences.
An out-of-the-box tool for processing and analyzing large-scale metabolomic data.
An integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
Aligning Gene Expression Patterns from the Larval Brain of Drosophila melanogaster.
Length-Aware Site Alignment Guided by Nucleotide Association algorithm for Transcription Factor Binding Site alignment. Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities.
C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes.
Comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.
A network inference toolbox for genome-wide mechanistic modeling.
Short read alignment program incorporating quality scores
A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.
Software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.
A Latent Gaussian Copula Model for Mixed Data Analysis in Brain Imaging Genetics. This gives the code for the latent Gaussian copula model.
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing.
LatPack is a collection of tools related to the folding simulations of lattice-protein models with arbitrary energy function.
Laue-DIALS is an open-source software pipeline for indexing and integrating polychromatic diffraction data based on DIALS, enabling analysis of data acquired with polychromatic X-ray sources, facilitating time-resolved applications.
Lightweight Association Viewer Across Ailments.
This tool implements a three-step latent vector autoregression method to correct for uncertainty in factor scores when modeling dynamic processes of latent variables. It is available as an R package using the lavaan framework.
An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies.
Tool created for visualizing viral variation from next generation sequencing data.
Molecular surface peeling algorithm and its applications to analyze protein structures.
A tool for visualizing and understanding deep learning models in biological sequence classification using UMAP.
A software suite for layer-fMRI. Revision 1. LayNii_extras (work in progress...). Here are some extra scripts that we use in combination with LayNii.
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data
LBD (Lymphoma Biomarker Database) is a manually curated database of literature-supported biomarkers for lymphoma. It contains 793 biomarkers (715 single biomarkers and 78 combined biomarkers) for different subtypes of lymphoma which have been verified by experiments. The biomarkers are collected from 978 literatures from PubMed and are categorized into molecular (DNA, RNA, protein, chemical), cellular (cells or cell counts), image (imaging technologies or parameters), histopathological (characteristics of individuals' histopathological functioning), physiological (characteristics of individuals' normal functioning) biomarkers. By browsing and searching LBD, users can get access to comprehensive information about lymphoma biomarkers conveniently.
Drug repurposing for COVID-19 via knowledge graph completion and literature-based discovery.
Efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.
LBFextract is a Python package designed for feature extraction from circulating cell-free DNA (cfDNA) data, facilitating the integration of preprocessing and postprocessing steps and enabling biomarker discovery by inferring transcription factor activity. It provides a comprehensive suite of tools to streamline liquid biopsy data analysis.
We developed a method LBtope for predicting linear B-cell epitopes. We developed several models using various techniques (e.g., SVM, IBk)on a large dataset of B-cell epitopes and non-epitopes (12063 epitopes and 20589 non epitopes obtained from IEDB database).
LC-IMS-MS Feature Finder is a command line software application that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time, and ion mobility drift time values.
A local consistency approach for nutrigenomics data analysis. Nutrigenomics aims at understanding the interaction between nutrition and gene information. Due to the complex interactions of nutrients and genes, their relationship exhibits non-linearity. One of the most effective and efficient methods to explore their relationship is the nutritional geometry framework which fits a response surface for the gene expression over two prespecified nutrition variables. However, when the number of nutrients involved is large, it is challenging to find combinations of informative nutrients with respect to a certain gene and to test whether the relationship is stronger than chance. Methods for identifying informative combinations are essential to understanding the relationship between nutrients and genes. Results< h4>We introduce Local Consistency Nutrition to Graphics (LC-N2G), a novel approach for ranking and identifying combinations of nutrients with gene expression
This function takes in images of cells infected with bacteria and quantifies intracellular signals from regions surrounding the pathogen.
Find the lowest common ancestor from a BLAST tabular file.
"This tool identifies the lowest taxonomic rank for which a metagenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input." - Galaxy tool wrapper
An R package to estimate the concordance correlation, Pearson correlation and accuracy over time. lcc is a package under development based on estimation procedures for longitudinal concordance correlation (lcc), longitudinal Pearson correlation (lpc), and longitudinal accuracy (la) through fixed effects and variance components of polynomial mixed-effect regression model. Longitudinal Concordance Correlation. Estimates the longitudinal concordance correlation to access the longitudinal agreement profile.
High-Specificity Identification and Functional Analysis of Low-Complexity Domains in Proteins.
Ensemble learning for COVID-19 multi-label classification.
The Lung Cancer Metabolome Database (LCMD), a freely available online database depositing 2013 lung cancer-related metabolites identified from 65 mass spectrometry-based lung cancer metabolomics studies.
R package using hierarchical mixture models for genomic data integration.
A generic and automatic pre-processing tool for high resolution (HR) LC-MS and GC-MS data.
High-Performance 3D Visualization Software for Mass Spectrometry.
An efficient lossless compression tool of quality scores with random access functionality. This software implements the LCQS algorithm described in: Fu J , Ke B , Dong S . “LCQS: an efficient lossless compression tool of quality scores with random access functionality” [J]. BMC Bioinformatics, 2020, 21(1).
LCRAnnotationsDB is a database storing functional and structural annotations for Low Complexity Regions (LCRs) in proteins. It consolidates knowledge about LCRs, categorizes redundant annotations, and links them to Gene Ontology terms, accessible programmatically via a REST API.
An R package and tutorial on latent change score modelling.
Assessing the low complexity of protein sequences via the low complexity triangle. LCT is a tool that analyzes a protein sequence and portrays its Low Complexity Triangle with information derived from its repeatability. You can read more about the Low Complexity Triangle here. LCT follows the following steps:.
Linear Combinations of Template Conformations (LCTC) is an efficient method to quantify structural distributions in heterogeneous cryo-EM datasets.
Analysis the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2.
The tool enables lipid annotation in high-throughput data derived from chromatography-coupled tandem mass spectrometry.
Discovering patients phenotypes and cell populations within a single Bayesian framework.
ldacov is an R package to estimate an LDA model with covariates using MCMC algorithms.
Latent Dirichlet allocation based generative adversarial networks. Latent Dirichlet Allocation in Generative Adversarial Network. Code for the image generation experiments in Latent Dirichlet Allocation in Generative Adversarial Network.
Fast and powerful gene-based association testing using summary statistics.
LDAK-KVIK is a computationally efficient tool for mixed-model association analysis in genome-wide association studies, designed for analyzing quantitative and binary phenotypes. Published in Nature Genetics, it offers increased statistical power and can be used to generate polygenic scores.
Define data structures for linkage disequilibrium measures in populations.
A fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. LDBlockShow is a fast and effective tool to generate linkage disequilibrium (LD) heatmap from VCF files. It is more time and memory saving than other current tools. LDBlockShow can generate the plots of LD heatmap and interested statistics or annotation results simultaneously. In addition, it also supports subgroup analysis.
Method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome.
An online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data.
LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.
Software program for statistical inference of fine-scale crossover recombination rates from population genetic data.
A parallel computing toolkit for linkage disequilibrium analysis. GUI package is under the GUI folder, please double-click the LDkit_GUI.jar to start. Run using Graphic User Interface (GUI).
Suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.
An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations. LDlinkR - An R Package for Calculating Linkage Disequilibrium.
A rarefaction-based extension of the LDM for testing presence-absence associations in the microbiome. Linear Decomposition Model.
Efficiently queryable compression of linkage disequilibrium matrices.
Program to mapping the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies.
Program of mapping disease genes (including location and confidence interval) by using haplotypes with disease mutation and the haplotypes without disease mutation (or allele frequencies in normal population).
Prediction of long non-coding rna and disease association using network feature similarity and gradient boosting. LDNFSGB:Predicting lncRNA-disease associations using network feature similarity and gradient boosting.
Method for detecting spurious associations using p-values. The strength of the method is its simplicity; it requires no other information but p-values.
Computing polygenic scores using LDpred2. prepare-corr: LD matrices for LDpred2 based on the 10K individuals in the validation set. prepare-genotypes: UKBB Europeans with imputed dosages for HapMap3 variants. This tutorial only uses fake data for educational purposes. You should also probably look at the code of the paper, particularly at the code to prepare summary statistics (including performing the quality control presented in the Methods section “Quality control of summary statistics” of the paper), at the code to read BGEN files into the data format used by bigsnpr, at the code to prepare LD matrices and at the code to run LDpred2 (genome-wide).
Legumes disease resistance genes database.
The Lung Donor Risk Index (LDRI) is a tool to assess the risk of graft failure in lung transplant recipients, developed using a Cox regression model based on donor and transplant factors. An online calculator is available for clinicians to evaluate donor lung offers.
ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
Pairwise Linkage Disequilibrium Estimation for Polyploids. Linkage Disequilibrium Shrinkage Estimation for Polyploids. Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2020) <doi:10.1101/2020.08.03.234476>.
Completely self-contained program written in Fortran90. It is a complete computer program for simulations of whole diploid population histories under various historical scenarios based on the gene-dropping method (MacCluer et al. 1986).
LDWeaver accepts a sequence alignment (fasta) and its reference annotation (genbank or gff) as inputs and identifies linkage disequilibrium (LD) between pairs of variants (links) that is unusually high given the genomic distance between the pair. This high LD could be the result of co-selection or epistasis. Approximate statistical significance is used to rank outlier links and the output is reported in tsv format, along with several other helpful annotations and figures. Additionally, LDWeaver has functions to assist the detection of genomic regions that have potentially undergone co-selection or epistasis.
Linked Region Detection without Pedigree is a software package for linkage analysis that finds the mutation regions for the case where the input individuals are closely related, but the pedigree is not known. It takes the genotype data of the individuals in the dotted rectangle and the diagnoses (diseased or normal) information of each individual in the dotted rectangle as its input, and report the mutation regions.
Quick bioInformatic phylogeny of prokaryotes.
R package for landscape genomics and ecological association tests. It can run analyses of population structure and genome scans for local adaptation. It includes statistical methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations; identifying genetic polymorphisms that exhibit high correlation with an environmental gradient or with variables used as proxies for ecological pressures, and controlling the false discovery rate.
A multimodal platform for deep brain stimulation surgery.
LEADD (Lamarckian Evolutionary Algorithm for de novo Drug Design) is a tool for molecular design and optimization.
An algorithm for outlier splicing detection in rare diseases. Alternative splicing quantification, differential splicing, outlier splicing detection, and splicing QTL mapping. LeafCutter: Annotation-free quantification of RNA splicing.
Using machine learning to automate leaf trait extraction from digitized herbarium specimens. LeafMachine is a GUI that autonomously extracts leaf trait data from herbarium vouchers using CNNs, SVMs, and CV algorithms. There are two GUIs: manual version for fine-scale analyses, batch version for local files or from a list of URLs.
LeafNet is a convenient tool that can robustly localize stomata and segment pavement cells for light-microscope images of leaves
Optimize leaf traits to different environments in silico.
An R Package for Multiomic Pathway Analysis Layered Enrichment Analysis of Pathways in R (leapR) a tool that carries out statistical enrichment analysis on single- or multi-omics data.
Multiple sequence alignment formulated as a statistical machine learning problem, where an optimal profile hidden Markov model for a potentially very large family of protein sequences is searched and an alignment is decoded.
R package for population genetic simulation and numerical analysis.
The LearnCoil Histidase Kinase program uses an iterative learning algorithm to detect possible coiled-coil domains in histidase kinase receptors.
An R package to apply machine learning methods for genomic prediction using multi-environment trial data.
Detect the features based on thesis LEAF RECOGNITION AND MATCHING WITH MATLAB
LEB is a software of biclustering gene expression data, based on Localize-and-Extract Biclusters
The BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.
This package creates a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, NGS peaks and signals and other numerical scores of the sequences using supervised classification. It contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences.
Program for the Bayesian reconstruction of ancient DNA.
lefser is an R package implementing the LEfSe method for identifying microbial biomarkers. It uses statistical tests and linear discriminant analysis to discover differences between microbial communities, and is distributed through Bioconductor with accompanying documentation and installation pathways.
Tool for functional characterization of proteins.
Performs in silico Legionella pneumophila sequence based typing
A Fast and Accurate Graphical User Interface for Automated Detection and Anatomical Localization of Intracranial Electrodes.
LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes.
A database of exclusive proteins from Leishmania parasite. Leishmania Exclusive Protein Database. The Leishmania Exclusive Protein database (Leish-ExP) is a repository of protein sequences specific to five Leishmania species and genus. Leishmania is a parasite known to infect people residing mainly in the tropical regions. Spread by sandflies, usually by Phlebotomus papatasi in the continents of Asia, Africa and Europe, and by sandflies of the genus Lutzomyia sp. in the North and South Americas. They are known to cause a variety of diseases which are included under the umbrella of leishmaniasis. Types of leishmaniasis include visceral leishmaniasis, cutaneous leishmaniasis and muco-cutaneous leishmaniasis.
protein motif scanning 2.0. run scan Need to enter motif alignments before running scan.
A Length-based Multi-species analysis by numerical simulation in R. Length-Based Multispecies Analysis by Numerical Simulation. Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment. LeMaRns is an R package to set up, run and explore the outputs of the Length-based Multi-species model LeMans, focused on the marine environment.
LeMeDISCO is a computational method for large-scale prediction & molecular interpretation of disease comorbidity.
A continuous benchmarking platform for metagenomics classifiers. A Live Evaluation of Computational Methods for Metagenome Investigation. Methods that completely or partially failed the LEMMI evaluation.
Lemon is a tool for mining features used in downstream structural biology software dealing with 3D Macromolecules. It is designed to be fast and flexible, allowing users to quickly query the 3D features of a given collection of 3D structures.
Algorithm to infer a module network from biological data. It can integrate heterogeneous data types such as expression data, copy number, microRNA, epigenetic profiles.
A software package for Learning Module Networks from gene expression data.
Library for the Enumeration of MOdular Natural Structures.
Landscape of effective neoantigens software.
A software to compress Next Generation Sequencing data.
Automated construction of linkage map anchored haploid genomes.
Robust linkage mapping software even for low coverage whole genome sequencing data
Genomics of two major lepidopteran pests.
This package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
A DICOM Anonymization pipeline in a Docker container. This pipeline is designed to anonymize DICOM files according to the EUCAIM standard and includes the following steps: Step 1 (Optional): Perform OCR on DICOM pixel data to remove sensitive information (burned-in information). Step 2: Deidentify DICOM metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script. Step 3 (Optional): Deidentify clinical data provided in CSV files so that the referenced patient id is anonymized the same way CTP does in Step 2.
leukemia cancer detection using mat-lab image processing.
leukemiaBD is a database of blood cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains following two modules for extracting data.
A database for miRNAs and their targets in acute lymphoblastic leukemia. Acute Lymphoblastic Leukemia (ALL) is one of the most common heterogeneous diseases observed in paediatric age group and it differs in both, immunophenotypic and molecular characters.
LEVELNET is a fully-automated and scalable database with a user-friendly web-interface designed to explore and infer either protein interactions or the absence of interactions based on known physical contacts and other annotations, including user-defined ones.
Collection of software tools for analyzing the development of proliferating (dividing) cells in time-lapse microscopy image sequences. It includes algorithms for segmentation, tracking and lineaging. It also includes a user interface that allows the segmentation, tracking and lineaging results to be validated, with any errors in the automated processing easily identified and quickly corrected.
Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images.
Fast lift-over of alternate reference alignments. levioSAM lifts alignments to the reference genome. Use a VCF file containing alternative haplotype information to lift SAM/BAM alignments from that haplotype to the reference sequence.
A system for automatically expanding concept lexicons for noisy biomedical texts.
LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes.
An R package and user interface for the controlled generation of word stimuli. An introduction to the LexOPS package and how to use it. LexOPS is an R package and shiny app for generating controlled word stimuli, for use in Psychology experiments.
LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.
A fundamentally different approach by directly modeling count ratios and reveal that bias also affects fold changes severely.
Unified framework for inferring population genetic structure and gene-environment associations.
Python package for calculation of extracellular potentials from multicompartment neuron models. It relies on the NEURON simulator and uses the Python interface it provides.
New lossless non-reference based fastq compression algorithm.
New analysis tool for label-free LC-MS/MS quantitative proteomics data. It is compatible with high-resolution mass spectrometers (Thermo RAW data) and two popular database search engines (SEQUEST and MASCOT) with target-decoy search strategy.
Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome. New features in 2.0.0: lfspro.mode is added to replace lfspro to account for additional utilities in cancer-specific and multiple primary cancer risk predictions. Simply specify parameter ‘mode’ to call desired functions. TP53 germline mutation carrier estimation and cancer risk predictions.
Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.
The code of Local Gravitation Clustering
Allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between amino acid residue and gene expression level.
Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.
Ligand-gated ion channel database (LGICdb)
An interpretable nonparametric method for inferring covariate effects from longitudinal Data. Longitudinal Gaussian Process Regression. R package for Longitudinal Gaussian Process Regression.
Tool to Align two RNA Secondary Structures Locally.
A web based application for predicting lung health severity.
IANA+ is an efficient framework that integrates and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data.
Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.
LIBFBAT programming library s robust both to genotyping errors and missing genotypes. The underlying method consists in considering an incomplete data model where the true unobserved genotypes produce the observed one through an explicit genotyping error model.
A portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from ground up. Currently, the enhanced suffix array is the only full-text index data structure supported.
bioinformatic pipeline for the design of information-enriched enzyme libraries
Reaction-based Generative Scaffold Decoration for in Silico Library Design.
Isotopic PAttern CAlculation library (MIT license).
A collection of data structures and algorithms. libmaus is a necessary component of Biobambam.
A flex/bison-based Mascot Generic Format (MGF) parser library.
An Open Source Library for Efficient Histopathological Image Processing. libMI is an histopathological image annotating library. LibMI is an histopathological image annotating library. This library is based on another library MMSI which proposes a new open data format for extremely large images. These two libraries are both written in C++, but python bindings are also available.
Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. libmolgrid is under active development, but should be suitable for use by early adopters. libmolgrid is a C++ library with Python bindings that generates tensors from molecular structures that are optimized for machine learning workflows.
Library for analysis of high resolution mass spectrometry data (including THRASH).
C library dealing with point group symmetry in molecules.
libOmexMeta is a library aimed at providing developer-level support for reading, writing, editing and managing semantic annotations for biosimulation models.
Ligand Binding site Recognition Application predicts the presence and identity of active sites and/or ligand binding sites. The software is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites.
A Java GUI component library for displaying and editing multiple sequence alignments and attached data.
Extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML).
A free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications.
A graph-based library for design and data exchange in synthetic biology.
libxtc is an efficient library for reading XTC-compressed MD trajectory data. It is used to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems.
LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution) is a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.
LICHEM is a software package that can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM calculations using multipolar/polarizable force fields.
Permorm Liddell's exact test on matched pairs.
LIden determines allele sharing status among family members using high-density SNP data. It takes SNP genotype data, pedigree structure and physical-locus-file as input, and outputs allele sharing graphical display files and linked regions
3D navigation tool for cells. Molecular Biology is a booming science with enormous scope and potential. In many ways its current status can be compared with the early days of the computer industry: it has the capacity to change the way we approach certain key technologies, such as medicine and manufacturing.
LifeMonitor is a service to support the sustainability and reusability of published computational workflows. It provides: * periodic testing; * test monitoring and notification; * automated checks and templates for workflow best practices.
Liferay, Inc., is an open-source company that provides free documentation and paid professional service to users of its software. Mainly focused on enterprise portal technology, the company has its headquarters in Diamond Bar, California, United States.
LifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.
A web based virtual gallery of biological specimens using X-ray microtomography. Micro-computed tomography or microCT is a method of non-destructive 3D x-ray microscopy, which allows the users to create 3D models of objects from a series of x-ray projection images, similar to the conventional clinical computer tomography.
An accurate gene annotation mapping tool.
LiftoffTools is a toolkit for comparing gene annotations mapped between genome assemblies, enabling the detection and analysis of gene sequence variants, synteny, and gene copy number changes. It leverages Liftoff for annotation transfer and offers modules for analyzing protein-coding genes, gene synteny, and gene copy number.
LiftOn is a homology-based lift-over tool that integrates DNA-DNA and protein-DNA alignments to improve genome annotation accuracy, particularly for eukaryotic species. It enhances annotation by maximizing protein-coding genes and finding additional gene copies.
This service converts genome coordinates and genome annotation files between assemblies.
Deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals.
LigAdvisor is a a versatile and user-friendly web-platform for drug design. Although several tools facilitating in silico drug design are available, their results are usually difficult to integrate with publicly available information or require further processing to be fully exploited. The rational design of multi-target ligands (polypharmacology) and the repositioning of known drugs towards unmet therapeutic needs (drug repurposing) have raised increasing attention in drug discovery, although they usually require careful planning of tailored drug design strategies. Computational tools and data-driven approaches can help to reveal novel valuable opportunities in these contexts, as they enable to efficiently mine publicly available chemical, biological, clinical, and disease-related data
LigAlign: an automated system and structure visualization tool for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.
A novel computational tool for scoring and ranking three-dimensional poses of small molecule ligands bound to RNA 3D structures.
Allows integrative analysis and visualization of multiple lineages over whole time-course profiles.
LigBind is a relation-aware framework with graph-level pre-training to enhance the ligand-specific binding residue predictions for 1159 ligands, which can effectively cover the ligands with a few known binding proteins.
A Multi-Target de novo Drug Design Approach. With the rapid development of systems-based pharmacology and poly-pharmacology, method development for rational design of multi-target drugs has becoming urgent. In this paper, we present the first de novo multi-target drug design program LigBuilder V3, which can be used to design ligands to target multiple receptors, multiple binding sites of one receptor, or various conformations of one receptor.
Spatial graph embedding and molecular descriptors assisted bioactivity prediction of ligand molecules for epidermal growth factor receptor on a cell line-based dataset. Predicting pIC50 and distinguishing hit compounds for ligands against human EGFR based on deep learning.
Jointly defining cell types from multiple single-cell datasets using LIGER. LIGER (Linked Inference of Genomic Experimental Relationships). LIGER (liger) is a package for integrating and analyzing multiple single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.
A tool for filtering docked poses to improve virtual-screening hit rates. LigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON). It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters. Jacob Durrant software July 7, 2020July 10, 2020.
Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.
Deep learning architecture and web server which predicts protein subcellular localization. It is based on protein language models and pre-trained Transformers.
Lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.
Computational prediction model of blood-brain-barrier penetration based on LightGBM. Identification of blood-brain barrier (BBB) permeability of a compound is a major challenge in neurotherapeutic drug discovery. Conventional approaches for BBB permeability measurement are expensive, time-consuming, and labor-intensive. BBB permeability is associated with diverse chemical properties of compounds. However, BBB permeability prediction models have been developed using small datasets and limited features, which are usually not practical due to their low coverage of chemical diversity of compounds.
A program for diagnosing IBD based on human gut microbiome data. The diagnosis of inflammatory bowel disease (IBD) and discrimination between the types of IBD are clinically important.
It is a protein-protein docking framework based on the Glowworm Swarm Optimization algorithm. The framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, and it has support for the use of pre-calculated conformers for both receptor and ligand.
Artificial Intelligence-powered modeling of macromolecular interactions.
Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
LightMyCells is a software resource within the BiaPy library that utilizes self-supervised Vision Transformers to predict fluorescence images from label-free transmitted light inputs, addressing phototoxicity limitations in fluorescence microscopy. It is described as a solution for the Cell Painting problem within the LightMyCells challenge.
Introducing the Library of Guidance for Health Scientists (LIGHTS).
LightStringGraphs (LSG) is an external memory string graph construction tool.
A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. Ligand-similarity-based virtual screening is one of the most applicable computer-aided drug design techniques.
Novel drug-design algorithm which combines structures of known binders to generate similar but structurally distinct compounds that can be tested for binding.
LigninGraphs is an open-source software package in Python to generate feasible lignin structures.
Program which plots schematic diagrams of protein-ligand interactions.
Identifies small molecules likely to bind to given protein.
New computational method for the structural alignment of small molecules.
A automated server for template-based small-molecule docking.
Ligand and structure-based target identification and activity prediction for small molecular compounds.
Sample data and code for the LRT for changes in HEB
Likelihood ratio test for changes in homeolog expression bias
Algorithm and software package for practical identifiability analysis in systems biology. LikelihoodProfiler is a Julia language package for identifiability analysis and confidence intervals evaluation. LikelihoodProfiler is a package for identifiability analysis and confidence intervals evaluation which was originally written in Julia language. See https://github.com/insysbio/LikelihoodProfiler.jl This is the translation of the original Julia code to Python.
An R package for the estimation of excess Life Years Lost among patients with a given disease or condition.
Online framework for the analysis of vascular networks in leaves.
Metagenomic analysis through the extended Burrows-Wheeler transform. LiME is a novel lightweight alignment-free and assembly-free framework for metagenomic classification that is combinatorial by nature and allows us to use little internal memory. In [1], a preliminary version of LiME has been introduced together with a new sequence similarity measure based on the properties of the extended Burrows–Wheeler transform. In [2], we now implement two variants of the above similarity measure and improve the overall classification. In addition, the new version of our tool allows to use multiple processors/cores.
Limelight is an open-source, web-based tool for analyzing, visualizing, and sharing mass spectrometry proteomics data. It supports various data formats from common search engines and enables collaborative interpretation of results.
Trimmed Constrained Mixed Effects Models. Linear Mixed Effects Model with Trimming.
Flexible and efficient linear mixed model library with interfaces to Python.
Data analysis, linear models and differential expression for microarray data.
A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.
Shiny app to determine differentially regulated features in data with few replicates and presence of missing values.
Latent Inceptionism for Targeted Molecule Generation.
Limonada (Lipid Membrane Open Network And Database) is a database dedicated to the simulation of biological membranes. limonada intends to provide an open library of membranes, along with the description of lipids, topologies and forcefields mandatory for their molecular dynamics simulations.
LIMS Tools is an integrated laboratory information and management system (LIMS) for our high-throughput TaqMan?-based SNP genotyping platform. Three new client tools (ProjectManager, AssayManager, OrderTool) for our LIMS improve quality control and workflow management. The programs support organizing multiple genotyping experiments as projects, managing reagents with barcodes, and automation of assay ordering.
A Linear Empirical Scoring Function for Protein-Ligand Docking.
LINADMIX is an algorithm that tests how well a mixture of ancient populations explains the genetics of a modern population.
This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with sets of protein-coding genes predict the biological contexts of lincRNAs according to the 'Guilty by Association' approach.
A deep learning model to identify and assign function to long noncoding RNA (lncRNA).
Deep learning method for lincRNA detection using auto-encoder algorithm.
Interactive web server to query, browse and interrogate LINCS L1000 gene expression signatures.
Database of linking disease-associated SNPs to human large intergenic non-coding RNAs.
Linear models for differential abundance analysis of microbiome compositional data.
A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples. Cell Type Deconvolution using gene expression data for bulk samples.
A lineage analysis algorithm called Label-free IdeNtification of Endogenous informAtive sinGle cell mitochondrial RNA mutation for lineage analysis and clonal Evolution (LINEAGE) by integrating the low cross-entropy subspaces identification with a consensus clustering method.
A comprehensive database that records lineage commitment across species.
It is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells. Expression model fits can be directly extracted from LineagePulse.
Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).
Linear-time approximation of RNA folding partition function and base-pairing probabilities. LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities. This repository contains the C++ source code for the LinearPartition project, the first linear-time partition function and base pair probabilities calculation algorithm/software for RNA secondary structures.
Fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.
Linesink-maker is a tool for rapid construction of streamflow routing networks from hydrography data. Nearfield (highest resultion), mid-field and farfield (least resolution, zero resistance) areas of a desired stream network can be defined by polygon shapefiles. The LinesinkData are then created from NHDPlus hydrography. The number of resulting linesink equations (level of detail) in the various areas of the stream network can be controlled by a distance tolerance parameter specified by geographic area (defined by one of the polygons).
LINflow a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments.
The core of this package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three- generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.
Produces high resolution, publication ready linkage maps and quantitative trait loci maps. Input can be output from 'R/qtl', simple text or comma delimited files. Output is currently a portable document file.
An R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.
Generation of linkage mapping input files for five different linkage mapping tools using as input genotype calls from Affymetrix and Illumina SNP chips or SNP genotypes inferred from sequencing data.
A linked data graph database for integrating immunological data.
LinkEHR is a set of tools that enables the semantic interoperability of your data by: Creating clinical information models (archetypes) Transforming clinical data into standards such as openEHR, HL7 CDA, or ISO 13606
Predicting, explaining and exploring links in large biomedical knowledge graphs.
A set of programs will allow you to analyze the segregation results from pairwise sets of loci in outbred families for possible linkage relationships. The same input data file may be used to analyze linkage relationships among loci using either parent as the mapping parent.
Linkprep create LINKAGE style .pre and .dat files from AGRF style data. This creates standard format input files for linkage analysis software from human genotyping data.
LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.
SNP detection tool with haplotype information from an individual sample.
R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large-scale count data. It transforms such datasets for parametric tests. Also the following pipelines are implemented: 1. Cell subpopluation analysis and visualization using PCA clustering, 2. Differential expression analysis or differential peak detection using limma, 3. Highly variable gene discovery and visualization, 4. Gene correlation network analysis and visualization. 5. Hierarchical clustering and plotting.
A database for cancer-cell-specific perturbations of biological networks.
A lipidomic data processing website aims to provide users a friendly pipeline for statistical analyses and lipidomic data mining.
Conveniently explore, share and present large-scale biological trajectory data from a web browser.
An integrated R package for effective prediction of ncRNA-protein interaction.
Software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA.
Single sample network inference in R. Single sample network reconstruction in R. LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (http: arxiv.org pdf 1505.06440.pdf). Modeling networks for individual samples using LIONESS. LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https: arxiv.org abs 1505.06440)
Flexible Matlab toolbox for fNIRS data analysis.
LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.
LipidCreator is a kick-off tool for targeted lipidomics providing both precursor / fragment mass transition list and a spectral library of MS2 spectra for lipids.
LipidCreator workbench to probe the lipidomic landscape. LipidCreator is a plugin for Skyline supporting targeted workflow development in lipidomics. It can be used to create user-defined target lists and fragment libraries for PRM and MRM experiments in Skyline. It also supports standalone and command-line operation. LipidCreator_HumanPlatelet_application.
Unraveling membrane properties at the organelle-level with LipidDyn.
A tool for high-confidence LC-MS/MS (Liquid Chromatography-Mass Spectrometry) lipid identification.
Advanced informatics pipeline for lipidomics discovery applications. LipidFinder is an open-source Python workflow designed to facilitate further targeted lipidomics analysis. LipidFinder: A computational workflow for discovery of lipids. LipidFinder is an open-source Python workflow which searches a number of different databases to obtain putative identification of lipids, and assigns them to a class based on the LIPID MAPS® classification system.
The LipiDisease tool performs disease enrichment analysis on lipids using biomedical literature data.
A data transfer hub to support integration of large scale lipidomics datasets. The LipidLynxX project is aimed to provide a unified identifier for major lipids, especially oxidized lipids in the epilipidome. LipidLynxX on LIPID MAPS® Lipidomics Gateway. A robust and accurate converter can only be achieved by community-wide collaborations, thus any issue reports from general users and developers are welcome and will improve LipidLynxX project.
Understanding the Lipidome at the Systems Level with lipidomeR. Integrative Visualizations of the Lipidome.
Current state of the art in a fast moving field. Lipidomics-Standards-Initiative (LSI). Regensburg, Lipidomics, LipidomicsRegensburg, LSI, Lipidomics-Standard-Initiative Lipidomics-Regensburg, Gerhard Liebisch, Silke Matysik, Lipid, Lipids, LCMS, GCMS, Mass Spectrometry, Gaschromatography, Analytical Chemistry, High-Resolution-MS. Welcome to the Lipidomics Standard Initiative (LSI)
LipidOne is a freely available and easy-to-use software to discover the deeper features of building blocks in a lipidomic dataset.
A Software Tool for Data Mining and Analysis of Lipidomics Datasets. Data Mining and Analysis of Lipidomics Datasets. lipidr: Data Mining and Analysis of Lipidomics Datasets in R.
LipidSig is a web-based tool for lipidomic data analysis. LipidSig is the first web-based platform which integrates a comprehensive analysis for streamlined data mining of lipidomic datasets. The user-friendly interface provides five main functions, namely Profiling, Differential expression, Machine learning, Correlation and Network, for assessment of lipid effects on biological mechanisms. The five functions provide unique aspects to analyze the lipidome profiling data based on different characteristics including lipid class, chain length, unsaturation, hydroxyl group, and fatty acid composition.', In summary, LipidSig enables users to perform intensive lipid analysis and create interactive plots with downloadable images and corresponding tables.
LipidSuite is an interactive web server for lipidomics differential and enrichment analysis.
An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry.
LipidXplorer is a software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra.
ImageJ Plugin for manual cell lineage tracking.
This tool can analyse polypeptide sequences encoded within the genome of Gram-negative bacteria and report the sequences with a possible lipo-box. The lipo-box is recognised on the basis of given the critera.
A mobile application for identification of rare lipodystrophy syndromes. LIPO-DDx® is a mobile app based on a personal algorithm developed by Prof. David Araújo-Vilar. With the support of the University of Santiago de Compostela, the Galician Health Service (SERGAS) and AELIP (International Association of Relatives and People with Lipodystrophy).
Predictions of lipoproteins and discrimination between lipoprotein signal peptides, other signal peptides and n-terminal membrane helices in Gram-negative bacteria.
Analyses grayscale images of liposomes, and produces different size and shape parameters.
Prediction of Lysine Lipoylation in Proteins based on the Support Vector Machine. A Predictor based on Support Vector Machine for lysine lipoylation in Proteins. The file named Algotithm contains python code for different classification algorithms: KNN, Decision Tree, Logistic Regression, Naive Bayes. The file named Encoding schemes contains code for different encoding schemes: PSSM, BPB, AAindex, BLOSUM62, Binary.
A Python module to manage individual fatty acid moieties from complex lipids. A small Python package to manipulate complex lipids.
A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data. lipydomics is a Python package for performing standard lipidomics analysis protocols on data in an efficient and reproducible fashion.
LiPyphilic is a Python toolkit for the analysis of lipid membrane simulations. LiPyphilic is a set of tools for analysing MD simulations of lipid bilayers. It is an object-oriented Python package built directly on top of MDAnalysis, and makes use of NumPy and SciPy for efficient computation. The analysis classes are designed with the same interface as those of MDAnalysis - so if you know how to use analysis modules in MDAnalysis then learning lipyphilic will be a breeze
Long-read Isoform Quantification and Analysis. A statistical tool to quantify isoform-specific expression using long-read RNA-seq. The input of LIQA is long-read RNA-seq read data in BAM format together with a refrence isoform annotation file.
LiqBioer is a manually curated database that contains multiple types of body fluid cancer biomarkers. LiqBioer can assist clinicians in diagnosis and scientific researchers in selecting the research objectives. LiqBioer will be updated regularly according to the newly available biomarkers and user-submitted data as an interactive website.
Pymol Plugin for Fuzzy Pharmacophore Models
The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.
Detection of epigenetic signatures in liquid biopsies based on whole-genome sequencing data.
Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks. Lesion Image Recognition and Analysis. This software seeks to improve the process of analyzing mouse lung slides for Tuberculosis lesions. By utilizing machine learning algorithms, the application is able to analyze Balb/c and Kramnik mouse lung and produces a CSV file with statistics for the user.
A comprehensive database of long inverted repeats in eukaryotic genomes.
Manually curated online database of experimentally validated functional LIR motifs. LIRcentral contains information about manually curated entries of LIR-motifs that have been experimentally tested for their ability to bind Atg8 homologs, often in a biologically relevant context.
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. LIkelihood Ratio Interpretation of Clinical AbnormaLities. LIRICAL is designed to provide clincially interpretable computational analysis of phenotypic abnormalities (encoded using the Human Phenotype Ontology, optionally combined with an analysis of variants and genotypes if a VCF file is provided with the results of diagnostic gene panel, exome, or genome sequencing.
The Legume Information System enables productive applied and basic research in the legumes by relating data from multiple crop and model species, and by helping researchers traverse among various data types.
Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Web version and documentation is hosted at http://lisa.cistrome.org. For large scale gene set analysis, we recommend user to install local version.
LISE is a web server for a novel method of predicting small molecule binding sites on proteins.
Taxonomy based sorting of deleterious missense mutations across species. LIST-S2: Taxonomy based sorting of pathogenic missense mutations across species. LIST-S2 predicts the deleteriousness of amino acid mutations in protein sequences based on Taxonomy distances.
This service returns the Ontologies registered on the NIF Ontoquest Server.
Shows the information of Annotation file: Number of genes, rRNA, tRNA.
Give a list of input files from different conditions/groups for DESeq analysis, DESeq can then charge these input files from the given list.
A database for the foodborne pathogen Listeria monocytogenes.
Write a list file of the logical OR of two sets of sequences.
LIT is an R package that uses a kernel-based approach to detect latent genetic interactions in genome-wide association studies (GWAS) leveraging information across multiple traits. It accepts standard PLINK files as input and has been applied to obesity-related traits in the UK Biobank.
An Unbiased Data Set for Machine Learning and Virtual Screening. 15 target sets, 9780 actives,and 407839 inactives from high-confidence PubChem Bioassay data. LIT-PCBA: A dataset for virtual screening and machine learninig.
An information resource for the COVID-19 literature.
Revisiting Data Fidelity and Regularization. Over four decades, the majority addresses the problem of optical flow estimation using variational methods. With the advance of machine learning, some recent works have attempted to address the problem using convolutional neural network (CNN) and have showed promising results. FlowNet2 [1], the state-of-the-art CNN, requires over 160M parameters to achieve accurate flow estimation. LiteFlowNet2 is built on the foundation laid by conventional methods and resembles the corresponding roles as data fidelity and regularization in variational methods. We compute optical flow in a spatial-pyramid formulation as SPyNet [2] but through a novel lightweight cascaded flow inference
An HTML5 web application for very fast 3D visualization of molecules and other related data. Very fast even for extremely large protein structures.
LiteQTL is a package that runs whole genome QTL scans near real-time, utilizing the computation power of GPU.
A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. It also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.
Literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, compounds, diseases and phenotypes, and tissues and organs.
Confidence-based visual text analytics tool for exploring literature-enriched pathway models.
LitSuggest is a web-based system for biomedical literature recommendation and curation.
LITT is an algorithm that can be used to integrate whole genome sequencing, clinical, and epidemiological data to identify and rank potential sources for tuberculosis cases.
Continuously running benchmark project for assessing the quality of protein structure prediction and secondary structure prediction methods. It focuses mainly on homology modeling and protein threading but also includes secondary structure prediction, comparing publicly available webserver output to newly deposited protein structures in the Protein Data Bank.
A large-scale dataset for label-free live cell segmentation
Extension to the SciXMiner MATLAB toolbox used for quantitative analysis of chromatin decondensation
A Semi-Automatic Software Program for Segmentation of Layers and Diabetic Macular Edema in Optical Coherence Tomography Images. Department of Electrical and Computer Engineering, Isfahan University of Technology. MISP Research Center, Isfahan University of Medical Sciences.
liver segmentation using levelset algorithm
Efficiently assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick 'single pass' analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. Its approach is kmer-based.
A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals.
LjaFGD is the Lonicera japonica functional genomics database..
An open-source computational pipeline for robust nanobody humanization.
LLMAIx is an open-source pipeline for information extraction from unstructured medical text using privacy-preserving large language models. It enables structured data extraction and anonymization of clinical letters, facilitating clinical research and improving patient outcomes.
Local Label Point Correction for Edge Detection of Overlapping Cervical Cells.
A database of proteins undergoing liquid-liquid phase separation in vitro. LLPSDB contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments.
Tool of predicting drug-target interactions using the node2vec and network path score methods.
A package of user-friendly terminal/command-line and interactive applications developed in Perl, to enable the high-throughput analyses of multiple genes/datasets in PAML (codeml). LMAP was designed for the workstation multi-core environment and enables all the codeml codon substitutions models: site models, branch models, branch-site models and clade models.
A user-friendly pipeline software package developed in Perl, to enable multiple genes/datasets high-throughput estimations of multiple sequence alignment (MSA) and phylogenetic trees (PT). Additionally, LMAP_S makes possible uncovering optimal estimations of both MSA and phylogenies. LMAP_S was designed for the workstation multi-core environment and integrates over 30 scientific software, for which provides easy installation. The LMAP_S package additionally includes our RYcode.pl application for purine/pyrimidine DNA/RNA (re-)coding.
Evaluating metagenomic short de novo assembly methods through defined communities.
Bioinformatic pipeline that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis.
Local manifold distance accurately measures beta diversity in ecological gradients.
Linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.
Fit linear and generalized linear mixed-effects models. Models and their components are represented using S4 classes and methods.
Linear mixed models with flexible covariance structure for genetic studies of related individuals.
An R package for analyzing transformed RNA-Seq data with linear mixed effects models.
Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning.
A package for analysis of microarray data using a linear model and glog data transformation.
LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.
Linear mixed-effects modeling to improve clinical metabolomics information.
LMME (Large Metabolic Model Explorer) is an add-on for the open-source software Visualisation and Analysis of Networks conTaining Experimental Data. (VANTED). It facilitates the exploration of large metabolic models by decomposing the large network into meaningful subsystems and by providing analytic techniques that may be applied successively.
LmRaC is an LLM-based tool designed to interrogate user experimental results by building domain-specific knowledge bases from PubMed sources and supporting quantitative experimental data through a customizable REST API.
Construction, validation and, visualization of a web-based nomogram for predicting the overall survival and cancer-specific survival of leiomyosarcoma patients with lung metastasis.
A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer. A modular approach to identify lncRNA related miRNA sponge modules in breast cancer. Until now, existing methods for identifying lncRNA related miRNA sponge modules mainly rely on lncRNA related miRNA sponge interaction networks, which may not provide a full picture of miRNA sponging activities in biological conditions. Hence there is a strong need of new computational methods to identify lncRNA related miRNA sponge modules. In this work, we propose a framework, LMSM, to identify LncRNA related MiRNA Sponge Modules from heterogeneous data. To understand the miRNA sponging activities in biological conditions, LMSM uses gene expression data to evaluate the influence of the shared miRNAs on the clustered sponge lncRNAs and mRNAs.
Novel Methodological Approach to Place Mouse Ultrasonic Vocalizations in Their Behavioral Contexts.
A Listeria monocytogenes fast-tracing platform for global surveillance.
Collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis, secondary structure prediction, and probe design for expression arrays, real time PCR, and SNP genotyping.
An updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. lncRNA and cancer association database. Lnc2Cancer, is a manually curated database that provides comprehensive experimentally supported associations between lncRNA or circRNA and human cancer.
An updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.
An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information.
A machine learning-based tool for long non-coding RNA detection from RNA-Seq data.
Novel computational method and tool to predict the associations between lncRNAs and diseases.
A comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution.
automated identification and conservation study of long noncoding RNAs.
An expression database of human long non-coding RNAs. Expression Database of Human Long non-coding RNAs. LncExpDB is a comprehensive database for lncRNA expression. It covers expression profiles of lncRNA genes across various biological contexts, predicts potential functional lncRNAs and their interacting partners, and thus provides essential guidance on experimental design.
A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.
A versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data.
Aggregated and inferred knowledge about human and mouse lncRNAs.
Lncident is a tool for rapid identification of long noncoding RNAs utilizing sequence intrinsic composition and open reading frame information.
LncInfo - A Comprehensive Resource For LncRNA Database And Subcellular Localization
A comprehensive compendium of human long non-coding RNA.
Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism.
A machine learning algorithm for long noncoding RNA annotation in plants. LncRNA prediction tool for plants. lncMachine requires python3 or newer.
Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer. Increasing lncRNA-associated competing triplets were found to play important roles in cancers.
Manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases.
A genome-wide lncRNAs regulated phenotypes database in plants.
A manually curated database for experimentally supported lncRNAs during various cancer metastatic events. A database for experimentally supported lncRNAs during various cancer metastatic events.
An updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients.
FANTOM-ZENBU provides an annotation of nuclear long non-coding RNAs based on chromatin interactions and Hi-C data, identifying potential target genes and regulatory factors. The results are accessible through an interactive visualization web portal.
New tool that calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames, translation scores based on ribosomal coverage, and conservation against characterized protein families.
An alignment-free predictor for long non-coding RNAs identification by multimodal deep learning. lncRNA_Mdeep is a computational tool for distinguishing lncRNAs from protein-coding transcripts. It efficiently incorporates the hand-crafted features and raw sequence information by a multimodal deep learning framework to predict the probability whether a transcript is lncRNA or not. LncRNA_Mdeep achieves a good performance on human dataset and multiple cross-species datasets.
Database containing a comprehensive list of long noncoding RNAs (lncRNAs) that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information.
Database of long non-coding RNA-associated diseases.
A knowledgebase of lncRNA function in human cancer.
Knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. Scripts for analyzing data displayed and deposited on the long non-coding RNA knowledgebase (lncRNAKB). LncRNAKB is an invaluable resource to understand the biological importance of long non-coding RNA (lncRNA) in tissue-specificity and disease association.
rms is an R package providing functions for regression modeling, testing, estimation, validation, and graphics. It assists in streamlining modeling design by storing enhanced model attributes and facilitates risk prediction.
An database for functional variants in long non-coding RNAs.
This tool aims to be the lncRNA (long non-coding RNA) portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were collected from TCGA, GEO, ENCODE, and modENCODE (Organism: Human, Mouse, Fly, Worm, and Yeast).
A web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs
LncRTPred is a target prediction tool to predict the interaction between lncRNA and mRNA for both Human and Mouse species.
A platform for long non-coding RNA related sets and enrichment analysis. Welcome to LncSEA a comprehensive human lncRNA sets resource and enrichment analysis platform.
LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms and tissue-specific therapeutic targets, especially the tissue elevated lncRNAs (TE lncRNAs), which expressed higher in a certain tissue or groups, and either not expressed or expressed at lower levels in other tissues.
Efficient tool for predicting RNA targets of lncRNAs (Long noncoding RNAs)
LNDb v4 is a resource providing pulmonary nodule annotations derived from medical reports linked to manually annotated lung scans. It aims to facilitate research into lung cancer diagnosis by connecting textual reports with annotated data.
LNetReduce is a tool for reducing linear dynamic networks with separated time scales. Dynamic networks, represented as digraphs labeled by integer timescale orders, can describe deterministic or stochastic monomolecular chemical reaction networks but also random walks on weighted protein-protein interaction networks, spreading of infectious diseases and opinion in social networks, communication in computer networks.
Efficient and effective method for constructing phylogenetic networks. It takes as input a set of rooted phylogenetic trees given in Newick format (inputfile shows an example of input data).
Live-Neighbor-Joining, a heuristic for building a live phylogeny. We presented Live Neighbor-Joining, that extends the rationale of Neighbor-Joining by introducing the case where the creation of a live internal node results in a smaller sum of branch lengths. Thus, at each step of Live Neighbor-Joining, two options may apply: one as in Neighbor-Joining and another admitting a live internal node.
A new converter from Linkage-style to Morgan ver 3 style data files.
The LnLCorr package is designed to detect pairwise coevolutionary among residues in a set of proteins using likelihood ratio tests.
Early distinction of lymph node metastasis in patients with soft tissue sarcoma and individualized survival prediction using the online available nomograms.
The web server LnSignal (Labelling N-terminal Signal petide cleavage site) was developed by integrating position-specific amino acid propensities based on the highest average positions and conditional random fields.
Load several FASTQ files from different conditions.
Loop modelling server for protein structures.
Multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. It applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA.
lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data
Database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.
Perform reciprocal blast against two databases to find RBH Orthologs
New algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data.
Fast and scalable local network alignment tool for the identification of functionally conserved modules in multiple networks.
Enables rapid and high-throughput analyses of a wide range of physico-chemical properties encoded by intrinsically disordered protein and region sequences.
Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence
This code is the detects abnormal region in retinal images using morphological operations
Localization of Hard Exudates in Retinal Fundus Images
Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.
Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Through a sequence of local moves, e.g. local backbone modifications, it walks through the conformational space, looking for a configuration as close as possible to the input 3D model, while keeping his points on-lattice. After a user-defined condition is triggered, the experiment stops and the currently best model can be retrieved as a PDB file.
A software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
A local stack-based RNA 3D structural alignment tool. LocalSTAR3D is a program for the local alignment of RNA 3D structures.
A local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar.
Local Z Projector is an ImageJ2 plugin to perform local-Z projection of a 3D stack, possibly over time, possibly very large.
A python library for analyzing single-molecule localization microscopy data.
Structure-based multiple alignment of RNAs.
Probabilistic structure-based multiple alignment of RNAs.
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.
Subcellular localization of long non-coding RNAs using nucleotide compositions. Predict the SubCellular Location of lncRNAs by using Nucleotide Compositions. The system will take one RNA sequence at a time.
LOCATER is an R package for testing tree structures (represented via discrete clades or relatedness matrices) for association with traits. It leverages genealogy-based methods to improve trait association power, especially in regions with allelic heterogeneity.
Manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Each database entry contains the experimentally derived localization in Gene Ontology (GO) terminology, the experimental annotation of localization, localization predictions by state-of-the-art methods and, where available, the type of experimental information.
locfdr is an R library for computeing Local False Discovery Rates.
LocHap is an ultra-fast computational pipeline for calling local haplotype variant using deep DNA-sequencing data to reveal cellular heterogeneity and somatic mosaicism.
loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.
Vector based protein structure superposition algorithm capable of recognizing distant structural similarities. Statistical significance values for alignments are provided.
Support Vector Machine (SVM) predictor that locates classical nuclear export signals (NESs) in CRM1 cargoes. Export-Karyopherinβ CRM1 recognizes hundreds of broadly functioning proteins. Most CRM1 cargoes contain the classical NES (also known as leucine-rich NESs), a peptide with 8-15 amino acids, regularly spaced with conserved hydrophobic residues.
Sequence-based genome size estimator for plants.
Designed to LOCate putative Pilus operons in Gram-positive prokaryotes. This is done in two steps: First, pilus-related sequences are identified by hmmsearch with a carefully selected set of profile Hidden Markov Models. Second, chromosome regions with statistically significant clustering of hits are located using hypergeometrical distribution and Monte Carlo simulations.
Tool for local structure prediction from protein sequence using a structural alphabet approach.
Produces piecewise polynomial models for one-dimensional signals of the type encountered in genomics.
Tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.
Framework to predict localization in life's three domains, including globular and membrane proteins (3 classes for archaea; 6 for bacteria and 18 for eukaryota). The resulting method, works well even for protein fragments. It uses a hierarchical system of support vector machines that imitates the cascading mechanism of cellular sorting.The method also accurately distinguishes membrane and non-membrane proteins.
Alexander von Humboldt Foundation through German Federal Ministry for Education and Research
Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea.
Locuaz is a computational platform for optimizing protein binders, enabling mutation selection, molecular dynamics simulations, and prioritization for in silico high-throughput screening. It supports parallel exploration of mutation streams and is highly customizable, with documentation and source code available on GitHub and Read the Docs.
LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a dynamic-programming algorithm for finding the optimal set of splice sites in a genomic region of interest with estimated prior length information.
A data visualization and exploration tool for genetic association data.
A web-based colocalization tool for the annotation and functional follow-up of GWAS. Explore GWAS Results with GTEx's eQTL Association Results. A Colocalization Tool to Prioritize Genes and Tissues from GWAS and eQTL Integration.
Computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci.
Interactive and embeddable visualization of genetic association study results. LocusZoom is a Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. To see functional examples of plots generated with LocusZoom.js see statgen.github.io/locuszoom and statgen.github.io/locuszoom/#examples. A Javascript/d3 embeddable plugin for interactively visualizing and navigating statistical genetic data from customizable sources. See github.com/statgen/locuszoom/wiki for full documentation and API reference. Shown here is a standard interactive LocusZoom plot, depicting GWAS association data with gene tracks loaded from a University of Michigan API. The LocusZoom.js library provides several pre-defined layouts for entire plots and subdivisions of plots such as panels, data layers, tool tips, etc.
Software package for genome-wide association anal-ysis of biomarkers with a limit of detection.
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
The Loss-of-Function ToolKit (LoFTK) allows efficient and automated prediction of LoF variants from both genotyped and sequenced genomes, identifying genes that are inactive in one or two copies, and providing summary statistics for downstream analyses.
Can be applied to relatively very large numbers (Total<100000)
Fast Algorithm for the Log P-value of Fisher s Exact Test or Hypergeometric Distribution
Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.
Probabilistic continuous logics in reconstructing gene regulatory networks.
Deontic logics, logic combinations and expressive ethical and legal reasoning (Isabelle/HOL dataset). LogiKEy Workbench (dataset of formalized knowledge): Flexible, Pluralistic Foundations for Legal and Ethical Reasoning, Metaphysics and Maths.
A database dedicated to long-range genome interactions quality assessment.
This library implements the Logit-t algorithm for use with Affymetrix data stored in an AffyBatch object in R.
Coronavirus Tracker - Log Live-Map of Spread
Logistic Multiple Network-constrained Regression.
Fit disruption replenishment time-intensity data with the lognormal perfusion model
Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution.
LogoBar is a Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments that show the amino acid incidence at every position.
Web based application designed to make the generation of sequence logos from biological sequence alignments simple.
A Javascript package for creating sequence logos and embedding them in web applications. Embeddable, customizable, and interactive sequence logos, all in Javascript. Create Logos: paste or upload data in common formats.
Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).
Produces logo plots highlighting both enrichment and depletion of characters, allows for plotting of string symbols, and performs scaling of position-weights adaptively, along with several fun stylizations.
A comprehensive database of transcription factor binding site profiles in Actinobacteria.
LOICA (Logical Operators for Integrated Cell Algorithms), Python package for designing, modeling and characterizing genetic networks.
Various optimization methods for Lasso inference with matrix warpper.
Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.
Interactive genomic locus overlap enrichment analysis.
Tool for Deconvolution for Wastewater Genomics - The LolliPop package comprises a python module and an optional set of command-line tools using it to build curves of viral variants over time within environmental sample. It runs a kernel-based deconvolution and leverages the time series nature of the samples.
Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes.
GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry.
Long-read-tools is an interactive database of software tools for the analysis of long read sequencing data.
Defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. LongAGE is a memory-efficient implementation of AGE (https://github.com/abyzovlab/AGE). Its memory footprint is less than hundreds of megabytes, while it is at most four times slower than AGE in terms of running time.
R package for covariate-sensitive longitudinal analysis of high-dimensional data.
A data hub for long genes. Long genes harbor specific genomic and epigenomic features and have been implicated in many human diseases. LongGeneDB is an interactive, visual database containing genomic information of 992 long genes (>200 kb) in 15 species.
Computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing.
Mixed-model-based approach for performing association mapping which utilizes multiple phenotype measurements for each individual.
LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies.
The LongITools toolbox is an open-source platform developed to support exposome research analysis. This cloud-based computational environment enables researchers to construct customized analytical platforms suited to their specific research requirements. The system provides a web-based interface that integrates various analytical resources, including statistical tools, computational pipelines, connections to external data repositories, and data visualization capabilities.
longmixr is an R package for robust consensus clustering of longitudinal data using finite mixture modeling techniques. It allows clustering of mixed data types and is documented with detailed examples and installation instructions.
Gene Length-Dependent Expression Analysis Tool in Neuronal Cells.
Long Ranger is a set of five analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF.
A genome assembly correction and scaffolding pipeline using long reads.
Automated Analysis of Long Read Spliced Alignment Accuracy.
AJAX-based browser for visualising deep sequencing data.
The Loop Catalog is a database of curated HiChIP data from published work, featuring over 1000 human and mouse samples and embedded analysis modules. It facilitates research areas like variant prioritization and SNP-to-gene linking.
Comprehensive feedback loop detection in ordinary differential equation models. Comprehensive Feedback Loop Detection in ODE Models. Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. LoopDetect - comprehensive detection of feedback loops in ODE models.
A web tool for transplanting dynamical loops for protein engineering.
Method based on the Random Forest automatic learning technique, designed to select structural templates for protein loops among a dataset of candidates.
LooplessFluxSampler is a toolbox for exploring the loopless mass-balanced flux solution space of metabolic models, based on an Adaptive Directions Sampling on a Box (ADSB) algorithm. It aims to provide efficient and reliable results for statistical inference in metabolic modeling.
A uLoop Assembly Clone Verification Tool for Nanopore Sequencing Reads. Cloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life. Cloning can be difficult and time consuming as each plasmid is unique to a particular project and each sequence must be carefully selected, cloned and sequenced to determine correctness. Loop assembly (uLOOP) is a recursive, Golden Gate-like assembly method that allows rapid cloning of domesticated DNA fragments to robustly refactor novel pathways. With uLOOP methodologies, one can clone several sequences directionally to generate a library of transcriptional units (TUs) in plasmids within a single reaction but analysis of the plasmid population has been impeded by current sequencing and analysis methods
Assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool.
Lipid over-representation analysis based on structural information.
LORD (linking opendata for rare diseases) - tool for browsing information about rare diseases. It aggregates the information from Orphanet, HPO and OMIM database.
Sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.
Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.
LoReTTA (Long Read Template Targeted Assembler) is a reference assisted de novo assembler specifically designed to deal with PacBio reads generated from viral genomes. It is a user-friendly tool for assembling viral genomes from PacBio sequence data.
Tools for M. tuberculosis DNA fingerprinting (spoligotyping)
LOw-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations.
On the stability of log-rank test under labeling errors.
LOT (Linkage analysis of Ordinal Traits) is a software program that performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait.
LOTUS is a comprehensive collection of documented structure-organism pairs. Within the frame of current computational approaches in Natural Products research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.
LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.
Detection and analysis of Lou Gehrig's disease by using Watershed Techniques as well as clustering.
Lou Gehrig s disease detection by using Watershed Technique
The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.
LoVis4u is a command-line tool and Python API for fast and customizable visualization of genomic loci, generating publication-ready vector images based on GenBank or GFF files. It is designed for comparative genomic analysis and can be used to highlight accessory and core genes.
Tool that searches for low complexity regions of DNA or protein sequences. Using it you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.
Moment Estimators of Relatedness From Low-Depth Whole-Genome Sequencing Data.
This package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or PFAM domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or PFAM domains of your interest.
Program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.
Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. The system LP-HCLUS and all the necessary files(lphclus.zip).
Allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user.
The Longitudinal Pediatric Data Resource (LPDR) is used for facilitating longitudinal collection of health information to inform clinical care and guide newborn screening efforts.
Used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. It is primarily used for analyzing data between two conditions. To use it for paired data, see library. For using it in multiple conditions, use HEM library.
Two options are added to the LPE algorithm, which original version sets all variances below the max variance in the ordered distribution of variances to the maximum variance. In the present version, this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default, the tool uses the sample size based variance adjustment.
Framework for exploring the wing color pattern formation of ladybird beetles in Python.
Prediction of lncRNA-protein interactions by using convolutional neural network with the copy-padding trick. LPI-CNNCP designs a copy-padding trick to turn the protein/RNA sequences with variable-length into the fixed-length sequences, letting them meet the input requirements of CNN model. Then, the high-order one-hot encoding way is used to transform the protein/RNA sequences into image-like inputs of non-independent for capturing the dependencies among amino acids (or nucleotides). In the end, these encoded protein/RNA sequences are feed into a convolutional neural network to predict the lncRNA-protein interactions.
A computational method LPI-CSFFR to predict lncRNA-protein interactions from sequences, secondary structure, and physicochemical property, which makes use of deep learning CNN and further improve its performance using feature reuse strategy.
Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions. This model is proposed to predict lncRNA-protein interactions, which can be summarized in four steps:.
Web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank.
A webserver for lncRNA-protein interaction extraction from the literature.
LPMX, i.e, Local Package Manager X, is a pure rootless composable container system. It helps researchers run genome analysis tools via existing Docker or Singularity (experimental) images without root/sudo privilege required. Besides, researchers can benefit from composability, e.g. allowing one to write a pipeline consisting tools from different containers.
This tool aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.
Linear-time program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model.In more population genetic terms, LPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets.
The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes and much more.
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus, the intention is to provide an easy to install interface to SYMPHONY.
The LPTD is an automatic topology determination method for intermediate resolution cryo-EM maps.
Lag penalized weighted correlation for time series clustering. Lag Penalized Weighted Correlation (LPWC) is a method for clustering short time series data. It is designed to identify groups of biological entities (for example, genes or phosphosites) that exhibit the same pattern of activity changes over time. LPWC allows lags to incorporate delayed responses in the biological data. For example, two genes may have similar expression changes over time, but one initiates those changes 5 minutes after the other. LPWC also supports irregular time intervals between time points collected in biological data. The LPWC website is available here.
Adapting Lot Quality Assurance Sampling to accommodate imperfect tests. This repository provides code that accompanies the Adapting Lot Quality Assurance Sampling (LQAS) to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti paper. The goal is to classify an area as “high” or “low” on some trait of interest. In our paper, we were interested in classifying hospitals as having high or low COVID-19 antibody prevalence among healthcare workers in Haiti. In the traditional form of LQAS, the sample size, n, and decision rule, d, are determined by the population size, N, and four parameters defined by users based on the specific context and goals.
the Long Read Aligner for Sequences and Contigs. LRA, the long read aligner for sequences and assembly contigs LRA is a sequence alignment program that aligns long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. LRA implements seed chaining sparse dynamic programming with a convex gap function to read and assembly alignment, which is also extended to allow for inversion cases. Through the Truvari analysis of LRA, Minimap2 and NGM-LR alignments. LRA achieves higher f1 score over HG002 HiFi, CLR and ONT datasets. Home: https://github.com/ChaissonLab/LRA. Long read aligner for sequences and contigs.
New method to discover molecular subtypes by detecting the low-dimensional intrinsic space of high-dimensional cancer multi-omics data.
Binning long reads in metagenomics datasets using composition and coverage information.
A computational method based on a combination of physicochemical and structural properties to predict the B-cell epitopes.
An R package and Shiny application for processing lexical data.
LRE analysis (Rutledge R.G. BMC Biotech 2008) on raw data from a real time PCR machine
LRensemble (LR Ensemble Localization Predictor) predicts 4 major locations for Yeast Proteins: Cytosol, Mitochondrion, Nucleus, Secretory. The prediction method is to build an ensemble over different available localization predictors. In the current version, our predict collects prediction results from up to 6 predictors and Logistic Regression is used as the ensemble algorithm.
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.
Predicting Associations between ncRNA and Drug Resistance via Linear Residual Graph Convolution.
Tool for the LRI prediction in full viral genomes based on a multiple genome alignment.
LRLoop is a full-featured R package for analyzing LR-Loops from bulk & single-cell RNA-seq data.
LRMotifs is a novel method of DNA sequence motif discovery based on logistic regression and rigorous hypothesis testing.
An Overlap Detection Algorithm for Long Reads Based on k-mer Distribution. LROD can detect overlap regions among long reads.
LRpath performs gene set enrichment testing using logistic regression, and allows the data to remain on a continuous scale.
Method that determines binding sites of small compounds (ligands) on the surface of proteinsExtraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.
An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors.
Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. scTCR-seq data compliments the scRNA-seq data in the sense that it provides the clonotype information for each cell, and it is generally assumed that cells sharing the same clonotype share the same progenitor. By integrating scTCR-seq data with scRNA-seq data, we could have a detailed insight of transcriptional changes that occur as clonal related cells differentiate. The LRT package utilizes the complementary nature of these two data type and investigate clonal differentiation heterogeneity by integrative analysis of scTCR-seq data and scRNA-seq data.
Linked-Read ToolKit (LRTK), is a unified and versatile toolkit to process human and metagenomic linked-read sequencing data from different linked-read sequencing technologies, including 10x Genomics, single-tube long fragment read (stLFR) and transposase enzyme linked long-read sequencing (TELL-Seq). LRTK provides functions to simulate linked-read sequencing data, perform barcode correction, barcode-aware alignment and metagenome assembly, reconstruction of virtual DNA fragments, and barcode-assisted genomic variant detection and phasing. LRTK also has the ability to perform automatic analysis from raw sequencing data to downstream analysis and support the analysis of multiple samples in parallel. In addition, LRTK could produce publication-ready visualizations and generate reproducible reports, summarizing the key parameters at multiple checkpoints such as library preparation.
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks.
Web tool for genome-wide annotation of human SNPs. The current version provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features, inferred from three-dimensional experimental structures.
A hybrid neural network incorporating double-layer LSTM and self-attention mechanism for the prediction of N4-acetylcytidine sites in human mRNA.
Accurately Resolving People in Dense Crowds via Detection. This repository is the pytorch implementation for the crowd counting model, LSC-CNN, proposed in the paper - Locate, Size and Count: Accurately Resolving People in Dense Crowds via Detection.
This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf senescence or morphological phenotypes. Users can browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases.
Fast dating using least-squares criteria and algorithms
LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press
This tool superposes macromolecular electron densities and computes a structural similarity score. Its computations scale linearly with the size of the molecules being compared.
Comprehensive drug discovery and genomic research workbench, knowledgebase and data management system.
Read image data from Zeiss Laser Scanning Confocal Microscope LSM files.
Zeiss Laser Scanning Confocal Microscope LSM file reader
MATLAB functions for reading info databases of Zeiss LSM confocal microscope files.
Scaling multimodal data integration for single-cell genomics data analysis.
LSNMF (Least Squared Non-negative Matrix Factorization) is a modified version of NMF (non-negative matrix factorization), it focus on gene expression patterns analysis on microarray datasets. The major improvement of LSNMF algorithm over NMF is that it incorporate uncertainty estimates into the update rules, so it is much more stable over the possible noise in the datasets, and it also more sensitive to the real signals.
Tool for leaderless secretory protein prediction in plants.
LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.
LSR (Longest Run Test) is an S-plus program computes the distribution and the first moment of the length of the longest k-interrupted run (Lk) in a binary sequence.
LSTM-PHV is a web application for the prediction of human-virus protein-protein interactions by LSTM with word2vec.
Large-scale transcriptome analysis pipeline.
A User-friendly Cloud Computing Pipeline to Infer Co-functional and Regulatory Networks. Large-Scale Transcriptome Analysis Pipeline on Cloud. If you use LSTrAP-Cloud in your research, please cite:. This repository is built upon wirriamm/CoNeGC. LSTrAP-Cloud is a pipeline designed for building co-expression networks from RNA-seq data (fastq files from ENA) on Goolge Colaboratory (Colab). Leveraging on the user-friendliness of the Colab interface, LSTrAP-Cloud allows users to analyse large scale transcriptome data without having to access the linux terminal, making it accessible to both bioinformaticians and biologist. To get started, we have provided a tutorial based on example data found here. While the pipeline was designed for plants, we have also made the script compatible with non-plant organisms.
An automated pipeline to generate annotated gene expression atlases for kingdoms of life. By NTU Plants Systems Biology and Evolution Laboratory.
LTM is an in silico screen to infer genetic influences on circadian clock function. LTM uses natural variation in gene expression data and directly links gene expression variation to clock strength independent of longitudinal data.
A comprehensive database for the linking of Traditional Chinese Medicine with modern medicine at molecular and phenotypic levels.
A transfer learning based end-to-end method for RNA secondary structure prediction.
Parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons | A parallel wrapper for LTR_FINDER | ~ ~ ~ Run LTR_FINDER in parallel ~ ~ ~ | This is a Perl wrapper for LTR_FINEDR. All rights reserved to the original author. It's free for non-commercial use. For commercial use, a software agreement is required for LTR_FINDER. LTR_FINDER_parallel is released under open source license CC BY 4.0
LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
New data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format.
Efficient tool to characterize structurally complex LTR retrotransposons and nested insertions on genomes.
Software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power.
R package implementing the methods for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions.
LuceGene is an open-source document/object search and retrieval system specially tuned for bioinformatics text databases and documents. LuceGene is similar in concept to the widely used, commercially successful, bioinformatics program SRS (Sequence Retrieval System).
Premade MSCV-based, VSV-G pseudotyped retroviral particles that contain luciferase reporter gene.
Site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.
A program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.
Metagenome SNP Calling via Read Colored de Bruijn Graphs. LueVari is a reference free metagenome SNP caller, based on the read-colored de Bruijn graph. LuVari is an extension of VARI (https://github.com/cosmo-team/cosmo/tree/VARI), in which the reads are stored as colors to allow the read-coherent traversal of de Bruijn graph.
LukProt is a database containing protein sequences from a variety of eukaryotic organisms, with a focus on undersampled animal taxa. It provides a resource for investigating animal evolution and is accessible via a BLAST server.
This package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
An Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites.
Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data. LUMINATE (longitudinal microbiome inference and zero detection) includes four programs for inference in longitudinal microbiome datasets:. Note: Estimates of cLV parameters with LUMINATE is considered experimental. To train model parameters using pseudo-counts instead of denoised estimates, pass the --use-pseudo-counts flag instead.
lumbar multifidus muscle segmentation from ultrasound images. LUMINOUS Database: Lumbar MUltifidus Muscle SegmentatIoN FrOm UltraSound.
A novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. We show that LUMPY yields improved sensitivity, especially when SV signal is reduced owing to either low coverage data or low intra-sample variant allele frequency.
Prioritizing virtual screening with interpretable interaction fingerprints.
Development and validation of the lung donor (LUNDON) acceptability score for pulmonary transplantation.
Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Kaplan Meier-plotter [Lung cancer]. Our aim was to develop an online Kaplan-Meier plotter which can be used to assess the effect of the genes on breast cancer prognosis. Notice: Use of undefined constant filterByMrna - assumed 'filterByMrna' in /var/www/kaplanmeier/analysis/index.php on line 94 Breast cancerOvarian cancerLung cancerGastric cancer Notice: Use of undefined constant filterByRnaseq - assumed 'filterByRnaseq' in /var/www/kaplanmeier/analysis/index.php on line 97 Liver cancerPan-cancer Notice: Use of undefined constant filterByMirna - assumed 'filterByMirna' in /var/www/kaplanmeier/analysis/index.php on line 100 Breast cancerLiver cancerPan-cancer Notice: Use of undefined constant filterByProtein - assumed 'filterByProtein' in /var/www/kaplanmeier/analysis/index.php on line 103 Breast cancer.
LungDWM is used for lung cancer subtype diagnosis using weakly paired multiomics data. LungDWM leverages attention-based feature encoders to extract the shared and specific features of multiomics data, imputes missing omics data from available ones through generative adversarial learning and makes the subtype diagnosis by fusing real and imputed data.
Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables.
Customizable tool for calling genome-wide germline and somatic short tandem repeat variants.
"De novo" peptide sequencing from MS/MS data.
Software for the de novo interpretation of peptide CID spectra.High quality tandem mass spectra of peptides are often obtained for which no exact database match can be made. Consequently, we are faced with the question of whether the protein under investigation is novel, or if the non-matching spectra are due to less exciting prospects such as inter-species variation, database sequence errors, or unexpected proteolytic cleavages.
The first method offering a metric to compare pairwise distances between complete lipidomics. We will offer LUXScore, as a standalone tool as well as a Knime node.
DNA methylation analysis with genome segmentation via hidden Markov model.
LuxRep is a genome wide methylation analysis tool that models different bisulphite-converted DNA libraries from the same biological replicate (i.e., technical replicates) thereby allowing use of libraries of even low bisulphite conversion rates.
DNA methylation analysis using generalized linear mixed model with spatial correlation. LuxGLM Using Spatial correlation (LuxUS) is a tool for differential methylation analysis. The tool is based on generalized linear mixed model with spatial correlation structure. The model parameters are fitted using probabilistic programming language Stan [2]. Savage-Dickey Bayes factor estimates are used for statistical testing of a covariate of interest. LuxUS supports both continuous and binary variables. The model takes into account the experimental parameters, such as bisulfite conversion efficiency.
Open-Source Routines for Building Personalized Left Ventricular Models from Cardiac MRI Data.
Uses a simple language for describing features on a genome or biological sequence and provides a browsable image of these features.
Customized Linux distribution for bioinformatics research. It aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure.
Tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.
A dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN2 as a regulator of effector functions. Shiny application to visualise phospho-kinetics upon TCR activation.
This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.
Programmatic access to the analytical tools (Enrichment Analysis, and Network-based gene prioritization) and annotations on the genes (integrated from over 35 databases).
A Machine Learning Model for Predicting the Pathogenicity of Missense Variants.
LZerD: Protein-Protein Docking Algorithm
Web server for protein-protein docking prediction using the LZerD algorithm.
Fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.
Software to implement an efficient method for the integration of biological knowledge with microarray gene expression data to enhance identification of differentially expressed genes.
MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Laboratory, appropriately filtered GOLM database peak information and Human Metabolome database information.
Calculates random combinations of a wide variety of reactions to list potential metabolic routes from initial to target compounds efficiently, which could be a heuristic approach in designing potential metabolic pathways in practical applications.
M²aia (MSI applications for interactive analysis in MITK) is a software tool enabling interactive signal processing and visualisation of mass spectrometry imaging (MSI) datasets. M²aia extends the open source Medical Imaging and Interaction Toolkit (MITK; https://www.mitk.org) and provides powerful methods that the MSI community can adopt, exploit and improve further. In it’s current state, it is designed to enable multi-modal 2D registration and 3D MSI reconstruction.
Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model. Predicting MiRNA-disease Associations by Multiple Meta-paths Fusion Graph Embedding Model（M2GMDA）. (1)M2GMDA.py：gereating meta-paths from the dataset of miRNA-disease associations,disease semantic similarity, miRNA functional similarity. all the result is saved in the folds named "5.mid result" and "6.meta path", which need to be created by yourselves.
A web server for microbiome and metabolome integrative analysis. M2IA is a web-based server for the Microbiome and Metabolome data integration analysis. M2IA integrates a variety of statistical analysis methods, including univariate analysis, multivariate modeling, and functional network analysis. Users can upload data, customize parameters, and submit a job by one click. An html-based summarized report will be generated automatically for overview, accompanied by supporting tables and high-resolution figures available for downloading.
Lightweight, easily pluggable, and extremely fast conversion software tool. It converts msf files to the proteomics community standard mzIdentML file format.
Comprehensive data about different olfactory receptor-ligand pairs
a computational model for predicting drug-targeted pathogenic proteins
A Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models. Microbiota-to-Recon (M2R) program.
Multimodal representation learning for predicting molecule-disease relations.
An improved SNP calling algorithm for Illumina BeadArray Data.
Genome-wide data is used to stratify patients into classes using class discovery algorithms. However, we have observed systematic bias present in current state-of-the-art methods. This arises from not considering reference distributions while selecting the number of classes (K).
MicroRNA childhood Cancer Catalog (M3Cs) is a high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases.
This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.
A novel machine learning approach for predicting the 3D printability of medicines. Select a tested drug product Example 1 Example 2 Example 3 Example 4 Load materials.
This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.
Comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.
A database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.
A novel method for predicting m5C sites of RNA. m5CPred-SVM: A webserver for predicting m5C sites of RNA based on SVM. A webserver for m5C Sites Identification of RNA. m5CPred-SVM was developed by using support vector machine based on six different kinds of features extracted from RNA sequences. Now it is for three different species including H. sapiens, M. musculus and A. thaliana. The benchmark datasets can be download here. The input for the server is the RNA sequence. More details can be found in the tutorial.
A Web Server for the Prediction of RNA 5-Methyluridine Sites from Sequences. As one of the widely occurring RNA modifications, 5-methyluridine (m5U) has recently been shown to play critical roles in various biological functions and disease pathogenesis, such as, under stress response and during breast cancer development.
Large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network.
Prediction of m6A regulated expression genes by integrating m6A sites and reader binding information in specific- context
Updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species. N6-methyladenosine (m6A) is the most abundant internal chemical modification on mRNAs and lncRNAs and has a broad function in biological metabolism. m6A-Atlas v2.0 was expanded to include 797,091 reliable m6A sites among 7 species , with 13 high-resolution technologies and 109 conditions.
Uncovering complex and condition-specific m6A regulation of gene expression.
Unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues.
A comprehensive database for targets of m6A writers, erasers and readers. N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs
A web server to predict tissue-conserved human m6A sites using machine learning approach.
m6ADD is a database containing manually collected experimentally confirmed m6A (N6-methyladenosine)-disease data and data obtained from high-throughput disease m6A modification profiles, aimed at exploring the association between m6A modified gene disorders and diseases
Analysis of m6A profile matrix based on graph regularized non-negative matrix factorization.
A Predictor for N6-Methyladenosine Sites Identification Utilizing Sequence Characteristics and Graph Embedding-Based Geometrical Information.
We have developed an algorithm called M6Allele for identifying allele-specific m6A modifications. To facilitate its usage by researchers, we have also encapsulated our analysis process into a pipeline.
Identifying RNA N6, 2'-O-dimethyladenosine (m6Am) sites based on sequence-derived information.
Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.
Epitranscriptome Target Prediction and Functional Characterization of a sequence-based N6-methyladenosine (m6A) modification site predictor. Among the various types of RNA modification, the methylation of adenosine at the N6 position (m6A) is characterized as the most abundant post-transcriptional modification in mRNA.
A database for m6A-centered regulation of disease development and drug response.
Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing | Code and data associated with m7G-MaP-Seq paper
Deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Search by RsID, Gene, Region or Disease:. Links MeT-DB Whistle DRUM DRRMSDB. A database for the disease-associated genetic variants that may affect m7G sites.
Machine learning computational tool designed to more accurately predict the effects of missense mutations on protein–protein interaction binding affinity.
Gene relevance based on multiple evidences in complex networks | Noemi Di Nanni (1, 2), Matteo Gnocchi (1), Marco Moscatelli (1), Luciano Milanesi (1) and Ettore Mosca (1, *)
A novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. mPies: metaProteomics in environmental sciences. Werner, J., Géron, A., Kerssemakers, J. et al. mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. Biol Direct 14, 21 (2019) doi: 10.1186/s13062-019-0253-x
Quality visualization tool specific for ribosome profiling data
This environment offers an interactive multi-user interface which includes all steps of a microarray study: from MIAME-compliant storage of experiments and raw data processing to analysis of differentially regulated genes. In addition, it offers functional insight into gene expression data by using an original approach combining biological knowledge annotation with gene expression data through interactive graph.
Comprehensive online resource to visualise mouse development and investigate gene expression in the mouse embryo.
Model-based Analysis of 2-Color Arrays is a model-based algorithm for analyzing 2-color microarrays.A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches.
A Multi-Arm Two-Stage (MATS) design for proof-of-concept and dose optimization in early-phase oncology trials.
Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.
MAAPER is a computational method for model-based analysis of alternative polyadenylation using 3’ end-linked reads. It uses a probabilistic model to predict polydenylation sites (PASs) for nearSite reads with high accuracy and sensitivity, and examines different types of alternative polyadenylation (APA) events, including those in 3’UTRs and introns, using carefully designed statistics.
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.
Genotyping thousands of microbial strains. Type SNPs from a set of whole genome assemblies and sequencing reads from beginning to end in one single command line.
An Integrated and Visual Tool for Microbiome Data Analyses. A Multifunctional and Visual Tool for Microbiomic Data Analyses.
Simulating continuous/discrete time Markov processes, applied on a Boolean network.
Marker-based automatic cell-type annotation for single cell expression data
A comprehensive platform for germplasm innovation and functional genomics in Macadamia.
MACARON (Multi-bAse Codon-Associated variant Re-annotatiON) is a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data. Starting from a standard VCF file, MACARON identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon.
Macarons is an algorithm designed to recover single nucleotide polymorphisms (SNPs) that are related with a phenotype in genome wide association studies (GWAS) by taking into account of the dependencies between them.
This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It implements an statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia.
Macaulay2 is a software system for research in algebraic geometry and commutative algebra. It includes a module NeighborJoining for analyzing phylogenetic trees under admixture, addressing clustering order, distance, and topological path length.
Visual interactive knowledgebase of metabolite-associated cell communications.
Computer program for phylogenetic analysis. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
A curated knowledgebase for metabolic associations across human cancers.
An Open Access Data Repository of Mass Spectra for Chemical Ecology.
Molecular Acquisition, Cleaning, and Evaluation in R (MACER) is an R package to assist biological researchers in assembling taxonomically and marker focused molecular sequence data set.
Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
Genotype imputation software that extends the capabilities of MaCH 1.0. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual. This reference selection method generates better imputation quality in shorter running time. It also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion.
MACH2 is a method for inferring migration histories of metastatic cancer cells from clone phylogeny and the location of extant clones. It systematically enumerates all plausible migration histories and includes an interactive webtool (MACH2-viz) for visualization and exploration.
Performs logic regression, using imputed SNP dosage data and adjusting for covariates.
QTL analysis based on imputed dosages/posterior_probabilities
Machado is a Django instance that provides data management, visualization, and searching functionalities to Chado databases. The resulting object-relational framework enables users, not only to set up a local instance containing data regarding their organisms of interest, but also to support the develop of new tools as a back end.
Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations.
A unified framework for developing and interpreting machine-learning models for chemosensory research. Machine-OLF-action: a machine learning-driven computational framework.
Rapid Prototyping of Bioinformatic Automata. Machine Boss allows you to manipulate state machines by concatenating, composing, intersecting, reverse complementing, Kleene-starring, and other such operations. Brief descriptions of these operations are included below. Any state machine resulting from such operations can be run through the usual inference algorithms too (Forward, Backward, Viterbi, EM, beam search, prefix search, and so on).
Mechanism, Annotation, and Classification in Enzymes: database of enzyme reaction mechanisms.
Automated pipeline that uses state-of-the-art machine learning algorithms to create a disease risk model based on a given GWAS SNP dataset and assesses its predictive performance for unseen datasets. The pipeline can either use a first dataset for training the model and a second for validation, or perform a nested k-fold cross-validation on a single dataset.
MACML is a program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
Multi-objective ant colony optimization algorithm for detecting the genetic interactions.
Graphically displays correlation in microarray data that is due to insufficient normalization.
A Database to Quickly Access All Tryptic Peptides of the UniProtKB
MaCPepDB - Mass Centric Peptide Database
It can be used for binding site analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM format and separates the data into Self-ligated, Intra- and Inter-chromosomal PETs. Furthermore, MACPET breaks the genome into regions and applies 2D mixture models for identifying candidate peaks/binding sites using skewed generalized students-t distributions (SGT). It then uses a local poisson model for finding significant binding sites.
mACPpred 2.0 is a web application for predicting anticancer peptides based on stacked deep learning and integrated spatial and probabilistic feature representations. It is designed to assist researchers in identifying potential ACPs for further testing.
Antimicrobial peptide screening in genomes and metagenomes. Macrel: (Meta)genomic AMP Classification and Retrieval. Pipeline to mine antimicrobial peptides (AMPs) from (meta)genomes.
macroMS is a image-guided analysis of random objects by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
A MATLAB package for the analysis of overlapping macrophages
It is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS making this program appropriate for simulating data for structured populations in genome wide association studies.
Aligning Protein-Coding Nucleotide Sequences with MACSE. MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. A wide range of molecular analyses relies on multiple sequence alignments (MSA). MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and or stop codons.
Multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods.
A high-quality SNV database for interspecies genetic divergence investigation among macaques. A database for genetic divergence investigation among macaques. MACSNVdb is an open-access SNV database comprising ~74.51 million high-quality non-redundant SNVs called from 20 macaques that may assist researchers to investigate interspecies genetic divergence between macaques.
Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.
a Python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.
Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees. A Tool for Multiple Accessions' Distinguishing through Hierarchical Decision Tree.
A deep U-shaped network combined with an attention mechanism for pancreas segmentation in CT images. Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras.
The Martini Database (MAD) is a web server dedicated to (a) sharing structures and topologies of molecules parameterized with the Martini coarse-grained (CG) force field; (b) converting atomistic structures into CG structures; (c) preparing complex systems (including proteins, nucleic acids, lipids etc.) for molecular dynamics (MD) simulations at the CG level.
An Open-Source Python Package for Annotation and Analysis of Time-Series Data.
A web service for analysing DNA methylation array data. MADA is developed for the whole process of methylation array data analysis
MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5&apos, and 3&apos,ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).
Mapping of Distances for the Categorization of Topology is a protein structure search tool
The Maryland Analysis of Developmental EEG (MADE) Pipeline. The Maryland Analysis of Developmental EEG (MADE) Pipeline. Version 1.0. Developed at the Child Development Lab, University of Maryland, College Park.
Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.
This R package fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver.
SoybeanMADisTool is a tool developed to identify multiple alleles and causative mutations in soybean GWAS datasets, addressing the limitations of existing methods that fail to account for the presence of multiple alleles. The tool computes a score for variant positions and is available as both a Python package and a web-based application hosted on SoyKB.
Data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.
A web application for processing and visualization of statistics for bone marrow donors registry - especially statistics of donors, executed searches for suitable donor, the typing and harvests before transplantation.
MadraX is a differentiable forcefield implemented as a PyTorch module that integrates physics into deep learning algorithms for structural biology. It provides tutorials and an installation guide accessible online.
This package provides a group of hierarchical Bayesian models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.
An Online Tool to Visualize Magnetostriction. MAELASviewer: Online visualization of magnetostriction. MAELASviewer is an online tool to visualize magnetostriction. This interactive applet shows the magnetostriction for some crystal systems. You can simulate the Joule and Wiedemann effects. A magnetostrictive material is one which changes in size due to a change of state of magnetization.
Multi AgEnt STability pRedictiOn tool for changes in unfolding free energy upon point mutation.
MAESTRO is a Multi AgEnt STability pRedictiOn tool for calculating changes in unfolding free energy upon point mutation. MAESTRO is structure based, which means that the 3-d structure of the wild type is required. It is able to predict single- and multi-point in monomeric and multimeric proteins.
MAESTRO-web is web interface to MAESTRO, a Multi AgEnt STability pRedictiOn tool for calculating changes in unfolding free energy upon point mutation. MAESTRO is structure based, which means that the 3-d structure of the wild type is required. It is able to predict single- and multi-point in monomeric and multimeric proteins. In addition, MAESTROweb provides mutation sensitivity profiles, a scanner for the most (de)stabilizing mutations and potential S-S bonds sites.
The MAExplorer is a Java-based bioinformatics exploratory data-analysis and data-mining program for analyzing sets of quantitative spotted cDNA or oligonucleotide microarray data . It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.
Laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it supports the widely used glass microarrays and oligo-chips, it was designed with the specific idiosyncrasies of Nylon based microarrays in mind.
Lossless compression tool specifically designed to compress MAF (Multiple Alignment Format) files.
A high-speed multiple sequence alignment program.
Multi-Sample Accurate and Flexible SNP Caller is a SNP caller using next-generation sequencing data from multiple samples.
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
MAG-SD is an image classification model focusing on pneumonia (including COVID-19) using CXR images.
A Supervised Method to Detect Motifs From Annotated Groups in Alignments. Motifs from Annotated Groups in Alignments. MAGA is a new simpler way to infer information from alignments. Based on a regular procedure usually done visually by experts, it looks for group-conserved residues in an alignment. Provided an alignment in FASTA format and a way to group the sequences in it, MAGA seeks to access an unexplored layer of information difficult to appreciate visually when many sequences are aligned, even for a trained bioinformatician.
A Platform-independent Java library of algorithms to built-up search engines to help in the discovery of services and datatypes specially oriented to deal with repositories of web-services and associated datatypes.
An Open-Source Tool for Meta-Analysis of Gene Expression Studies.
MAGE-ML visualize script will read any MAGE-ML file and generate a graph showing the links between BioMaterials all the way through to BioAssays, and include information on sample characteristics and experimental factor values in the output.
Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.
It is designed to surporting downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis.
An online tool that facilitates curation of MAGE-TAB. It combines text-mining and the Experimental Factor Ontology (EFO) to create a semi-automatic environment for faster annotation, guided data-manipulation and content summary.
MaGelLAn is a software that facilitates quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information
A multi-agent architecture for feature selection, called MAgentOmics, to consider all omics data together. MAgentOmics extends the ant colony optimization algorithm to multi-omics data, which iteratively builds candidate solutions and evaluates them. Moreover, a new fitness function is introduced to assess the candidate feature subsets without using prediction target such as survival time of patients.
A software for analyzing UMI-tagged data for detecting ultra-rare variants.
Leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. MAGGIE provides a framework for identifying DNA sequence motifs mediating transcription factor binding and function. By leveraging measurements and genetic variation information from different genotypes (human individuals, animal strains, or alleles), MAGGIE associates the mutation of DNA sequence motif with various types of epigenomic features, including but not limited to transcription factor binding, open chromatin, histone modification, and stimulus response of regulatory elements.
Sharing descriptive metadata is the first essential step towards the “Open Data” approach. With this in mind, the Maggot tool was specially designed to allow users to easily add descriptive metadata to datasets produced within a collective (research unit, platform, multi-partner project, etc.), thus promoting the sharing of metadata within this same collective and beyond.
Single-animal tracking system for Drosophila larval locomotion analysis.
Publicly available web application to explore and annotate cancer genomics data.
Merging affected genes into integrated networks - multiple seeds: Seed-centric module discovery using multiple seeds.
Web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene expression data.
Access portal to a cross-platform gene expression compendium for maize.
MAGIC (Multi-scAle heteroGeneity analysIs and Clustering) is a multi-scale semi-supervised clustering method that aims to derive robust clustering solutions across different scales for brain diseases.
A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. The manuscript accompanying this script is: MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. Roopra, A. 2020 PLoS Computational Biology.
Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach.
Navigation in the Ring Chemical Space Guided by the Bioactive Rings.
MAGIC Tool is an integrated microarray data analysis software.
Machine-learning-based genotype imputation quality calibration.
Large-scale short reads and sequencing depth visualization.
MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.
MAGinator is a tool for profiling shotgun metagenomics datasets, enabling accurate identification of subspecies-level microbes and reconstruction of phylogenetic relationships between MAGs.
A computational framework to explore cellular response mechanisms from multi-omics datasets. MAGINE : Mechanism of Action Generator involving Network Analysis. MAGINE is a framework for the analysis of quantitative multi-omics data. It was designed to handle multi-sample (time points) and multi-omics (rnaseq, label-free proteomics, etc). Users are provided access to tools driven around their experimental data. Provides access to enrichment analysis, biological network construction and various visualization methods.
This tool can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.
The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples
Fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes
MagMD is a database mainly describing the interactions between human gut microbes, enzymes and active substances. Later, we may add some prediction results of the interaction of gut microbes, enzymes and active substances(mainly pharmaceutical).
A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum.
Software tool for pairwise global network alignment. It is an extension of MAGNA. An example of an application domain where this tool is useful is computational biology – It can be used for biological network alignment.
Microarray Gene Expression and Network Evaluation Toolkit (MAGNET) is a web tool with three components: generation of coexpression networks, weighted protein-protein interaction networks and bimodality of coexpression.
Efficient method to measure the magnetic susceptibility of the materials with arbitrary shape using B0 inhomogeneity map.
An interactive web application to explore transcriptome signatures of heart failure.
An automated workflow for genome-resolved metagenomics
MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.
MAGPIE is a web server application that enables researchers from different domains to publish, exchange and execute models on-line, as well as publish and exchange data.
Accurate pathogenic prediction for multiple variant types using machine learning approach.
Interactive tool for visualizing and analyzing many simultaneous protein interactions with a binding partner.
Software which was developed for predicting highly polymorphic gene alleles using unphased SNP data.
MAGpy is a Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs).
MAGqual is a command-line pipeline for assessing the quality of metagenome-assembled genomes based on MIMAG standards, built with Snakemake, R, and Python, and openly available on GitHub under the MIT license.
Multiple Sequence Alignment using Graph Clustering. A few basic ways of running MAGUS are shown below. MAFFT (linux version is included).
This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data.
Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin. MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map. MAINMAST is a fully automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. This new de novo modeling method has several advantages; (1) It does not require reference structures; (2) It does not requre manual interventions; (3) a pool of candidate models are generated.
Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map. MAINMAST is a fully automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. This new de novo modeling method has several advantages; (1) It does not require reference structures; (2) It does not requre manual interventions; (3) a pool of candidate models are generated.
Privacy-Preserving Record Linkage using Secure Multi-Party Computation. This repository is a fork of the official Mainzelliste project, embodying the features described in the paper “Mainzelliste SecureEpiLinker (MainSEL): Privacy-Preserving Record Linkage using Secure Multi-Party Computation”. It is intended that these new features will eventually be integrated back into the official Mainzelliste software.: https://bitbucket.org/medicalinformatics/mainzelliste/src.
MainzelHandler is library for a simple integration and usage of the Mainzelliste, a web-based first-level pseudonymization service.
Mainzelliste is a web-based first-level pseudonymization service. It allows for the creation of personal identifiers (PID) from identifying attributes (IDAT), and thanks to the record linkage functionality, this is even possible with poor quality identifying data. The functions are available through a RESTful web interface. Mainzelliste also includes built-in consent management and supports FHIR APIs.
A web service for predicting blood-stage malaria inhibitors. Prediction platform to give access to a consensus approach of anti-malaria models.s. MAlaria Inhibitor Prediction platform. The malaria inhibitor prediction (MAIP) platform is the result of a public-private collaboration whose aim is to develop a consensus model for predicting blood stage malaria inhibition. Five Pharma and not-for-profit partners trained a model (using code developed by EMBL-EBI) on their private datasets. The resulting models were combined by EMBL-EBI and made available through this public prediction platform.
MAISEN is the first web tool to combine advantages of automatic and manual genome annotation. MAISEN lets you browse results of many functional annotation programs in one place.
Fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms.
This package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.
Biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information.
Maize genetics and genomics database (MaizeGDB)
Encyclopedia of RNA splicing variations in human tissues and cancer.
This tool is designed to facilitate automated analysis of miniature inverted repeat transposable elements (MITEs).
Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.
Make a FASTA file non-redundant, with a Galaxy wrapper This tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved. This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative.
Generate random database through Markov process.
This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
Fully Automated Generation of UCSC Genome Browser Assembly Hubs. MakeHub is a command line tool for the fully automatic generation of of track data hubs1 for visualizing genomes with the UCSC genome browser2. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.
Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
Pipeline designed to annotate novel plant genomes and is build on the MAKER annotation tool. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes.
MakeSBML is a web-based tool for converting between Antimony and SBML, facilitating model creation and editing for systems biology researchers. It provides an installation-free application accessible via a GitHub page and leverages the Antimony language for human-readable model definition.
Create a .png file with distribution of peaks heights for ChIP and Control sample.
Development and internal validation of a prediction model for hospital-acquired acute kidney injury. ACUTE KIDNEY INJURY RISK CALCULATOR. MAKIPS ACUTE KIDNEY INJURY RISK CALCULATOR.
Mako is a bottom-up guided model-free CSV detection tool. It first builds a mutational signal graph and utilizes pattern growth to detect maximal subgraphs as CSVs.
Computational prediction of protein Malonylation sites via machine learning based feature integration. Mal-Prec is a supervised machine learning classification to predict malonylated sites. In Mal-Prec, three encoding method including One-hot encoding, physiochemical properties (AAindex), and composition of k-spaced acid pairs (CKSAAP) were initially performed to extract sequence features. PCA was then applied to select optimal feature subsets while SVM was adopted to predict the malonylation sites. Five-fold cross-validation test and independent test results showed that Mal-Prec can achieve better prediction performance compared with other approaches.
Designed for the analysis of Microarray data. The rational data representing the gene expressions is discretized into a limited number of intervals for each cell of the array; the obtained discrete variables are then used to select a small subset of the genes that have strong discriminating power for the considered classes. The optimization algorithms for feature selection and logic formula extraction are then used to identify networks of genes that characterize the classes.
Bayesian modelling of high-throughput sequencing assays with malacoda. The goal of malacoda is to enable Bayesian analysis of high-throughput genomic assays like massively parallel reporter assays (MPRA) and CRISPR screens.
A program for automatic detection of aligned blocks in multiple protein alignment.
BLAST search against protein targets stored in Malaria Data database.
Search against small molecules stored in Malaria Data database.
Association testing of bisulfite sequencing methylation data via a Laplace approximation.
Package for standardized implementation of batch correction methods for omics data.
A web-based application for gene regulatory network analysis in Plasmodium falciparum.
MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
R package and Shiny app for more specific identification of MALDI imaging proteolytic peaks using LC-MS/MS-based proteomic biomarker discovery data.
A tool to quantify MALDI peptides (SILAC) from Phenyx output
Admixture mapping of complex trait loci, using case-control data.
Tool for aligning molecular or insilico restriction maps to a reference map.
Program for screening 16S rRNA clone libraries, and similar multiple sequence alignments for chimeras and other anomalies.The program is based on the Pintail algorithm which works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene.
Automated landmarking through pointcloud alignment and correspondence analysis.
MaLTA is a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf, mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata.
MALVIRUS is a fast and accurate tool for genotyping haploid individuals that does not require to assemble the read nor mapping them to a reference genome. It is tailored to work with virological data and can genotype an individual directly from sequencing data in minutes. MALVIRUS is divided into two logically distinct steps: the creation of a variant catalog from a set of assemblies and the genotype calling. The first step is based on mafft and snp-sites, whereas the second step is based on KMC and MALVA. The variant catalog can be built once and reused for genotyping multiple individuals. Please see the website for additional details. MALVIRUS is distributed as a Docker image and is publicly available on GitHub and Docker Hub under the terms of the GNU General Public License version 3 or later. MALVIRUS was mainly developed and tested under Ubuntu GNU/Linux version 18.04 but works wherever Docker is available.
Takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.
Monoallelic DNA-methylation pipeline for enrichment-based sequencing technologies.
Perception of Chemical Bonds via Machine Learning. A tool for the perception of chemical bonds via machine learning. A python tool for the perception of chemical bonds via machine learning. Internally uses RDKit, numpy, pandas and scikit-learn python packages.
MAmBA is an analysis pipeline to assess m5C in microRNAs following Bisulfite small RNA sequencing. Bisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs.
MAMBO (Metabolomic Analysis of Metagenomes using fBa and Optimization) is an algorithm which assesses and optimizes correlations between genome-scale, constraint-based metabolic models and microbial abundance profiles obtained from shotgun sequence data.
An automated machine learning pipeline with a microbiome repository for human disease classification. Flowchart of the mAML pipeline. Two files indicated at the beginning of the pipeline should be submitted to the mAML web server. Operation steps before training are indicated in the blue inverse-trapezoids. Automated machine learning model building pipeline for microbiome data.
Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.
cancer cell localization using image processing matlab function
Enhancement of mammogran images for clear view of pictorial muscles and cancer affected region
MammOnc-DB is a web platform designed for in-depth analysis of breast cancer RNA-sequencing, proteomic, and epigenetic data. It provides access to multiple datasets and offers tools for data visualization and biomarker discovery.
Detecting and genotyping deletions and insertions based on long reads and a deep learning approach.
It is a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization.
MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.
The rmams package and associated standards provide metadata standards for single-cell data matrices and analytical workflows. It facilitates harmonization, integration, and reproducibility of single-cell data across platforms.
A Web Based Dynamic MANA Nomogram for Predicting the Malignant Cerebral Edema in patients with large hemispheric infarction.
Merged Affinity Network Association Clustering (MANAclust) is a coding-free, automated pipeline enabling integration of categorical and numeric data spanning clinical and multi-omic profiles for unsupervised clustering to identify disease subsets. Using simulations and real-world data from The Cancer Genome Atlas, it is demonstrated that MANAclust's feature selection algorithms are accurate and outperform competitors.
A GUI designed to management of big amount of accession numbers.
Management of Accession Numbers and sequences
MANA is a Python module that detects metabolic changes induced by chemical exposure by computing condition-specific metabolic models and analyzing their impact on metabolic networks. It provides a workflow to identify mechanisms of action (mMoA) through network analysis and visualization of metabolic changes.
MANA (mMoA identification Assisted by modelling and Network Analysis)
Visualising microbial population structure by embedding millions of genomes into a low-dimensional representation.
Complete ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag sequencing) data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.
Exploratory Data Analysis for Large-Scale Sequencing Datasets. Mango User Guide — bdgenomics.mango 0.0.5 documentation. Free document hosting provided by Read the Docs.
MANGO: Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
mango : Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)
A Genomics Portal and Gene Expression Atlas for Mangifera indica.
A function for plotting a Manhattan Plot in MATLAB directly from a text file of GWAS statistics from PLINK, BOLT-LMM or SAIGE.
Manhattan Plots for visualisation of GWAS results
MANIEA is a microbial association network inference method based on improved Eclat association rule mining algorithm.
A novel manifold learning approach to reveal the functional links between gene networks. A novel manifold learning approach to reveal thefunctional links between gene networks.
Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.
A machine learning platform to guide protein-ligand design by anchors and influential distances.
Simple and effective method for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications.
MAnorm2 for quantitatively comparing groups of ChIP-seq samples. To pre-process a set of ChIP-seq samples. MAnorm2_utils is designed to coordinate with MAnorm2, an R package for differential analysis with ChIP-seq signals between two or more groups of replicate samples. MAnorm2_utils is primarily used for processing a set of ChIP-seq samples into a regular table recording the read abundances and enrichment states of a list of genomic bins in each of these samples.
Tools for robust comparative metatranscriptomics.
Integrative database and analysis platform that relates microbiome and phenotypic data. MANTA (Microbiota And pheNotype correlaTion Analysis platform) is an integrative database and analysis platform that relates microbiome and phenotypic data. MANTA is a web application that works on most of the modern web browsers. Microbiota And pheNotype correlaTion Analysis platform.
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
Machine learning-based tool to automate the identification of biological database IDs.
Performs Mantel-Haenszel's test for k strata of 2x2 tables. Mantel and Haenszel proposed this asymptotic test based on the chi-2 distribution. Assuming no three-way interaction (k independent strata).
Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).
MANTI is an tool for automated annotation of protein N-termini for rapid interpretation of N-terminome data sets.
An R package that simulates multilocus models of pathogen evolution.
Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.
Flexible and consensus-driven genome annotation. This tool can be used for protein function annotation, it is a standalone tool that uses HMMER to match sequences against multiple reference datasets, producing a consensus annotation using text mining. It accepts as input one or multiple aminoacids sequence fasta.
Mantis is a space-efficient data structure that can be used to index thousands of raw- read experiments and facilitate large-scale sequence searches on those experiments. Mantis uses counting quotient filters instead of Bloom filters, enabling rapid index builds and queries, small indexes, and exact results, i.e., no false positives or negatives.
Mantis is a homology-based protein function annotation tool that integrates multiple reference data sources. It uses multiple high-quality data sources as a reference, however custom reference data sources can also be added. Mantis does not use a pre-built database, instead, it dynamically integrates the multiple sources into a consensus-driven output. Mantis is extensively customizable and is available on Linux.
Computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”. It is based on network theory and non-parametric statistics on gene expression data.
An efficient and flexible library for training and validating protein folding models.
One Molecular Fingerprint to Rule them All. Extended-Benchmark: compounds and query lists used for the peptide benchmark. MAP4-Similarity-Search: source code for the similarity search app. Supplementary Material for the manuscript: "One Molecular Fingerprint to Rule them All: Drugs, Biomolecules, and the Metabolome". TMAPs of the ChEMBL, non-Lipinski ChEMBL, Human Metabolome, SwissProt up to 50 residues sequences, and Drugbank MAP4 Chemical Space.
Lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake.
MAP (Microtubule-associated Proteins) analysis tool.
Shiping Yang (for database-related issues)
Yuan Zhou (for prediction server-related issues)
Easy and reliable maximum a posteriori Bayesian estimation of pharmacokinetic parameters with the open-source R package mapbayr.
Identify and quantify DNA damage patterns in ancient DNA.
A ShinyR package to chart ancient DNA data through space and time.
Performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs.
MAPDISTO is a program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes.
A Cloud-Based Computational Platform for Immunopeptidomics Analyses. MHC-associated peptide discovery platform.
The algorithm is a post-variant-calling filter for variants that uses BLASTN to determine the fraction of reads supporting a variant call that align best to the site of the variant.
Uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences.
Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony. Data Repository for "MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.". This repository can be used to reproduce source data and results contributing to all figures and tables presented in:.
Framework for the development of desktop client applications. It is able to integrate meta-data of different Web-services catalogues. Its main characteristic is that it is modular and adaptable to different usage scenarios.
Deep exploration of quality issues and error profiles in high-throughput sequence data.
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes.
We propose a hybrid FS method, which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.
A user friendly web-application for spatio-temporal malaria prevalence mapping.
MAPLE is a microbiome analysis pipeline enabling optimal peptide search and comparative taxonomic and functional analysis.
An extensible R toolbox for modular and reproducible metabolomics pipelines.
User-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.
mapMECFS is an interactive data portal providing access to research results across many biological disciplines from studies that are focused on advancing our understanding of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME/CFS).
A tool designed to locate miRNA precursor sequences in existing genomic sequences (e.g Ensembl and Ensembl Metazoa), using potential mature miRNA sequences as input.
Considers the physicochemical variation present in a column of a protein sequence alignment and, on the basis of this variation, predicts the impact of all possible amino acid substitutions on the function of the protein.
Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats.
Contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.
A Massively Parallel, Portable, and Reproducible Tractography Pipeline. Massively Parallel, Portable, and Reproducible Tractography (MaPPeRTrac) is a brain tractography workflow for high performance computing. It incorporates novel technologies to simplify and accelerate neuroimaging research.
data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform. MAPPI-DAT (Mappit microArray Protein Protein Interaction- Data management & Analysis Tool) is an automated high-throughput data management and analysis system for microarray-MAPPIT system. MAPPI-DAT is capable of processing many thousand data points for each experiment, and comprising a data storage system that stores the experimental data in a structured way.
Mapping Tool is a tool to assist name mapping if different nomenclatures are used by different models (e.g. metabolic networks).
Analyses taxoptimizer output file to find the most relevant database's sequence using taxonomics informations (kronaextract output) and draw picture(s) with the mapping of all hsp on it.
Multiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces.
MapPop is a software for choosing good samples from mapping populations and for locating new markers on pre-existing maps.
Image analysis" of LC-MS features, deconvolution etc.
This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.
MAPS is a machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy.
A E-scape tool for interactive visualization of spatial clonal evolution.
MAPSCI is an algorithm to compute a multiple structure alignment for a set of proteins and to generate a consensus structure.
Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .
Highly sensitive and specific tool in the detection of splices as well as CPU and memory efficiency. It can be applied to both short (<75 bp) and long reads (>=75 bp) and it is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. The tool leverages the quality and diversity of read alignments of a given splice to increase accuracy.
MAPtools is an open-source Python3 application for analyzing genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. It provides command-line tools for calculating allele count-based statistics, generating plots, and annotating effects of mutations.
An information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. It supports a compact alignment view for both single-end and pair-end short reads, multiple navigation and zoom modes, and multi-thread processing. It offers automated genetic variation detection.
Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.
Complete pipeline for mutant discovery, with web front end.
Graphical read alignment viewer. It is specifically designed for the Maq alignment file and allows visualization of the mismatches, base qualities and mapping qualities. Maqview is nothing fancy as Consed or GAP, but just a simple viewer for visualizing what happens in a particular region.
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS.
MARBL is an open-source package for indexing the text components of GenBank records and the NLM article abstracts associated with them. A few demonstrations of the package are also available at this website.
MarblingPredictor is a software tool designed to analyze and predict the marbling score of dry-cured ham slices, aiding in quality control and categorization within the ham industry. It estimates marbling and fat content from image analysis and can be used for both research and industrial applications.
MarCat is a gene (protein) catalogue of uncultivable and cultivable marine microorganisms derived from metagenomics samples.
predicting coiled-coils in protein sequences
A method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering.
Includes all non-complete marine microbial genomes regardless of the level of completeness.
Processing Big Data with application containers on Apache Spark. Italian, pronounced: /ˈmare/. Noun: Sea. MaRe has been developed with scientific application in mind. High-throughput methods produced massive datasets in the past decades, and using frameworks like Spark and Hadoop is a natural choice to enable high-throughput analysis. In scientific applications, many tools are highly optimized to resemble, or detect some phenomena that occur in a certain system. Hence, sometimes the effort of reimplementing scientific tools in Spark or Hadoop can't be sustained by research groups. MaRe aims to provide the means to run existing serial tools in MapReduce fashion. Since many of the available scientific tools are trivially parallelizable, MapReduce is an excellent paradigm that can be used to parallelize the computation.
Tool to evaluate the effectiveness of no-take marine reserves.
Replicable pipeline and curated reference database for marine eukaryote metabarcoding. Building custom reference databases for metabarcoding. This pipeline can be used to develop a de-contamination database (i.e used to create a database of potential contaminants), or as a database for general purpose metabarcoding. We have provided three databases - a very small database composed of common contaminants (i.e human, sheep, goat, flies etc), as well as two metabarcoding databases for marine eukaryotes. These scripts support the MARES (MARine Eukaryote Species) pipeline used to create the MARES database of COI sequences for metabarcoding studies (presented in Arranz, Pearman, Aguirre, Liggins, in prep.).
Predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.
Open-source, version-controlled reference library of marine microbial eukaryote functional genes.
MARGARET is a computational tool for Trajectory Inference i.e. for inferring trajectories underlying biological developmental processes like cell-differentiation.
It is a robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. The framework has three main functions: MARGE-potential, MARGE-express, and MARGE-cistrome.
Assess downstream causality between two variables.
The marginAlign package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads.
MarginPhase is a program for simultaneous haplotyping and genotyping.
Algorithm for metabolite and reaction inference based on enzyme specificities. It has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.
Database of biosynthetic gene clusters in marine species.
Marigold is a free and open-source web application for analyzing zebrafish behavior, featuring a graphical user interface for tracking keypoints and exporting kinematic parameters. It leverages a custom neural network architecture for efficient pose tracking, accessible through standard web browsers.
MarineMetagenomeDB provides standardized and manually curated metadata for 11,449 marine metagenomes from SRA and MG-RAST. It enables users to search, filter, visualize, and download metadata through a web application equipped with quick and advanced search options, interactive map selection, and export tools. The database enhances data findability and reuse for comparative and large-scale meta-analyses in marine microbiome research.
mariner is an R/Bioconductor package for exploring Hi-C data that provides functions for manipulating, extracting, and aggregating chromatin interaction data. It simplifies the process of querying and extracting contacts from multiple Hi-C files and enables complete analysis and visualization of Hi-C data in R.
Citizen Science for Mining the Biomedical Literature. Scientific communication is broken. Progress in biomedical science is all about incrementally building off of the work of others. Currently, it takes far too long for one scientist's work to reach all the other scientists that would benefit. Mark2Cure will make scientific communication more efficient for everyone, leading to faster discoveries and cures for disease.
Marks all duplicate reads in a provided SAM or BAM file and either removes them or flags them.
A joint method for marker-free alignment of tilt series in electron tomography | This is an alpha version of the joint method for marker-free alignment. Currently, it may be not so robust and include third-part modules. The third-part modules will be removed in beta version | The files is build in fedora 25.
Explainable Single Cell Typing using Capsule Networks. MarkerCapsule is a genneral framework for identifying cell types from single cell scRA-seq data. MarkerCapsule is based on Capsule Networks, which reflect most recent and most advanced progress in deep learning, automatizes the annotation step, enables to coherently integrate heterogeneous data, and supports a human-mind-friendly interpretation of results, by relating marker genes with the fundamental units of capsule networks.
An online database of molecular biomarkers. MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and a selected set of pre-clinical biomarkers into a single resource.
NLP-enabled text-mining system for biomedical entity relation extraction.
Linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads.
Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning.
markerpen is an R library for the identification of cell-type-specific marker genes from co-expression patterns in tissue samples.
Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects.
Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data.
Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data. MarkovHC is an open-source R package designed for explore hierarchical structures of biological data, especially in cell type and critical point identification and cell transition tracking in development.
MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.
It is able to annotate biomedical texts using different annotation classes. You only need a server with php technology and one database to annotate documents with a browser. Users can enter biomedical documents to be annotated by other users and get annotations for relevant terms, such as diseases, symptoms and treatments.
MARome is a resource for annotation of Scaffold and Matrix Attachment Regions (S/MARs) in Human Genome such as associated genes, genomic region, associated S/MAR binding proteins, associated Retroviral Integration sites for HIV and HTLV (Source: RID) etc. MARome is interlinked to other genomic resources such as, UCSC Genome Browser (For visualization of S/MAR genomic location), ensemble, NCBI-Gene.
Web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.
This app provides a user interface for the open-source R package marr, which implements the method Maximum Rank Reproducibility (MaRR), a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data.
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
MArray is a tool for analysing single, replicated or reversed microarray experiments.
MarRef is a manually curated marine microbial genome database that contains complete genomes.
Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar couplings can be used to enhance assignment.
A software pipeline for automated analysis of social behaviors in mice. Assessing Apps for Patients with Genitourinary Tumors Using the Mobile Application Rating Scale (MARS). The Mouse Action Recognition System (MARS) is a deep learning based system for automated pose estimation and social behavior classification in pairs of interacting mice. It combines a user-friendly graphical user interface with fast and powerful computer vision and machine learning algorithms. MARS's novel approach to extracting features from the animals' poses and trajectories allows for highly accurate classification of social behavior.
A package for Multiple Samples Alignment-base SV Calling and Refinement.
Find matrix/scaffold recognition (MRS) signatures in DNA sequences.
Metabolite Analogues for Strain Improvement.
Prediction method for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs.
martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.
Martini 3 is a general purpose force field for coarse-grained molecular dynamics with an eye for atomic detail. The Martini force field is a coarse-grain (CG) force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parametrized in a systematic way, combining top-down and bottum-up strategies: Non-bonded interactions are based on the reproduction of experimental partitioning free energies between polar and apolar phases of a large number of chemical compounds, whereas bonded interactions are derived from reference all-atom simulations.
Tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface it allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats.
Multi-phenotype Analysis of Rare Variants.
An integrated alternative splicing analysis platform for single-cell RNA sequencing data.
Algorithm that models linkage-disequilibrium (LD) using a simple multivariate Gaussian distribution.
Manual Annotation Studio (MAS) is a web server which assists users in the process of identifying coding regions and determining the function of genes.
Perl implementation of our MaSC approach to estimating fragment length from short-read high-throughput sequencing data.
Converts Mascot search results in .dat files to pepXML (.xml) format.
A library to fully parse and analyse MASCOT MS/MS search results.
Proteomics aggregation utility that queries and aggregates information from a variety of online Arabidopsis proteomic resources.
Tool designed to simplify the manipulation of aligned sequence sets. It contains functionality for many of the common tasks related to this goal. In addition, mase was designed with a very modular approach, making additions or modifications to the code straightforward.
Fast genome and metagenome distance estimation using MinHash.
MASH-Ocean is an interactive platform for investigating microbial diversity, function, and biogeography using marine metagenomic data. It integrates global datasets and provides analysis modules for sample view, diversity, function, biogeography, and interaction networks.
A Universal Software Environment for Top-Down Proteomics. A Comprehensive User-friendly Software Environment for Top-Down Proteomics. MASH Explorer is a comprehensive and user-friendly software environment for top-down proteomics, which includes a downloadable software package, MASH Explorer App, as a versatile, comprehensive platform for top-down proteomics with the capability to process data from various vendor formats and incorporate multiple algorithms for deconvolution and database searching. It is developed by an interdisciplinary team consisting of experts in top-down mass spectrometry-based proteomics, computational data science, and bioinformatics/biostatistics.
MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using k-mers
Microbiota-active substance interactions database. Active Substance Interaction database. Try Examples: Bifidobacterium adolescentis, Enterococcus faecalis, Acarbose, Caffeic acid, Oxaprozin, Obesity, Colorectal cancer. A centralized and standardized database to catalog Microbiota-Active Substance Interaction (MASI) will be very useful for related research fields, including microbiota-related precision medicine, pharmaceutical research, food and nutrition research, clinical pharmacy, health management studies. Accumulating evidence about the interaction between human microbiota and active substances, especially for those therapeutically-relevant substances such as clinical used drugs and traditional medicines/herbs, is deepenning our understanding in the role of "our second genome" in human health and diseases, and opens new avenue for managing/treating human healthy problems/diseases by manipulating microbiota-human interactions.
Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.
Mapping and Analysis of SIreVirus Elements is an expertly-built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis, and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences.
Mask all ambiguity characters in nucleotide sequences with N.
Mask all ambiguity characters in protein sequences with X.
Package includes functions to analyze and mask microarray expression data.
Effects of spaced k-mers on alignment-free genotyping.
A deep learning framework for fully supervised, weakly supervised, and unsupervised mitosis detection in histopathology images. Codes for our Medical & Biological Engineering & Computing paper "MaskMitosis: a deep learning framework for fully supervised, weakly supervised, and unsupervised mitosis detection in histopathology images". Please see the paper for more details.
Masks recombinant regions in an alignment based on ClonalFrameML or Gubbins output
A fast, feature-rich and hackable read simulator for the simulation of NGS and Sanger data.
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server.
Freely available platform for integrating MS protein identifications with information from the major bioinformatics databases (ontologies, domains, literature, etc.)
Provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization.
“Mass++” is open-source software for visualizing and analyzing mass spectrometric data.
Predict the global qualities of individual protein models using random forests and novel statistical potentials. MASS: Protein Single-Model Global Quality Assessment by Random Forest and Various Energies. Tong Liu and Zheng Wang. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. BMC Bioinformatics (2020) 21:246.
Open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.
A software platform for analysis and visualization of label-free and tandem mass tag (TMT) data-dependent acquisition (DDA) bottom-up proteomics data, including pathway and gene set enrichment analyses.
Free (Windows/WINE) tool for analysis of MS/MS, bottom-up proteomics data, including non-standard PTMs and more.
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package.
MassBank is a public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains spectra from EI‐MS, fast atom bombardment MS, electrospray ionization (ESI)‐MSn data of thousands of authentic standards, EI‐MS and other‐MS data of thousands of volatile natural and synthetic compounds, and ESI‐MS2 data of synthetic drugs contributed by research groups worldwide. ESI‐MS2 data were analyzed under nonstandardized, independent experimental conditions. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS2 data. MassBank is useful for the identification of chemical compounds and the publication of experimental data.
A large-scaled depository of mass spectrometry datasets for metabolome analysis.
XIC extraction and quantitation from LC-MS data.
massdatabase is an R package that operates the online public databases and combines with other tools for streamlined compound annotation and pathway enrichment analysis. massDatabase is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the users to leverage all the online public databases for biological function mining.
Bottom-up parameterization of enzyme rate constants.
Robust linear deconvolution by optimal transport. This repository contains software tools which allow to compare spectra using the Wasserstein distance and estimate relative abundances of molecules from the spectrum by minimizing the Wasserstein distance. The tools are distributed as a Python3 package called masserstein. Basic functionality is also available as a set of commandline applications: WSDistance to compute the Wasserstein distance and WSDeconv to estimate proportions.
Access raw data from Agilent MassHunter GC/MS and GC/MS/MS, export to plain text.
Kalman filter based on binless peak picking and quantitation in XCMS.
Predicts the sex of samples in gene expression microarray datasets.
MassiveFold allows massive sampling with AlphaFold2, AlphaFold3 or ColabFold, automatically splitting the computing on CPUs and many GPUs.
A Mann-Whitney-Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis.
A two-stage microbial association mapping framework with advanced FDR control.
Web based tools for peptide identification and quantitation.
Provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.
MASSPEC is (or was) a computer program for the complete sequence analysis of large proteins from a single mass spectrum, a precursor to modern-day software for de novo sequencing and top-down proteomics.
Processes high resolution mass spectrometry imaging data, performs multivariate statistics (PCA, clustering) and lipid identification.
Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. MASSpy is a package for kinetic modeling and simulation of biological networks. MASSpy - Mass Action Stoichiometric Simulation in Python.
Software tool for doing blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm relies on overlapping peptides for the two proteases used, and can indicate both modifications and amino acid substitutions. The method can help restrict the area where the modification has occurred.
Search by molecular mass or elemental composition within ChemSpider or within particular data source(s).
A web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.
Processing Mass Spectrometry spectrum by using wavelet based algorithm.
With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.
Peptide identification and FDR calculation.
Tool for analysis of polymer and peptide/protein mass spectra.
A lightweight Linux live distribution prepackaged with a wide range of tools for MS and MS/MS data analysis.
Data processing tool for targeted high-throughput MALDI-MS data extraction.
Methods and models for handling zero-inflated single cell assay data.
A tool that converts from MasterVar to pgSnp format, so it can be viewed in browsers or used with the phenotype association and interval operations tools. .
masterVar2VCF converts a Complete Genomics masterVar file to a file in VCF v4.1 format.
Network analysis of functional genomics screening data. MasterPATH is an exploratory network analysis method that employs the shortest path approach and centrality measure to uncover members of active molecular pathways leading to the studied phenotype based on the results of functional genomics screening data.
The Staphylococcus aureus MLST tool is a web-based resource for determining the multi-locus sequence type of *Staphylococcus aureus* isolates. It facilitates bacterial typing and allows for comparative genomics studies.
Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach.
Multiple alignment and secondary structure prediction on a set of structural RNA sequences.
MAximal tumor treeS TRajectOries (MASTRO), to discover significantly conserved evolutionary trajectories in cancer.
Software for phylogenetic tree-to-tree distance comparison by calculating these trees’ “Maximum Agreemen SubTrees” in order to improve the visualization of tree “landscape”
Whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).
MAT2 (Manifold alignment of single-cell transcriptomes with cell triplets) is designed to align multiple single-cell transcriptome datasets. The operation steps include Manifold alignment based on contrastive learning and Reconstruction of gene expression profile.
Matlab implementation of Thermodynamics-based Flux Analysis.
Laboratory of Computational Systems Biotechnology
Reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
Platform for high throughput collaborative genome wide association studies (GWAS). Computational time is reduced by processing user-supplied trait data in parallel. Result analysis is facilitated by displaying annotated candidate markers in tabular format and in a genome browser.
The development of Matataki can overcome current limitations in reanalyzing RNA-Seq data toward improving the potential for discovering genes and pathways associated with disease at reduced computational cost. Thus, the main bottleneck of RNA-Seq analyses has shifted to achieving the decompression of sequenced data.
Weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use it.
Open source software matching patients across genomic centers and finding the individual patients with the same candidate gene and overlapping phenotypic feature. Search for novel genetic causes of rare disease is based on the algorithm that determines the similarity between two distinct patients.
Probing multi-way chromatin interaction with hypergraph representation learning. This is the implementation of the algorithm MATCHA for analyzing multi-way chromatin interaction data via hypergraph representation learning.
A guide to student-faculty connections in PhD programs. R Shiny app to match two sets of people based on mutual interests (e.g. students and faculty based on research interest). Created for the Matchathon event for the Program in Biomedical Sciences (PIBS) incoming first-year student Matchathon event. To help students find faculty members with mutual research interests, we use this algorithm to match first-year PhD students and faculty who are in search of trainees based on mutual research interests. Then these students and faculty meet during a two hour Matchathon event. At the event students meet individually with 12 different faculty members for 5 minutes each.
This package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.
Waterman-Eggert local alignment of two sequences.
Pairwise sequence alignment of DNA or protein sequences using Waterman-Eggert local alignment.
Finds the best local alignments between two sequences. It compares two sequences looking for local sequence similarities using a rigorous algorithm.
A Deep Learning Framework for Drug Synergy Prediction. Drug combination therapies have been a viable strategy for the treatment of complex diseases such as cancer due to increased efficacy and reduced side effects.
A platform for rare disease gene discovery. It connects databases of genotypes and rare phenotypes via a common application programming interface (API).
MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.
An open-source platform for cancer precision medicine.
A cross-platform normalization method for gene expression data integration. MOTIVATION:Combining gene expression (GE) profiles generated from different platforms enables previously infeasible studies due to sample size limitations. Several cross-platform normalization methods have been developed to remove the systematic differences between platforms, but they may also remove meaningful biological differences among datasets. In this work, we propose a novel approach that removes the platform, not the biological differences. Dubbed as 'MatchMixeR', we model platform differences by a linear mixed effects regression (LMER) model, and estimate them from matched GE profiles of the same cell line or tissue measured on different platforms. The resulting model can then be used to remove platform differences in other datasets
Tool to import, process, clean, and compare mass spectrometry data.
Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. This repository provides the following 3 perl scripts for reconstructing the structure of double-stranded DNA fragments from deeply sequenced single-stranded DNA libraries:. Each script includes a help menu with further instructions and available options (accessible by executing the scripts without specifying an input file).
Measure fluorescence signal colocalisation in biological systems.
A MATLAB toolbox for feature ranking. The matFR toolbox has already integrated 42 methods. Among them, 12 methods are from FSLib [1], 9 methods from mutual information (MI) based feature selection repository [2], 7 methods are used in MATLAB (“rankfeatures”, “relieff” and “lasso”), and others are accessible online. FR methods can be grouped into supervised and unsupervised methods. In this toolbox, there are 29 supervised and 13 unsupervised methods. FR methods can also be categorized from theoretical perspective. The matFR contains 12 MI based methods, 8 statistical analysis based methods, 8 structure learning based methods and others.
Facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots
MatHeat transforms your gene expression data into powerful insights, delivering interactive heatmaps, DEG analysis, volcano plots, advanced clustering, UMAP/K-Means, and Reactome pathway exploration.
Feature Extraction Package for Biological Sequences Based on Mathematical Descriptors. Home • Documentation • List of files • Dependencies • Installing • Descriptors • How To Use • Citation. Feature Extraction Package for Biological Sequences. Machine learning algorithms have been very successfully applied to extract new and relevant knowledge from biological sequences.
Multi-task framework for learning from single-cell multimodal omics data.
MATISSE is a method for improved single cell segmentation in imaging mass cytometry. MATISSE method combines fluorescence microscopy and multiplex IMC to achieve improved segmentation.
MATLAB is a general use development environment and scientific computing language.
This repository aim to share some of my matlab functions for biomechanical data analyses
Motion-Attentive Transition Network for Zero-Shot Video Object Segmentation. Motion-Attentive Transition for Zero-Shot Video Object Segmentation. [2020/06/15] Update results for DAVIS-17 test-dev set!. This is a PyTorch implementation of our MATNet for unsupervised video object segmentation. [2020/03/04] Update results for DAVIS-17 validation set!.
matOptimize is a program to rapidly and effectively optimize a mutation-annotated tree (MAT) for parsimony using subtree pruning and regrafting (SPR) moves within a user-defined radius.
Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible.
Automated classification and characterization of the mitotic spindle following knockdown of a mitosis-related protein.
MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.
In-silico definition of the Drosophila melanogaster matrisome. The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster< i> has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans< i>
Taking as input one or several sets of position-specific scoring matrices, this program applies hierarchical clustering to identify clusters of similar motifs. It produces a set of trees (one per cluster) and builds branch motifs at each node of each tree by merging the matrices of all descendent nodes.
Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast,easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. A web interface is included.
Model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors.
MatrixCGH is an extensible software framework for array CGH processing
A Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network.
It is a database focused on interactions established by extracellular proteins and polysaccharides. It takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes.
Ultrafast exhaustive epistasis scan for quantitative traits with covariate adjustment.
MatrixMatchMaker or MMM predicts interacting proteins using coevolution
shiny-based interactive data quality exploration for omics data.
Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.
Matroid intersection algorithm, i.e., find the maximum cardinality intersection of two matroids
Multi-Agent Thompson Sampling for Bandit Applications with Sparse Neighbourhood Structures. An efficient version of MATS that was used to perform the experiments in the article titled 'Multi-Agent Thompson Sampling for Bandit Applications with Sparse Neighbourhood Structures' (https://arxiv.org/abs/1911.10120).
MATSAS is a package of programs that analyse small angle scattering of neutrons and X-rays data obtained from porous systems. MATSAS has initially been developed for sedimentary rocks but can be used for other microstructures such as biological macromolecules, composite nanomaterials, or polymers.
Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature | Public API for the Materials Scholar database | matscholar (Materials Scholar) is a Python library for materials-focused natural language processing (NLP). It is maintained by a team of researchers at UC Berkeley and Lawrence Berkeley National Laboratory as part of a project funded by the Toyota Research Institute
Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations.
Protein structural alignment benchmark that may be used to test and refine protein sequence aligners.
Pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis.
Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays. This package is designed to be used as a back-end for Cardinal for working with high-resolution mass spectrometry imaging data.
Tool for finding mature miRNA within a miRNA precursor sequence using a Naive Bays classifier.
Maud is a command-line application that implements Bayesian statistical inference for kinetic models of biochemical metabolic reaction networks, incorporating quantitative omics data and structural information. It is designed to facilitate the quantitative modeling and analysis of cell metabolism.
Inferring expression changes in sorting-based CRISPR screens. MAUDE: Mean Alterations Using Discrete Expression. MAUDE is an R package for finding differences in means of normally distributed (or nearly so) data, via measuring abundances in discrete bins.
A Cross-sectional Analysis of the US Food and Drug Administration Manufacturer and User Facility Device Experience Database.
MAUI (MBI Analysis User Interface) is an image processing pipeline for Multiplexed Mass Based Imaging. MIBI_GUI is a set of three graphical user interfaces (GUIs) for low-level analysis of MIBI data. The three steps of low-level analysis (after you've extracted your data) are background removal, denoising, and aggregate removal.
Mauve Genome Alignment software, for comparing two or more draft or finished genomes
Learning genotype-phenotype maps from multiplex assays of variant effect. learning genotype-phenotype maps from multiplex assays of variant effect — mavenn 0.24 documentation.
Compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny.
A web resource for planning experimental tests of human variant effects. Explore potential assays and phenotypes for human gene variants. MaveQuest is an online database for querying literature-curated functional assays, phenotypes and clinical interests of human genes for Multiplex Assays of Variant Effect (MAVE) studies.
A collaboration platform for multiplexed assays of variant effect. We use cookies to offer you a better experience. By using the Service, you agree to our Terms and Privacy Policy . MaveRegistry is a collaborative resource for sharing progress on Multiplexed Assays of Variant Effect (MAVE).
Performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.
MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.
Metabolome Annotation Workflow for untargeted tandem mass spectrometry.
MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the alignment.
Scientific problems: Rodrigo Gouveia-Oliveira
Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
Command-line tool for the comparison of protein structures. It provides a simple interface for a large number of common structure comparison tasks. A key feature of the program is the ability to process thousands of structures, either against a single reference protein or in an all-verses-all comparison.
A problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem.
Novel approach to estimate gene expression from RNA-seq data that reduces length bias. Once reads have been aligned to a reference genome or transcriptome, using any alignment tool, the expression of a genomic feature, such as a gene, transcript or exon, can be estimated as the maximum read coverage along its sequence. The method is available as a patch for bedtools.
Evaluation of ontology annotation for protein-protein interactions using Maximum Entropy.
A greedy algorithm, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space.
Robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments. MaxHiC is a background correcting model for General and Capture Hi-C experiments that assigns significance to the recorded interactions. You can become more familiar with MaxHiC by reading the paper or the short summary presented in the About MaxHiC section that gives you enough information to understand the tool's arguments.
The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.
Systems Proteomics Laboratory, Institute of Information Science, Academia Sinica
Automated tool for quantifying the total and air-free volume of the maxillary sinus based on computed tomography images. The quantification tool seeks to standardize maxillary sinus volume measurements, thus allowing better comparisons and determinations of factors that influence maxillary sinus size. The automated tool utilized image processing techniques (watershed, threshold, and morphological operators).
MIP-viewer, in which the color represents the depth of the voxel with the maximum intensity.
Maximum Intensity Projection with color coding for depth
Hybrid reference and de novo assembly pipeline
Thus tool find and rank cancer gene candidates by their connectivity to known cancer genes. Using a comprehensive protein interaction network, it searchs for genes connected to known cancer genes.
Standalone Graphical User Interface (GUI) of the MODELLER program which combines profile Hidden Markov Model (profile HMM) method with Clustal Omega for the construction of protein homology models.
Web portal for maximum occurrence analysis.
Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
An Enhanced Proteomic Result Reporting Tool for MaxQuant.
Statistical classifiers for diagnosing disease from immune repertoires.
Generate protein backbone and side chain co-ordinates from a C(alpha) trace.
Extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets.
Estimates protein identification false discovery rates.
To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from a given microbial abundances and compute simulated abundances that are indistinguishable from it. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently. MB-GAN is freely available at: https://github.com/zhanxw/MB-GAN
Java program for automated assignment and assessment of uncertainty of protein backbone NMR. It is based on a statistical model for NMR spectra, and employs a tree-based algorithm of stochastic optimization.
This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.
mBARq is a framework and web application for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations, designed to simplify statistical analysis and visualization for a variety of experimental setups.
The package implements the corresponding algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.
Workflow-simplified ancestral state reconstruction of discrete traits with MrBayes in the R environment. MrBayes Ancestral States with R. Contribute to stevenheritage/MBASR development by creating an account on GitHub.
An efficient approach for metagenomic binning based on clustering.
This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.
Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data.
Microbiome data denoising using zero-inflated probabilistic principal components analysis.
Microbiome batch effects correction suite.
An R package for bending non-positive-definite symmetric matrices to positive-definite.
Minimizer-based Sparse de Bruijn Graph Construction. Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify. Suggested input is PacBio HiFi/CCS reads. May or may not work with Illumina reads. Algorithmic details: https://www.biorxiv.org/content/10.1101/2020.09.18.303156v1.
A Shiny application for teaching model-based geostatistics to population health scientists.
Multiple Bacteria Genome Compressor. Multiple Bacteria Genome Compressor (MBGC) is a tool for compressing genomes in FASTA (or gzipped FASTA) input format. It is tailored for fast and efficient compression of bacteria species collections.
The microbial genome database for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature is that it allows users to create ortholog groups using a specified subgroup of organisms.
Search MBInfo database for interactions using a protein id.
Fast clustering for single cell data using mini-batch k-means. Mini-batch K-means Clustering for Single-Cell RNA-seq. Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation. Clustering, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics.
Search nucleotide database with nucleotide query sequence(s).
A curated database for microbes across human body and their associations with health and diseases.
Multi-omics boolean omics network invariant-time analysis.
Integrated database for curating metalloproteins in all aspects.
Estimates the DNA copy number profile by detecting regions with copy number changes.
Profile Hidden Markov Model based method capable of predicting membrane binding proteins (MBPs).
R/Bioconductor package for microbial quantitative trait loci (QTL) estimation.
Microarray Blob Remover is a microarray tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step. The software allows rapid visualization, detection, and removal of blob defects of a variety of sizes and shapes from different types of microarrays using their .CEL files. Removal of the affected probes in the blob-defects using MBR was shown to improve sensitivity and FDR compared to leaving the affected probes in the analysis.
A Web Server for Cross-Modal Coherent Registration of Whole Mouse Brains.
Server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.
Improved functional enrichment of chemical compounds for metabolomics data analysis.
Simulation program to generate patterns of single nucleotide polymorphism (SNP) data in a region that is linked to a biallelic site targeted by selection. The software was developed by modifying the commonly used Hudson’s ms simulator
Web server for accurate prediction of true or functional miRNA binding sites.
This high power, high conservativeness of FDR estimation and high stability method is suit-able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.
Method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets.
Fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome.
A MATLAB implementation of Monte Carlo simulation for photon migration inside tissue.
Monte Carlo Simulation for Photon Migration Inside Biological Tissue
Steady-state Model and Constraint Consistency Checker for biochemical networks.
A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies.
Multi-scale cross co-attentional U-Net for automatic medical image segmentation.
Microbial community analysis GUI for R using gWidgets.
Novel computational algorithm and platform for constructing and visualizing haplotype networks.
Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.
A powerful integration method for identification of causal pathways from genetic variants to complex disease. ADnet: An integration powerful method(MCC-SP) for Identification of Causal Pathways from genetic variants to complex disease.
A framework MccDTI for DTIs prediction by integrating heterogeneous information of drug and target. MccDTI adopts multiview network embedding to integrate heterogeneous information.
An open-source software application for Monte Carlo simulations of radiative transport.
A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.
Integrating long-range connectivity information into de Bruijn graphs.
A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.
This tool is proposed to identify disease-related genes. It is divided into three steps: module partition, genes prioritization in each disease-associated module, and rank fusion for the global ranking.
MCell4 is a Monte Carlo simulator of rule-based reaction-diffusion systems with a Python interface and native BioNetGen language support. It allows modeling of biological systems previously inaccessible and integrates with external simulators.
Image segmentation algorithms and example code for automated single cell analysis.
MCGAE is a deep computational framework for spatial transcriptomics data analysis, designed to create multi-view representations from gene expression and spatial adjacency matrices. It demonstrates improved performance in spatial domain detection, data denoising, trajectory inference, and 3D feature extraction.
Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome.
Premade MSCV-based, VSV-G pseudotyped retroviral particles that contain mCherry reporter gene.
Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence. Using a sequence similarity-based annotation and an ensemble of a support vector classifier and a multi-layer perceptron, MCIC (metagenome cellulase identification and classification) aims to identify and classify cellulolytic enzymes from a given metagenomic data as well as any other amino-acid sequence on the basis of optimum temperature and pH.
Development of machine learning algorithms to predict achievement of minimal clinically important difference for the KOOS-PS following total knee arthroplasty.
MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure.
MCLand is a Python-based software tool with a graphical user interface for modeling and visualizing Waddington's epigenetic landscape using Monte Carlo simulations. It allows users to explore gene regulatory networks and quantify landscape characteristics.
MCLEAN (Multilevel CLustering Exploration As Network) proposes a visual analytics clustering methodology for guiding the user in the exploration and detection of clusters. We thereby combine a graphical representation of the clustered dataset as a network with the community finding algorithms into one coherent framework. Our approach entails displaying the results of the heuristics to users, providing a setting from which to start the exploration and data analysis. This is considered multilevel because allows the user to have an overview and detailed of the merging of elements into clusters.
Adaptive Metropolis-coupled MCMC for BEAST 2. Installing the CoupledMCMC package.
C++ program that estimates posterior probabilities of identity by descent (IBD) sharing between multiple individuals using unphased single nucleotide polymorphism (SNP) data.
Program implementing some codon models allowing \omega = d_N/d_S to vary among sites (M0, M2a, M3, M7, M8) in a Bayesian framework.
MCMICRO (Multiple-choice microscopy pipeline) is an end-to-end processing pipeline for multiplexed whole slide imaging and tissue microarrays developed at the HMS Laboratory of Systems Pharmacology. It comprises stitching and registration, segmentation, and single-cell feature extraction. Each step of the pipeline is containerized to enable portable deployment across an array of compute environments.
Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. This is the repo for the mcmseq R package, which has the wrapper functions to run the MCMSeq method described in "MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments".
mCNA is a tool for Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers.
Critical chemical classes for the classification and boost identification by visualization for untargeted LC-MS/MS data analysis.
Multiple convolutional neural networks for RNA-protein binding sites prediction.
A Cytoscape plugin that finds clusters in different types of networks. An automated method for finding molecular complexes in large protein interaction networks.
MCoM is a dataset containing long-term monitoring data of contaminants in fish, mussels, and bird eggs from the Baltic Sea, collected since 1978. The dataset is available through an R package and GitHub repository, providing valuable insights into environmental contamination trends.
MCPath is a Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.
A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data.
Used in the analysis of pooling experiments for library screening. Pools are collections of clones, and screening a pool with a probe is a group test, determining whether any of these clones are positive for the probe. The results of the pool screenings are interpreted, or decoded, to infer which clones are candidates to be positive using a Markov chain Monte Carlo approach.
The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an online resource for viewing and exploring bacterial microcompartment (MCP) proteins and other large proteinacious assemblies like encapsulins. The MCPdb utilizes existing structural information to make learning about MCPs accessible to expert and novice learners alike.
The MCPep server for Monte Carlo simulations of peptide-membrane interactions
Monte Carlo penalty selection for graphical lasso. Monte Carlo Penalty Selection (MCPeSe) for graphical lasso.
Parallel maximum capacity-based genome-scale gene network construction framework.
The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.
R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison.
Program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.
A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data.
MCRA stands for Monte Carlo Risk Assessment. It is a web-based platform containing various models that users can use to assess these health risks for specific populations in various scenarios. In MCRA, more than 50 modules are available to address all major areas of risk assessment, including hazard identification, hazard characterisation, exposure assessment and risk assessment. MCRA contains models following the guidelines of the European Commission and the European Food Safety Authority (EFSA), and also includes novel scientific models that could improve or refine future risk assessment.
This package includes a function for combining preprocessing and classification methods to calculate misclassification errors.
MCSdb is a manually curated database documenting proteins residing in membrane contact sites. It provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering, cataloging 7010 protein entries and 263 complexes across 11 species.
Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.
Multiparticle Tracking algorithm for cell motion and morphology
Web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures
Predicting the effects of mutations on transmembrane proteins. mCSM-membrane: effects of mutations on transmembrane proteins. Douglas E. V. Pires & David B. Ascher.
Quantitatively predict the effects of mutations in protein coding regions on nucleic acid binding affinities.
McSNP is a relatively cheap and handy genotyping technique as it is an extension of the RT-PCR technique. It make use of the difference in melting temperature of PCR products for different alleles.
A probabilistic model for estimating splice site usage from RNA-seq data. McSplicer is a probabilistic model for estimating splice site usages, rather than modeling an individual outcome of a splicing process such as exon skipping.
A web server for predicting metal ion effects in RNA structures.
Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media.'
Modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing.
A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.
Tool suite for analysing molecular dynamics trajectories using network analysis and PRS.
Interactive Data Visualization of Protein Molecular Dynamics.
A webserver integrating database and prediction tools for microbe-disease associations.
Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs. Inferring Causal Network from Mixed Observational Data Using a Directed Acyclic Graph. Learning a mixed directed acyclic graph based on both continuous and categorical data.
Potent antibiotic design via guided search from antibacterial activity evaluations.
MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see the supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol
Microarray Data Analysis Toolbox (MDAT) contains functions for normalization, adjustment and analysis of gene expression data.
A toolkit to optimize the performance of molecular dynamics simulations. Benchmark molecular dynamics simulations. MDBenchmark — quickly generate, start and analyze benchmarks for your molecular dynamics simulations. MDBenchmark is a tool to squeeze the maximum out of your limited computing resources. It tries to make it as easy as possible to set up systems on varying numbers of nodes and compare their performances to each other. Benchmark molecular dynamics simulations — MDBenchmark 3.0.1 documentation. MDBenchmark: Benchmark molecular dynamics simulations¶.
Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly.
A PyMOL plugin for the preparation of molecular dynamics simulations.
A tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts.
The MDCS provides maximal margin Linear Programming method (Antonov et al., 2004) for classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types.
Web server for identifying carbonylation sites. Protein carbonylation, is an irreversible non-enzymatic post-translational modification (PTM) which is often used as a marker of oxidative stress. Despite the used of Protein Carbonylation as a biomarker of oxidative stress, the substrate motif of carbonylation remains unknown.
Web server for identifying S-sulfenylation sites
Predicting multi-type drug-drug interactions via supervised contrastive learning.
A web portal for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.
Novel Multi-Channel protein featurization for deep learning based binding affinity prediction in drug discovery. MDeePred: Multi-Channel Deep Chemogenomic Modeling of Receptor-Ligand Binding Affinity Prediction for Drug Discovery.
A multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies. MDEHT is termed as Multivariate Differential Expression by Hotelling’s Test.
A multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.
Functions to preform a Gene Set Analysis in several genomic dimensions. Including methods for miRNAs.
Improved implementation of a Bayesian correlated clustering algorithm, that permits integrated clustering to be routinely performed across multiple datasets, each with tens of thousands of items.
A microRNA-drug interaction prediction approach based on non-negative matrix factorization. A microRNA-drug interaction prediction ap-proach based on nonnegative matrix factoriza-tion Ali Akbar Jamali, Anthony Kusalik, Fang-Xiang Wu. A microRNA-drug Interaction Prediction Approach.
MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters.
User-friendly environment for prototyping molecular dynamics simulation protocols and numerical methods, built with the scripting language Python.
Dependency-Based Protein Subcellular Location Predictor.
A web platform for protein dynamic residue networks and modal analysis. Interactive homology modeling pipeline. A platform for the analysis of molecular dynamics trajectories using dynamic residue network analysis, perturbation response scanning, essential dynamics, dynamic cross-correlation, and for large-scale motion analysis of protein complexes using normal mode analysis.
Freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota.
Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. The Molecular Detection Mapping and Analysis Platform for R (MDMAPR) is an open-source bioinformatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format and geospatially visualizing the distribution of the data and relative intensity of the qPCR results.
Set of semantic Web-Services to help access to molecular dynamics (MD) simulations. Semantic information is added using the BioMoby library and a MD Ontology.
MDock is a suite for molecular inverse docking and target prediction. MDock is an automated molecular docking software which can simultaneously docking ligands against multiple protein structures/conformations by using the ensemble docking algorithm. It supports docking/optimizing ligand(s) against either a single protein structure or an ensemble of multiple protein structures and score calculations for given protein-ligand complexes. The energy function used in MDock is the knowledge-based scoring function, ITScore.
A Web Server for Blind Prediction of Protein-Peptide Complex Structures. MDockPeP server predicts protein-peptide complex structures starting with the protein structure and peptide sequence.
MDockPeP2_VS is a structure-based in silico peptide screening program that integrates molecular docking with structural conservation to identify peptide inhibitors. It is written in python2.7 and uses AutoDock Vina, PCalign, and Naccess, and has been applied to develop peptide inhibitors against antibiotic resistance.
The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases. Molecular Data Organization for Publication (MDOP). The Molecular Data Organization for Publication (MDOP) R package has functions to assist researchers in uploading molecular sequence data and associated metadata to public databases.
The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls.
MDPath is a tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral angle movements throughout an MD simulation.
MDPET is a unified motion correction and denoising adversarial network for low-dose gated PET.
Package for identifying driver pathways promoting cancer proliferation and filtering out the unfunctional and passenger ones.
Multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.
Medium-chain dehydrogenases/reductases database.
Mutation-induced drug resistance DataBase.
This tool merges the MDR method with the genotype-Pedigree Disequilibrium Test (geno-PDT). It allows identification of single-locus effects or joint effects of multiple loci in families of diverse structure. We present simulations to demonstrate the validity of the test and evaluate its power.
The web-based application for rapid determination of multidrug-resistant Staphylococcus aureus with MALDI-TOF mass spectra
Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
MDSCAN is a Python command-line interface (CLI) conceived to speed up and significantly lower the RAM memory needs of the HDBSCAN clustering of long Molecular Dynamics.
Microbial Dynamical Systems INference Engine for microbiome time-series analyses.
A posteriori sampling of important protein conformations from biomolecular simulations.
MDSuite is a software designed specifically for the molecular dynamics community to enable fast, reliable, and easy-to-run calculations from simulation data.
It prepares a raw frequency table, given information from MODELLER alignments and/or PDB files. The sample for generating the frequencies N is obtained depending on the type of features a, b, c, …, d. The sample can contain individual proteins, pairs of proteins, pairs of residues in proteins, pairs of aligned residues, pairs of aligned pairs of residues, chemical bonds, angles, dihedral angles, and pairs of tuples of atoms.
A deep learning approach replicating ophthalmologist's diagnostic process of arteriolosclerosis.
A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.
Web-based platform to help access to molecular dynamics (MD). The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories are also incorporated.
Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. ME-Scan analysis codes for the Alu, LINE, and SVA libraries. MEScanner is an intergrated tool for identifying polymorphic mobile element insertions (MEIs) using targeted high throughput sequencing.
A site to help depressed patients select an antidepressant tahat is most likely to help them
A Methylomic and Epigenomic Allele-specific analysis pipeline
Fortran program to estimate the admixture proportions and genetic drift using DNA sequence data, based on a coalescent estimator.
Performs functional/pathway enrichment test while integrating network information from biological interactome (e.g. protein-protein interaction network) using graphical algorithm techniques.
Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.
The process of mean-centering is to calculate the average spectrum of the data set and subtract that
A tool for comparative genomics aiming to aid researchers in identifying and visualizing Structural Variations with the use of Hilbert curves
An efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data.
Moment Expansion Approximation, iNference and Simulation (MEANS) is a tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment
MEAP is an R package for large-scale exon array data analysis.It includes a novel algorithm (PM-BayesBG) to estimate sequence-based backgrounds that allows more reliable expression estimation than the existing background correction methods. MEAP also contains algorithms for generating robust expression estimates at exon, alternatively spliced variant and gene levels that facilitates the quantitative analysis of alternative spliced variants in the whole transcriptome.
A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity. MEArec: Fast and customizable simulation of extracellular recordings on Multi-Electrode-Arrays.
The M-file is to calculate the g-ratio for Scanning or Transmission Electronic Microscopy.
Measure a point spread function and other parameters on a microscope
A method for annotation of metal binding functionality encoded in protein sequences.
Software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.
A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses.
Mapping, error correction, and de novo assembly for single-molecule sequencing reads.
A knowledge representation framework for genetic disease mechanism.
Clarified Drug-Drug Interaction Mechanism Facilitating Rational Drug Use and Potential Drug-Drug Interaction Prediction.
An algorithm for standardization and automation of compression test analysis.
Mechnetor lets you quickly explore and visualize integrated protein mechanism data, enabling a better understanding of the functional context of genetic variants.
Prediction of lncRNA mechanisms from RNA–RNA and RNA–protein interactions.
MeCOM is a versatile tool for metalloenzyme active site comparison, which is based on the pharmacophore and α-carbon patterns. It can automatically recognize the active site of the given metalloenzyme, extract active site features, and superimpose metalloenzymes. This tool can be used to find important information to develop new specific metalloenzyme inhibitors, and it will be also useful for protein function prediction, drug repurposing, inhibitor selectivity investigation, and so on.
A new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites.
An R package for measurement error correction in linear regression models with a continuous outcome.
MED is a non-supervised prokaryotic gene prediction method which integrates MED2.0 and TriTISA, an iterative self-learning translation initiation site (TIS) prediction algorithm. As the update of MED2.0, MED 2.1 modifies the TIS model by replacing the previous one to TriTISA, which imoroves the prediction accuracies for both 3′ and 5′ ends.
A clinical decision support tool for differential diagnosis of TMA with enhanced accuracy using an ensemble method. Failed to generate visualization... MED-TMA: Machine learning-based Ensemble model for Diagnosis of TMA.
A medication extraction algorithm for electronic health records using the R programming language | Objective: We developed medExtractR, a natural language processing system to extract medication dose and timing information from clinical notes. Our system facilitates creation of medication-specific research datasets from electronic health records. Materials and Methods: Written using the R programming language, medExtractR combines lexicon dictionaries and regular expression patterns to identify relevant medication information ('drug entities'). The system is designed to extract particular medications of interest, rather than all possible medications mentioned in a clinical note. MedExtractR was developed on notes from Vanderbilt University's Synthetic Derivative, using two medications (tacrolimus and lamotrigine) prescribed with varying complexity, and with a third drug (allopurinol) used for testing generalizability of results
medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.
Single-cell copy number lineage tracing enabling gene discovery. This package performs lineage tracing using copy number profile from single cell sequencing technology. It will infer:. An rooted directed minimal spanning tree (RDMST) to represent aneuploidy evolution of tumor cells. The focal and broad copy number alterations associated with lineage expansion.
A Metazoan Developmental Alternative Splicing database. This repository contains the pipeline for generating exonic PSI used in MeDAS.
MeDBA is an integrated, distinctive, practicable, user-friendly metalloenzyme data bank and analysis platform. It comprehensively integrates information regarding metalloenzymes, ligands, metalloenzyme-ligand associations with metalloenzyme-specific computational analysis tools.
Comparison between the accuracy of Montreal Cognitive Assessment and Mini-Mental State Examination in the detection of mild cognitive impairment. MedCalc is a comprehensive statistical software package for biomedical research. Free trial available.
Analysis of transcription factor binding motifs in accessible chromatin. MEDEA identifies lineage-specifying transcription factors (TFs) from chromatin accessibility assays by:.
Computational method for decomposition of heterogeneous DNA methylomes. It applies matrix factorization with biologically motivated constratints and regularization to discover and quantify latent components in methylomes of multi-cellual samples.
A MP(Membrane proteins)-specific homology-based coordinate generation method, which is optimized to build highly reliable core models.
MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data.
Comprehensive database on cultivation media and growth conditions for all domains of life. Data derived from culture collections and individuals.
SPARQL endpoint for the MediaDive cultivation media database.
How to create, train and evaluate SegNet for medical image segmentation
Positive-pressure medical ventilator system using Simscape™
A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning. The depository support training and testing BERT-CNN model on three medical relation extraction corpora: BioCreative V CDR task corpus, traditional Chinese medicine literature corpus, and i2b2 temporal relation corpus. This is an implementation of BERT-CNN model used in our paper "A General Approach for Improving Deep Learning-based Medical Relation Extraction using a Pre-trained Model and Fine-tuning".
A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. MEDICASCY is a multi-label based boosted random forest machine learning method that predicts small molecule’s side effects, indications, efficacy and mode of action proteins. MEDICASCY server takes a small molecule’s SMILES string (example: CC(C)(c1ccc(O)cc1)c2ccc(Cl)cc2 ) as input and predicts the molecule’s side effects and indications and sends output via user provided email to the user.
Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2. Chromosomal instability (CIN) and somatic copy number alterations (SCNA) play a key role in the evolutionary process that shapes cancer genomes. SCNAs comprise many classes of clinically relevant events, such as localised amplifications, gains, losses, loss-of-heterozygosity (LOH) events, and recently discovered parallel evolutionary events revealed by multi-sample phasing. These events frequently appear jointly with whole genome doubling (WGD), a transformative event in tumour evolution, which generates tetraploid or near-tetraploid cells. WGD events are often clonal, occuring before the emergence of the most recent common ancestor, and have been associated with increased CIN, poor patient outcome and are currently being investigated as potential therapeutic targets
MedicDeepLabv3plus is a convolutional neural network based on DeepLabv3+ implemented in Python and Pytorch to extract the brain mask and the contralateral hemisphere of rodent MRI brain scans with lesions.
Automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.
This tool was developed for analyzing data derived from Methylated DNA ImmunoPrecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, it provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.
medkit is an open-source Python library designed to facilitate the development and reproducibility of phenotyping pipelines, particularly when working with clinical text data from electronic health records.
This web server offers a flexible and fast statistical ranking of PubMed abstracts for topics of interest without expert knowledge.
The MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge.
A tool allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.
MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords.
An open-source data management system for tracking environmental DNA samples and metadata.
MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site.
MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex and rarely explored domain of Mediator proteins and its implications in all eukaryotic kingdoms.
MedSavant is a tool that helps find the genetic causes of disease.
A portable and customizable annotation tool for biomedical documents.
MedTator is a serverless text annotation tool for corpus development. It is built on HTML5 techniques and many open-source packages, and was designed to be easy-to-use for your annotation task.
Algorithm for genome scaffoldin which exploits information obtained from a set of genomes from related organisms to determine the correct order and orientation of the contigs. It formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. It does not require either prior knowledge on the microrganisms dataset under analysis or the availability of paired end read libraries.
MEDUSA (Multiclass flexibility prediction from sequences of amino acids) is a deep learning approach for prediction of protein flexibility from sequence. MEDUSA takes as input an amino acid sequence and returns a flexibility class of each residue in terms of the expected normalized B-factor value range. Prediction is simultaneously performed in two-, three- and five classes using a convolutional neural network trained on a dataset of non-redundant X-ray structures.
Visualization of networks with multi-edge connections
Integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting, to enable feature selection from the high-dimensional search space of candidate binding sequences while avoiding overfitting.
Tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects.
Software to build and analyze ensembles of genome-scale metabolic network reconstructions. Medusa - Analysis of ensembles of metabolic network reconstructions. Medusa is a tool for constraint-based reconstruction and analysis (COBRA) of ensembles. It builds on the COBRApy package (https://github.com/opencobra/cobrapy) by extending most single-model functionality to efficient ensemble-scale analysis. Additionally, Medusa provides novel functions for the analysis of ensembles. Welcome to medusa’s documentation! — medusa 0.2.0 documentation. Free document hosting provided by Read the Docs.
Medical Vision Language Learner (MedViLL), which adopts a BERT-based architecture combined with a novel multi-modal attention masking scheme to maximize generalization performance for both vision-language understanding tasks (diagnosis classification, medical image-report retrieval, medical visual question answering) and vision-language generation task (radiology report generation).
Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks.
Meerkat is designed to identify structure variations (SVs) in human cancer genomes from paired end high throughput sequencing data.
Application of the Meet-URO score to metastatic renal cell carcinoma patients treated with second- and third-line cabozantinib.
Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO. This repository contains application of MEFISTO to simulated and multi-modal omics data:. MEFISTO provides an unsupervised approach to integrate multi-modal data with continuous structures among the samples, e.g. given by spatial or temporal relationships. The aim of MEFISTO is to exploit such relationships between samples in the dimensionality reduction and disentangle smooth sources of variation given by factors that change gradually along the covariate and other source of variation that are independent of the covariate. Furthermore, it enables to interpolate/extrapolate to unseen timepoints or locations.
This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality.
A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite And Therapeutics (MeFSAT) is a curated database which has been constructed via literature mining followed by manual curation of information gathered from more than 900 published research articles, 6 specialized books on medicinal fungi and other existing resources.
Software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments.
Mega-scale Bayesian Regression methods for genome-wide prediction and association studies with thousands of traits.
Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples.
Megadepth is also available under R/Bioconductor. megadepth: BigWig and BAM related utilities. This package provides an R interface to Megadepth by Christopher Wilks available at (). It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by .
Fft-based protein-protein docking system for all-to-all protein-protein interaction predictions.
It is an integrated database of high-throughput structure-based PPI predictions.
A fast yet powerful approach to assess functional similarity across meta-omics data sets. Calculate semantic distance for sets of Gene Ontology terms.
Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.
Mega-scale linear mixed models for genomic predictions with thousands of traits. Scripts to run all analyses and make all figures in the paper: MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits, by Daniel Runcie, Jiayi Qu, Hao Cheng and Lorin Crawford.
Web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.
Computational pipeline for positional cloning of mutations by whole genome sequencing.
Merge two large overlapping DNA sequences.
Merge two large overlapping nucleic acid sequences.
Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.
Comprehensive toolbox for interactively analyzing microbiome data. It can perform taxonomic analysis using the NCBI taxonomy. Perform functional analysis using InterPro2GO, SEED, eggNOG or KEGG. Make bar chartsm word clouds, Coronoi tree maps and other charts. Perform PCoA, clustering and networks.
Facilitating interactive access to metagenomic data on a server.
Perform genomic sequence annotations by uploading a sequence and selecting the species to query. Automatically runs several analysis and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with GBrowse and the results can be downloaded in Microsoft Excel format.
Sensitive and rapid pathogen detection using metagenomic NGS data. Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference sequence of a close relative, or with a high load of mutations compared to its predecessors, read mapping fails due to a low similarity between the pathogen and reference sequence, which in turn leads to insensitive and inaccurate pathogen
An interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning. MegaR: A user-friendly interactive machine learning interface for metagenomic analysis to identify and predict disease sample accurately. Machine learning has been utilized in many applications from biomedical imaging to business analytics. Machine learning is stipulated to be a strong method for diagnostics and even for determining therapeutics in future as we move to personalized medicine. MegaR provides an unprecedented opportunity to develop machine learning models from metagenomic data available publicly as well as to perform classification of data samples based on the optimal model we developed.
Web server for large scale microsatellite identification, classification, and marker development.
A parametric class of general hazard models for clustered survival data.
ur company provides aeps cash withdrawal service to the best of our abilities. It is easy to start serving customers once you download the mego app, register & begin using it.
Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.
MEGU is a web application that visualizes complex omics data of multiple layers simultaneously, including transcriptome, pro-teome, and metabolome, onto an integrated pathway diagram de-rived by connecting the individual KEGG pathway maps; the mapped images are generated in Scalable Vector Graphics for easy editing by hand or with computer programs or drawing software.
Open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
A software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis.
Improving score-based motif enrichment by incorporating sequence bias covariates. Motif Enrichment In Ranked Lists Of Peaks. This project analyzes the relative enrichment of transcription factor binding motifs found in peaks at the top or bottom of a given ranking/score. It does this by calculating motif enrichment using a logistic regression model that describes the likelihood of a motif being present in sequences with higher/lower scores, while accounting for the effect of multiple covariates. The design is based on MOODS and statsmodels. To get started using MEIRLOP, see our documentation, which gives you a quick idea of what goes into and out of MEIRLOP so you can use it for your own experiments. For a full usage example that downloads and generates all the data it needs on the fly, see our walkthrough, which recreates commands and output for the section "MEIRLOP identifies enriched TF binding motifs in DNase I Hypersensitive Sites" from the MEIRLOP manuscript.
MEL-MP is a tool for De novo prediction of moonlighting proteins using multimodal deep ensemble learning.
Offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels.
Spanish National Bioinformatics Institute
Predictors of lesion location and postsurgical seizure freedom in focal cortical dysplasia. Website for Multi-centre Epilepsy Lesion Detection (MELD) Project. Updates from the Multi-centre Epilepsy Lesion Detection (MELD) Project. The Multi-centre Epilepsy Lesion Detection (MELD) project is an international collaboration dedicated to improving the detection of lesions in patients with drug-resistant epilepsy.
Run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.
The Mellorater is an animal welfare monitoring app based on the 2020 Five Domains Model, allowing animal guardians to record structured observations and trends. It aims to help owners improve animal welfare through reflective self-reporting.
Melodia is a Python library for protein structure analysis that utilizes differential geometry and knot theory to generate robust geometric descriptors. The library allows for advanced similarity analysis, incorporating sequence structural annotation and 3D visualizations.
Open source framework providing analysis methods for raw GC- and LC-MS metabolome datasets and offers methods to combine the respective results. Flexible tool pipelines allow both the import of pre-processed data as well as the integration of existing open source analysis packages such as XCMS, MassSpecWavelet or metaB. For the identification of metabolites based on mass spectra either the GMD database or user defined libraries in NIST are queried.
Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA.
A user-friendly online tool for epidemiological investigation using High Resolution Melting data. R script for strains clustering/typing and epidemiological investigation using High Resolution Melting (HRM) temperatures. MeltingPlot is a tool for strains clustering/typing and epidemiological investigation using High Resolution Melting (HRM) temperatures.
MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. Each dataset can be also accessed through ExpressView gene clustering and visualisation, and DiffExp for differential expressed genes search.
A two-layer multi-label predictor for identifying multi-functional types of membrane proteins.
Assembly of protein complexes in and on the membrane with predicted spatial arrangement constraints.
Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry.
MemBlob web application calculates the membrane boundaries of transmembrane proteins using cryo-EM densities. The membrane environment used during transmembrane protein structure determination cannot be resolved at the atomic level, but it produces density, which can be utilized to dissect the membrane embedded part of the protein.
Membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.
Web server developed for transmembrane protein structure prediction. It contains two main prediction functions, i.e., transmembrane helix (TMH) prediction and TMH-TMH residue contact prediction.
A Deep Learning-aided Pipeline for Automated Detection of Membrane Proteins in Cryo-electron Tomograms.
This tool inserts channels in a membrane and see what happens. See how different types of channels allow particles to move through the membrane.
Visualising transmembrane protein structure and topology.
An α-Helical Membrane Protein Docking Algorithm.
Tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. This tool represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern.
A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices.
An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
Unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.
memes is an R interface to the MEME Suite family of tools, which provides several utilities for performing motif analysis on DNA, RNA, and protein sequences. memes works by detecting a local install of the MEME suite, running the commands, then importing the results directly into R. A docker container for motif analysis in R using the memes packge. Currently, this container is build from the development branch of bioconductor_docker_meme, which builds a bioconductor docker image + the most current MEME Suite version. This container additionally contains an install of the most recent {memes} package along with all dependencies. It can be used to test out {memes} or to perform containerized data analysis. This repository contains all analysis code associated with the paper 'Memes: an R interface to the MEME Suite'. motif matching, comparison, and de novo discovery using the MEME Suite.
Creates multi-component lipid bilayer membranes for molecular dynamics simulations.
This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.
Structural Mass Spectrometry and Proteomics
Predictor for the subcellular localization of proteins associated or inserted in eukaryotes membranes.
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. MemMoRF database of membrane associated disordered protein regions. Membrane-binding Molecular Recognition Features.
Server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).
Ms2 basEd saMple vectOrization (MEMO) is a method allowing a Retention Time (RT) agnostic alignment of metabolomics samples using the fragmentation spectra (MS2) of their consituents. The occurence of MS2 peaks and neutral losses (to the precursor) in each sample is counted and used to generate an MS2 fingerprint of the sample. These fingerprints can in a second stage be aligned to compare different samples.
Method for identifying mutually exclusive driver networks in cancer. The method identifies networks defined by three properties: first, member genes are recurrently altered via somatic mutation or copy number changes; second, member genes are likely to participate in the same biological pathway or process, as determined from prior pathway and network knowledge; and third, genomic events within the network exhibit a statistically significant level of mutual exclusivity.
Memoir is a web server for template based structure prediction for membrane proteins. Input is a structural template and sequence to be modelled.
Web based bioinformatics platform for the management, storage, and development of metabolic models. It supports the development of new models by providing a built in version control system which offers access to the complete reconstruction history.
Database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable.
Memprot GPCR-ModSim is a web server and associated modules for modeling and simulation of membrane proteins, including GPCRs, using molecular dynamics. It accepts sequence or 3D structures and generates equilibrated systems ready for further simulations.
MemProtMD is a database of over 5000 intrinsic membrane protein structures identified in the Protein Data Bank, inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations.
Prediction of topology and subcellular localization of Eukaryotic membrane proteins.
Allowing mutations in maximal matches boosts genome compression performance. Memrgc is a tool for compression genome sequence. The program is written in C++11 and tested on Red Hat Enterprise Linux 7.5 (64 bit).
MEMSATSVM is a SVM (support vector machines) based TM (Transmembrane Protein) protein topology predictor.
Correctness and response time distributions in the MemTrax continuous recognition task.
2-layer predictor for predicting membrane protein types, the first layer will predict whether the query sequence belongs to membrane proteins or not; and the second layer aims to predict exactly the membrane protein types when the output of the first layer is “membrane proteins”.
This software program performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several novel, statistical genetic tests. Data sets can consist of qualitative or quantitative traits, pedigree or population samples, limited loci or dense SNPs.
This tool uses OpenCL kernels to rapidly impute genotypes using linkage disequilibrium patterns in unrelated subjects. It is appropriate for resequencing data.
Mendelgen is a plasmid editing app that features cloning, sequencing alignment, vaccine design tools, and more.
R-package for heuristic variant filtering.
Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.
Online tool created to help doctors and scientists to identify disease causing variants in human exome/genome sequencing data from patients with Mendelian disorders.
Gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. Initial set-up for standalone MendelVar usage. A new tool that blends your everyday work apps into one. It's the all-in-one workspace for you and your team.
A Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications. Public databases for molecular typing and microbial genome diversity. A collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.
MENDS-on-FHIR leverages the OMOP Common Data Model and FHIR standards to create a pipeline for national chronic disease surveillance, facilitating interoperable data exchange and transformation for distributed data networks.
Topological gap-filling of genome-scale draft metabolic networks.
Individual-patient prediction of meningioma malignancy and survival using the Surveillance, Epidemiology, and End Results database. Meningioma.app is the companion app to our paper, "Individual-patient prediction of meningioma malignancy and survival using the Surveillance, Epidemiology, and End Results database". Individual-patient prediction of meningioma malignancy and survival.
In silico typing of Neisseria meningitidis contigs.
Multi-start Evolutionary Nonlinear OpTimizeR (MENOTR).
MENSAdb (Data-Driven Molecular Design) is a thorough structural analysis of membrane protein dimers.
A MLST caller based on a k-mer counting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes.
Resource for protein-protein interactions (PPI). It integrates data curated by experts in compliance with IMEx curation policies, using the PSICQUIC protocol to implement an automatic procedure that automatically aligns the integrated database with data regularly annotated by the primary databases
An interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny. Medical and Pharmaceutical Statistics Based on Shiny. MEPHAS is a shiny-based statistical software that was developed to support statistical data analyses for medical and pharmaceutical students, researchers, and doctors.
Motif Enrichment Positional Profiling (MEPP) quantifies a positional profile of motif enrichment along the length of DNA sequences centered on e.g. transcription start sites or transcription factor binding motifs.
Cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective.
MeQA is a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets.
De novo genome assembler from short reads.
Versatile high performance toolkit for complete analysis of methylated RNA data.
Web-based tool that can query a database comprising ～4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors.
A versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data.
It is an orthology mapping program suitable for multiple genomes.Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes.
Web server for genome scale functional annotation of plant sequence data.
An R Package for Visualization of Distance Matrices | Clustering and Visualizing Distance Matrices | Defines the classes used to explore, cluster and visualize distance matrices, especially those arising from binary data
Evaluate variant calls and its combination with k-mer multiplicity
Multifunctional R pipeline for small molecule LC-MS/MS data processing, searching, and organizing.
This R extension studies gene expression array data. Its main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculates the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival.
Multidimensional Data Integration. This web aplication serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts: a Marker Set Enrichment Analysis (MSEA) and a weighted Key Driver Analysis (wKDA).
Mergeomics is a computational pipeline consisting of independent modules that 1) leverage multi-omics association data to identify biological processes that are perturbed in disease, and 2) overlay the disease-associated processes onto molecular interaction networks to pinpoint hubs as potential key regulators.
Merges two files containing the results of a sliding windows clustering.
Merge the elements of two lists of genomic coordinates.
Clusterizes the reads when their genomic intervals overlap.
MERIDA (MEthod for Rule Identification with multi-omics DAta), a tool for drug sensitivity prediction in cancer.
An easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data.
An integrated analysis pipeline for MeRIP-seq data based on Nextflow.
Mutation Error Rare Identification Toolkit is a comprehensive pipeline designed for in-depth quantification of erroneous substitutions and small indels in high-throughput sequencing data, specifically, for ultra-deep applications. It considers the genomic context of the errors, including the nucleotides immediately at their 5’ and 3’, and establishes error rates at 96 possible substitutions as well as four single-base and 16 double-base indels.
Web-based integrated Mycobacterial PE/PPE protein database.
Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation
Merlin is a simple, graphical and user-oriented solution for the reconstruction of genome-scale metabolic models. It will guide you along the model reconstruction, providing several tools that help to improve and curate the model throughout the whole process.
An open source automated hit-to-lead method based on deep reinforcement learning.
Collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database can distinguish one peptidase from another through identifying the specificity of the peptidase in terms of where it will cleave substrates and with which inhibitors it will interact.
Free, open-source tool designed to streamline and automate large-scale Mendelian Randomization analysis.
Reference-free quality, completeness, and phasing assessment for genome assemblies. Evaluate genome assemblies with k-mers and more. Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. Merqury provides a set of tools for this purpose.
Micromagnetic Earth Related Robust Interpretated Language Laboratory.
Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.
Automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors. A flexible DNA Error Detection and Simulation Framework. MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing, and PCR errors.
microRNA expression and sequence analysis database is a database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets.
Fast and accurate cDNA mapping and splice site identification.
A powerful statistical framework for Genome-Scale mutual exclusivity analysis of cancer mutations. MEScan is an accurate and efficient statistical framework for genome-scale mutual exclusivity analysis of cancer mutations. We provide an example dataset from TCGA Ovarian Cancer to demonstrate the pipeline for large scale ME patterns survey using MEScan. The pipeline has several steps as shown in the DAG below.
High-quality clustering of DNA sequences using the mean shift algorithm and alignment-free identity scores.
The package is a unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interfaced to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.
NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. This tool supports enrichment analysis of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups.
A set of annotation maps describing the entire MeSH assembled using data from MeSH.
Provide for measuring semantic similarity over MeSH headings and MEDLINE documents.
A tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations.
Scientific tool designed to identify characteristic structures or components in heterogenous solutions from bulk-average data. It does this by evolving a population of ensembles containing candidate components, selecting only ensembles that fit the available experimental data better than their peers.
Open-source light-sheet microscopes for imaging cleared tissue | Hardware documentation for the mesoSPIM microscope project | Control software for mesoSPIM microscopes | MATLAB tools for handling mesoSPIM data | The mesoSPIM (mesoscale selective plane illumination microscopy) project creates open-hardware microscopy platforms for imaging cleared tissue | Members of the mesoSPIM initiative organize a variety of workshops for the community
A mesocosm database management system for environmental nanosafety.
A tool for stochastic simulation of reactions and diffusion.
Mesoscope is a web-based data integration and curation tool. Mesoscope allows users to begin with a listing of molecules (such as data from proteomics), and to use resources at UniProt and the PDB to identify, prepare and validate appropriate structures and representations for each molecule, ultimately producing a portable output file used by CellPACK and other modeling tools for generation of 3D models of the biological mesoscale.
Database of metal coordination groups in proteins.
Snakemake pipeline for simulating shotgun metagenomic samples
Automated recommendation of metabolite substructures from tandem mass spectra. MESSAR 0.1 (MEtabolite SubStructure Auto-Recommender).
Software for transforming messy research datasets into clean submissions to metabolomics workbench for public sharing.
Identifying signaling genes in spatial single cell expression data. MESSI (Mixture of Experts for Spatial Signaling genes Identification) is a predictive framework to identify signaling genes active in cell-cell interaction. It jointly models gene interactions within and between cells, using the recently developed spatial single cell expression data. MESSI combines the ability to subdivide cell types with multi-task learning to accurately infer the expression of a set of response genes based on signaling genes and to provide useful biological insights about key signaling genes and cell subtypes.
Collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.
The Motif Enrichment Tool (MET) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif. The tool is available for a number of model organisms (human, mouse, zebrafinch, stickleback, fruitfly, etc). It incorporates transcription factor DNA-specificity motifs taken from literature curation, bacterial one-hybrid assays, high-throughput SELEX experiments, and protein binding microarrays.
Mass spectrum-oriented computational method for ion mobility-resolved untargeted metabolomics.
Java library for metabolic networks. Singularity and docker containers allow to use met4j without installing Java or computational skills. Met4j apps allow to parse and edit SBML and to analyse the network with graph analysis.
meta is a program to produce and to align the TF-maps of two gene promoter regions. meta is very useful to characterize promoter regions from orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites.
A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads.
Meta-Analysis Accelerator is a web-based tool designed to simplify statistical data conversion for systematic reviews and meta-analyses, offering 21 different conversions between common statistical measures.
META-BASE is a big repository of genomic datasets homogenized with the Genomic Data Model format, including Encode, TCGA, Roadmap Epigenomics, 1000 Genomes and others.
A tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.
META-BOA (METAbolomics data Balancing with Over-sampling Algorithms) is a software solution for handling sample imbalance primarily for metabolomics and lipidomics datasets.
A web application for meta-analysis of diagnostic test accuracy data.
A generalised, dynamic DNA reference library for metabarcoding of fishes
Set of post-processing tools aimed at improving the taxonomical classification and at providing additional information to enhance metagenomics analyses. The developed tools provide additional proofs in the presence of low-abundant species, information of the mapping quality in coding and noncoding regions, etc.
An interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. DNA N6-Methyladenine Site predictor.
A sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation. PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using Scoring Card Method. In this work, we developed a novel PVP predictor named PVPred-SCM which is an efficient and interpretable method for predicting and analyzing PVPs.
Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.
Similarity search in heterogeneous knowledge graphs via meta-paths.
Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation. Meta-Prism aims to conduct quick query in large-scale metagenomics database. The method is based on three computational techniques: dual-indexing approach for sample sub-grouping, refined scoring function that could scrutinize the minute differences among samples, and parallel computation based on GPU computing.
Meta-predictor of disease causing variants.
Metagenomic database system toolkit to systematically and efficiently organize and search metagenomic data.
Meta4P (MetaProteins-Peptides-PSMs Parser) is an easy-to-use bioinformatic application designed to integrate label-free quantitative metaproteomic data with taxonomic and functional annotations. Meta4P can retrieve, filter and process identification and quantification data from three types of inputs (proteins, peptides, PSMs) in different file formats. Abundance data can be combined with taxonomic and functional information and aggregated at different and customizable levels, including taxa, functions, pathways, as well as taxon-specific functions. Meta4P output tables, available in various formats, are ready to be used as inputs for downstream statistical analyses.
The metaFALCON (metadynamics package For the Automatic Localization of CONical intersections) software package for automatic sampling of conical intersection seams using multistate metadynamics.
metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.
The metaRbolomics Toolbox in Bioconductor and beyond | Metabolomics in R and Bioconductor | The term metaRbolomics has been coined for a workshop at the 2016 annual conference of the international Metabolomics society in Dublin, Ireland | Jan Stanstrup, Corey D
A 16S rRNA gene sequencing count data simulator. A rule-based model of insulin signalling pathway. Di Camillo B, Sambo F, Toffolo G, Cobelli C. ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. Bioinformatics 30(3):384-391. Patuzzi I., Baruzzo G., Losasso C., Ricci A., Di Camillo B. "metaSPARSim: a 16S rRNA gene sequencing count data simulator", Submitted to BMC Bioinformatics, October 2018
A comprehensive database on adverse drug events. MetaADEDB is an online database we developed to integrate comprehensive information of adverse drug events (ADEs). The new version consists of 744,709 drug-ADE associations between 8,498 compounds (including more than 3000 drugs) and 13,193 ADEs by integrating more and newer data from U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Data-base in addition to the Comparative Toxicogenomics Database (CTD), SIDER and OFFSIDES. Additionally, Compared to the previous version, MetaADEDB 2.0 has an over 40% increase in drug-ADE associations and almost 200% growth in the total number of compounds. Notably, we directly generated a unique identifier for each compound based on the chemical structure, and UMLS ID was used as unique identifier for ADE to ensure the quality of data.
MetaAnalysis Online is a web-based bioinformatics tool for fast and user-friendly meta-analysis of clinical and epidemiological data. It supports importing various input types (HR, OR, RR with CI, means ± SD, proportions, incidence rates) and automatically generates forest, funnel, and Z-score plots, as well as summary tables. Key features: Fixed or random effects models, heterogeneity estimation (I², τ²) Subgroup analysis and flexible method selection (e.g., Mantel–Haenszel, DerSimonian–Laird) Exportable plots (PDF, PNG) and customizable result displays
A user-friendly tool for metagenomic biomarker detection and phenotype classification.
Data transformation for meta-analysis of microarray data: Transformation of gene expression data to signed probability scale (MCMC/EM methods). Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.
R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, it considerably speeds up the data mining process in metabolomics and produces better quality results.
An R package for the evaluation and improvement of DNA metabarcoding data quality. Evaluation and Improvement of DNA Metabarcoding Data Quality. metabaR is an R package enabling the import, handling and processing of DNA metabarcoding data that have been already processed through bioinformatic pipelines. It provides functions to reveal and filter common molecular artifacts produced during the experimental workflow. This package can be easily used in combination with others R packages commonly used in ecology (vegan, ade4, ape, picante, etc.), and provides flexible graphic systems based on ggplot2 to visualise the data under both ecological and experimental perspectives.
The database of biological databases. A community-curated database containing more than 2000 commonly used biological databases.
Metagenomics binning by coverage and composition for long reads.
metabCombiner is a R package for paired untargeted LC-HR-MS metabolomics feature matching and concatenation of disparately acquired datasets.
Program for accurate, fast and highly sensitive taxonomic assignments of metagenomic sequences
A high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities.
MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.
Mixed model normalization method for metabolomics data.
Statistical, functional and integrative analysis of metabolomics data , interpretation, and integration with other omics data.
MetaboAnalystR is an R-based workflow designed to streamline LC-MS metabolomics data analysis, covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. It provides a unified, end-to-end pipeline for metabolomic research.
Web portal to gather tools to improve metabolomic annotations through API microservices based on a cloud infrastructure.
Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.
An analytical pipeline for the processing of FT-ICR MS-based metabolomic data. A comprehensive command-line based pipeline for the analysis of direct injection FT-ICR mass spectrometry data.
A comprehensive data extraction tool for untargeted metabolomics. We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis
A scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes | A scalable high-throughput metabolic and biogeochemical functional trait profiler | This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets. These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or pure culture sequenced genomes. It can also calculate the genome coverage. The information is parsed and diagrams for elemental/biogeochemical cycling pathways (currently Nitrogen, Carbon, Sulfur and "other") are produced
Linking metabolic network features to phenotypes using sparse group lasso.
A deep learning architecture for metabolic pathway prediction. This code is an implementation of our graph-convolutional network (GCN) and random forest (RF) classifiers for predicting one or many metabolic pathway classes for a query compound (paper accepted at Bioinformatics, Oxford University Press). Baranwal, Mayank, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, and Alfred Hero. "A deep learning architecture for metabolic pathway prediction." Bioinformatics (2019).
Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications. Metabolic Atlas is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. In short, the vision is to create a one-stop-shop for everything metabolism related.
Database for Metabolomics experiments and derived information.
A web application for Streamlined Processing and Analysis of Large-Scale Untargeted Metabolomics Data.
Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs. metabolisHMM: a tool for exploration of microbial phylogenies and metabolic pathways. Constructing phylogenies and performing functional annotations with HMM markers. Welcome to the metabolisHMM wiki!. metabolisHMM is a pipeline for visualizing the distribution and evolutionary relationships using curated and custom Hidden Markov Model (HMM) profiles. metabolisHMM is a tool for visualizing the distributions and evolutionary histories of specific metabolic markers
An integrated userfriendly workflow for metabolomics multi-study analysis. This is a Shiny-App with the aim of facilitating association and covariate selection for targeted metabolomics data from multiple studies with a wide range of factors (demographic, lifestyle, etc.). Features of the App are:.
An application to process and visualise metabolite data in the web-browser.
QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments.
Metabolizer is a web tool for analysis of modular architecture of metabolic pathways using transcriptomic data. Metabolizer calculates impact of modules on production of metabolites. These modules are conserved part of metabolism which starts with substrate(s) and ends with a product.
Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability.
An international data aggregation and notification service for metabolomics.
MetabolomicsR is a streamlined R package to preprocess, analyze, and visualize metabolomic data.
Freely-available software tools for metabolomics analysis.
Pathway sharing and multi-omics data visualization in metabolic context. MetaboMAPS is a web project for manipulating metabolic pathways in SVG format. MetaboMAPS consists of two main parts: the visualization tool, where users can plot their own data set, and the plot box editor, where users can add or change the areas for visualization (plot boxes) and assign identifiers to them.
Tool which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. It is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data.
The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.
A toolbox to interactively create, customize and explore multi-systemic metabolic reaction networks
A pipeline of metabolomics data processing and quality control
MetaboReport is a versatile web application designed to simplify metabolomics data analysis and reporting. It provides tools for experiment design, data preprocessing, statistical analysis, visualization, and report generation, tailored for research labs and metabolomics core facilities.
Performs mass-based metabolite search simultaneously against the four major metabolite databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LipidMaps.
R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling or enzymatic genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.
Exploring Individual Variation in Metabolite Levels.
Automated exploration and contextualization of metabolic data. Visualizing and Analyzing Metabolic Networks. Integrating multi- or single-omic metabolic data upon the metabolic network can be challenging for a variety of reasons. Metaboverse seeks to simplify this task for users by providing a simple, user-friendly interface for layering their data on a dynamic representation of the metabolic network and automatically searching the network for interesting regulatory or other patterns. Additionally, Metaboverse provides several tools to enable the contextualization of metabolic data:.
Enabling network-based integrative analysis via direct protein interactors of metabolites.
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid
A big data approach to metagenomics for all-food-sequencing.
Performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.
Distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.
Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning. MetaChrom is a transfer learning framework that takes advantage of both an extensive compendium of publicly available chromatin profiles data, and epigenomic profiles of cell types related to specific phenotypes of interest. It's capable of predicting the genomic variant effect on epigenomic profiles with single-nucleotide resolution. Please see paper for details.
A machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data. Detection of Low-Quality Peaks in Untargeted Metabolomics Data.
Unsupervised binning method for metagenomic sequences. Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorganisms and phylogenetic markers.
A consensus approach to infer accurate copy numbers from low coverage data. The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples.
MetaCoAG is a metagenomic contig binning tool that makes use of the connectivity information found in assembly graphs, apart from the composition and coverage information. MetaCoAG makes use of single-copy marker genes along with a graph matching technique and a label propagation technique to bin contigs. MetaCoAG is tested on contigs obtained from next-generation sequencing (NGS) data. Currently MetaCoAG supports contigs assembled using metaSPAdes and MEGAHIT.
Package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data.
Tool for meta-omics comparative analysis.
MetaCompare is a bioinformatic pipeline and web service that ranks resistome risks across metagenomic sequencing data, differentiating between human health and ecological risks. It projects samples into a hazard space and calculates risk scores based on antibiotic resistance gene (ARG) mobility.
MetaCompass is a software package for comparative assembly of metagenomic reads. MetaCompass achieves comparable assembly performance to the state of the art de novo assemblers, but these two different approaches complement each other a lot. So combining contigs between MetaCompass and other independent de novo assemblers give us the best overall metagenomic assembly.
Capturing variation in metagenomic assembly graphs with MetaCortex.
A web-application for living meta-analyses of COVID-19 trials.
Pipeline for taxonomy identification and lossless compression of FASTA-format metagenomic reads. It integrates algorithms for taxonomy identification, read alignment, assembly, and finally, a reference-based compression method in a parallel manner.
Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models.
MetaCV is a composition and phylogeny based algorithm to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. MetaCV performs (for both sensitivity and specificity) as good as BlastX-based methods on simulated short reads, but runs 300 times faster thus provides effectively and efficiently analysis on huge amount of NGS data.
The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.
This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.
A method of using global evidence for local decision making. Metadataset (www.metadataset.com) is a collection of open data from scientific publications. These publications are about the management of agricultural and natural resources (e.g., crops, soil, water, and wildlife). The data are extracted from scientific publications, standardized, and summarized using dynamic meta-analysis. Metadataset is a collection of open data from scientific publications.
Meta web server to predict DNA-binding residues for DNA-binding proteins. It integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED and it solely uses sequence information of proteins.
meta-analysis of differential expression analyses (metaDEA) is a simple package that provide easy functions to integrate the results of previously computed differential expression analyses to find out the genes that are more consistently differentially expressed across different comparisons and their statistics.
MetaDegron is a web service and deep-learning framework for predicting E3 ligase targeted degrons by integrating protein language models and comprehensive featurization strategies. It allows prediction of targeted degrons for 21 E3 ligases and provides functional annotations and visualization of degron-related features.
A background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.
Java/R-based software package that performs differential expression analysis on RNA-Seq based data.
Prediction method that molds various sources of information predominantly obtained from orthogonal prediction methods which focus on different types of disordered regions.
A Combinatorial Molecular Docking Approach.
An R shiny application for meta-analysis of diagnostic test accuracy and sensitivity analysis of publication bias.
An interactive web viewer of metadynamics results.
University of Chemistry and Technology Prague, Czech Republic
Molecular simulations are slow because the system usually gets stuck in local energy minima. To address this problem, metadynamics uses an artificial bias potential calculated adaptivly during the simulation. Metadynminer is R package for analysis and visualization of metadynamics results, primarily from popular Plumed package.
Metadynreporter is a Galaxy portal that generates a PDF report based on data from metadynamics simulation done in Plumed (https://www.plumed.org/).
MetaFetcheR is an R package designed to link metabolites IDs from different Metabolome databases with eachother in a step to resolve ambiguity and standardize metabolites representation and annotation. Currently the package supports resolving IDs for the following databases: Human Metabolome Database (HMDB), Chemical Entities of Biological Interest (ChEBI) PubChem, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Lipidomics Gateway (LipidMaps).
Java-based feature analysis tool that enables real-time, interactive correlation analysis of feature sets, discovery of addtional related features and analysis of related metabolites. It is designed specifically to aid feature analysis within NMR metabolomics data.
MetaFun is a web tool for the integration and functional characterization by unveiling sex differences in multiple omics studies through comprehensive functional meta-analysis.
Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes. Create the nrgo database for the metafunc workflow.
An Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes.
A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates.
MetaGenomic analysis of short and long reads. This directory contains the query files used to test MetaG. Due to file size limitations, the databases can be found here:.
MetaGate is an R package and shiny-based web application for interactive statistical analysis and visualization of high-dimensional cytometry data, facilitating data sharing and integration with metadata.
Reconstruction of genome scale metabolic models directly from metagenomes. A Snakemake-based workflow to generate high quality metagenome assembled genomes from short read paired-end data, reconstruct genome scale metabolic models, and perform community metabolic interaction simulations on high performance computing clusters. metaGEM integrates an array of existing bioinformatics and metabolic modeling tools using Snakemake, for the purpose of interrogating social interactions in bacterial communities of the human gut microbiome. From WMGS datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for in silico simulations of cross feeding interactions within sample based communities. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification.
metagen performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables
User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.
This package produces metagenic plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.
Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.
A standardized database to study deep sequenced metagenomic data from human fecal specimen.
MetaGeneMark is a tool for gene prediction in metagenomes, utilizing metagenome parameters and gene prediction.
Managing and analytical bioinformatics framework that is engineered to run dedicated Galaxy workflows for the detection and eventually classification of pathogens.
Metagenome@Kin is an automated high throughput sequencing data analysis tool for the 16S/28S/ITS rRNA genes. It measures the composition and diversity of microbial and fungal species in natural environments.
Pipeline for parallel computing of improved metagenomic assembly using Spark-based computing and Hopsworks platform
Developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.
Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Comprehensive inference and meta-insights for microbial correlation networks. Microbial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations.
MetaGenyo is a simple, ready-to-use software which has been designed to perform meta-analysis of genetic association studies.
metaGOflow is a pipeline based on MGnify and its workflows, aiming to address the challenges of the analysis of the European Marine Omics Biodiversity Observation Network (EMO BON) data. EMO BON is a long-term omics observatory of marine biodiversity that generates hundreds of metagenomic samples periodically from a range of stations around Europe.
Indexing and Analysing Nucleotide Archives at Petabase-scale. This repository contains resources related to the manuscript describing the MetaGraph framework, such as supplemental data tables containing sample metadata, example scripts and interactive notebooks. Please find below a more detailed description of each category under the respective section. The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest. Read more in the paper preprint.
metaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by transcripts.
Novel gene prediction method for metagenomic fragments based on a machine learning approach of SVM.
metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.
A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.
MetaHD is an R package for multivariate meta-analysis of high-dimensional metabolomics data, designed to account for correlation between metabolites, missing values, and variability across studies. The package is available on CRAN and includes a detailed vignette with example datasets and code.
Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.
A metaheuristic method based on the reactive model of neighborhood consensus for continuous optimization.
Metaheuristic reactive model-based on neighborhood consensus for continuous optimization
An information repository of mammalian imprinted genes.
Tool to perform meta-analysis of summary statistics obtained from a series of related studies. The special feature of it is the ability to meta-analyze the results of multiple linear and logistic regression models, broadly used in genome-wide association studies (GWAS).
Pseudoalignment for metagenomic read assignment.
Program that facilitates the meta-analysis of genomewide association scans.
A flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. MetaLAFFA is a flexible, end-to-end, and compute cluster-compatible metagenomic functional annotation pipeline. MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional orthology groups. This process consists of several steps to go from raw FASTQs (with sequencing adapters removed) to functional profiles:.
MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.
An open-access docking tool for easy and reproducible docking of metal complexes.
Efficient alignment-based metagenomic profiling via containment min hash. Metalign is a method for estimating the taxonomic composition and relative abundances of organisms in a metagenomic sample based on whole-genome shotgun sequencing reads.
A Simple Open-Source Laboratory Information Management System for Small Metagenomic Labs.
metagenomics Taxonomic Assignation pipeline in Snakemake
Novel bioinformatic method for predicting metal-binding sites in RNA structures.
METALizer predicts the coordination geometry of metals in metalloproteins. Potential coordination geometries of metals are matched onto the found metal interactions in the examined structure. The predicted coordination geometries and the observed metal interaction distances can be compared interactively to statistics calculated on the PDB.
Metabolic analysis of logical models extracted from molecular interaction maps.
MetaLogo is a tool for making sequence logos. It can take multiple sequences as input, automatically identify the homogeneity and heterogeneity among sequences and cluster them into different groups given any wanted resolution, finally output multiple aligned sequence logos in one figure. Grouping can also be specified by users, such as grouping by lengths, grouping by sample Id, etc. Compared to conventional sequence logo generator, MetaLogo can display the total sequence population in a more detailed, dynamic and informative view.
Knowledge on metal sites in biological macromolecules, built on structural information in the Protein Data Bank (PDB).
Allows two metal-binding sites to be structurally aligned, independently of protein fold.
Simulating electrochemical interfaces between polarizable electrolytes and metallic electrodes.
Integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks.
MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.
MetAMDB is a software/database for the analysis of metabolic models and specifically the work with atom mappings.
MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity.
Meta-analysis of genome-wide DNA methylation and integrative OMICs in human skeletal muscle. EWAS meta-analysis of age in human skeletal muscle.
Integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.
metaMIC is a fully automated tool for identifying and correcting misassemblies of (meta)genomic assemblies with the following three steps. Firstly, metaMIC extracts various types of features from the alignment between paired-end sequencing reads and the assembled contigs. Secondly, the features extracted in the first step will be used as input of a random forest classifier for identifying misassembled metagenomic assemblies. Thirdly, metaMIC will localize misassembly breakpoints for each misassembled contig and then correct misassemblies by splitting into parts at the breakpoints.
R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models.
Metagenomic microbial interaction simulator based on microbial community profiles.
Bayesian mixture model framework for resolving complex metagenomic mixtures.
MetaMobilePicker is an open-source pipeline for identifying antimicrobial resistance genes (ARGs) associated with mobile genetic elements in metagenomic data. It combines existing tools to streamline the process of identifying ARGs linked to plasmids, insertion sequences, and phages, starting from short metagenomic sequencing reads.
A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics.
A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta analysis.
MetAMOS is an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations.
MS-based metabolomics data processing and compound annotation pipeline.
A multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.
An R package for multi-environment trial analysis. metan (multi-environment trials analysis) provides useful functions for analyzing multi-environment trial data using parametric and non-parametric methods. The package will help you to:.
MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.
Software tool in MATLAB for network construction and biologically significant module detection.
A new paradigm for data sharing in photonics research. Jonathan Fan, Stanford University. GLobal Optimization NETwork or GLOnet is a global optimizer, based on a generative neural network, which can output ensembles of highly efficient topology-optimized metasurfaces. This is a toolbox to convert .mat files on MetaNet into GDS files.
MetaNetX/MNXref allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models.
metano is an open-source software toolbox for analyzing the capabilities of metabolic networks and for assisting in metabolic reconstruction.
An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.
Tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experiment data in mind.
The server automates data analysis for the processing of metabolomics experiments.
A Web Application for Analyzing the Biological Activity Spectrum of Organic Compounds Taking into Account their Biotransformation.
MetaPath is a tool for meta analysis pathway enrichment.
MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.
A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.
MetaPathways is a meta’omic analysis pipeline for the annotation and analysis for environmental sequence information. MetaPathways include metagenomic or metatranscriptomic sequence data. The pipeline consists of four operational stages including: Quality Control, Feature Prediction, Functional Annotation, Pathway Inference.
MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.
An automated pipeline for analyzing, annotating, and classifying bacteriophages in metagenomics sequencing data.
Detecting and Decomposing Multivariate Associations From Univariate Genome-Wide Association Statistics. MetaPhat is an open sourced program to detect best subset traits on lead multivariate SNP associations from related sets of GWAS summary results. Best traits are derived from systematic decomposing multivariate associations into central traits based on optimal BIC and P-value from multivariate CCA models. Variant trace results are plotted and clustered to dissect and improve the specificity of phenotype(s)-genotype associations.
Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. Currently, over 117,131,162 of unique homologs are deposited in MetaPhOrs database. These predictions were retrieved from 8,246,911 Maximum Likelihood trees for 4,094 species. For each prediction, MetaPhOrs provides a Consistency Score and Evidence Level describing its goodness, together with number of trees and links to their source databases.
Novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length.
Virtual laboratory which aims at assisting modellers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes. Its framework is based on a core module which enables to design and manage biological models, and an extensible set of plugins by which MP models can be generated, optimized, simulated and analysed.
metaplasmidSPAdes - tool for assembling plasmids from metagenomic data sets
MetaPlatanus is a de novo assembler for metagenome (microbiome). The features of this tool are as follows: (1) It can utilize various types of long-range information such as Oxford-Nanopore/PacBio long reads, mate-pairs (jumping libraries), and 10x linked reads (experimental). (2) Coverage depths, k-mer frequencies and results of the binning tool are also employed to extend sequences and correct mis-assemblies, reducing inter-species misassemblies. (3) Contig-assembly, scaffolding, gap-closing and binning are automatically executed at once. (4) MetaPlatanus requires at least one short-read paired-end library.
A Bioconductor package for joint pathway testing for untargeted metabolomics data.
A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
The metaPR2 database contains processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. Version 2.0 of the database contains 41 datasets corresponding to more than 6,000 samples and 90,000 ASVs. The database is accessible through both a web-based interface (https://app.metapr2.org) and an R package.
MetaPred is a meta-learning framework for Clinical Risk Prediction using limited patient Electronic Health Records (EHRs).
Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs).
MetaPred : A webserver for the Prediction of Cytochrome P450 Isoform responsible for Metabolizing a Drug Molecule
A machine learning-based tool for predicting protein disorder.
MetaPredictor is a rule-free and prompt-based method for in silico prediction of human drug metabolites using deep language models. It leverages prompt engineering to improve accuracy and generalization compared to traditional approaches.
Metapreg is a Stata tool for performing meta-analysis, network meta-analysis, and meta-regression of binomial proportions, employing advanced statistical procedures and generalized linear models.
A Toolkit for Joint Taxa/Gene Analysis of Metagenomic Sequencing Data. MetaPrism: A Toolkit for Joint Analysis of Meta-genomic Sequencing Data. MetaPrism provides joint profile (infer both taxonomical and functional profile) for shotgun metagenomic sequencing data. It also offer tools to 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) build asso-ciation and prediction models for comparative analysis.
A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. MetaPro: Meta-analysis pipeline for Transcriptomics + Genomics. The MetaPro Meta Transcriptomics/Genomics Pipeline is a software tool that will perform Transcriptomics and Genomic analysis on Paired and Single Reads of FASTQ data.
An MS1 Profiling Approach for Large-Scale Microbiome Screening.
MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant genetic variants
Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics. This repository contains the source code of the MetaProfiler software package. It provides calculations for local false discovery rates of protein-based stable isotopic probing (SIP) results and performs taxonomic, functional, phylogenetic, and time series analysis of microbiome dynamics.
Pipeline to analyze metaproteomics data, supporting MGF and X!Tandem, OMSSA and Mascot.
Algorithm incorporating different approaches of contact predictions implemented with a neural network in order to improve the accuracies of the predicted contacts.
MetaQC: A diagnosis tool for assessing quality of genomic studies for meta-analysis and determining inclusion/exclusion criteria.
MetaQTL is a Java package designed to perform the integration of data from the field of gene mapping experiments (e.g molecular markers, QTL, candidate genes, etc…). This package consists in a modular library and several programs written in pure Java. These programs can perform various tasks, including formatting, analyzing and visualizing data or results produced by MetaQTL.
MetaQuad is a tool designed to detect shared informative variants in a population of shotgun metagenomic data. It uses a density clustering model to assess the informative variants among background noise. MetaQuad is an extension of MQuad, specifically tailored to support shotgun metagenomic data.
Evaluates and compares metagenome assemblies based on alignments to close references. It is based on QUAST genome quality assessment tool, but addresses features specific for metagenome datasets.
Web application for rapid and quantitative analysis of specific genes in the human gut microbiome.
Prioritization of the entire protein-coding part of the human genome based on heterogeneous user-specified data sets.
R package for motif discovery via meta-analysis of microarrays and RNA-Seq. metaRE R Package for Meta-analysis of Transcriptome Data to Identify the Cis-regulatory Code behind the Transcriptional Reprogramming.
metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.
MetaRNN and MetaRNN-indel are pathogenicity prediction scores for human nonsynonymous SNVs (nsSNVs) and non-frameshift (NF) indels. They integrated information from 28 high-level annotation scores (16 functional prediction scores) and produce an ensemble prediction model with a deep recurrent neural network (RNN). The final prediction is the likelihood of a nsSNV or NF indel being pathogenic.
A pipeline for prediction of Metagenome and whole-genome opeRons. MetaRon (Metagenomic opeRon prediction pipeline) is a computational workflow for the prediction of operons from metagenomic data. The pipeline predicts metagenomic operons without any any functional or experimental data. It comes with options to process the metagenomic data starting from filtered raw reads, which includes: assembly into scaffolds via IDBA, data manipulation, gene prediction via prodigal and lastly operon prediction based on gene's co-directionality, intergenic distance (IGD) and promoters.
MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.
Metaphase selection tool using a Gaussian-based classification technique.
The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
metaseqR2 provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way. In the new version, the underlying PANDORA algorithm has been extended with additional statistical analysis tools, the report has been completely redesigned and is fully ineractive, there is an annotation database building system and all actions run 5-50x faster.
Interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.
Accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
Metashot/prok-quality is a comprehensive and easy-to-use pipeline for assessing the quality of prokaryotic genomes.
The software can be used to generate collections of synthetic reads.
R package for multiple marker meta-analysis. It can carry out meta-analysis of SKAT, SKAT-O and burden tests with individual level genotype data or gene level summary statistics.
Pipeline for calling metagenomic single nucleotide variants (SNVs). It was designed to scale well with the exponentially increasing amount of metagenomic datasets and is capable of handling large multi-species references.
Cloud engine and platform for metabolite annotation for imaging mass spectrometry
Genome assembler for metagenomics datasets.
Unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering. It clusters all experimentally observed MS/MS spectra based on their spectral similarity and create a representative consensus spectrum for each cluster by using the spectrum clustering algorithm implemented in the spectral library search engine, SpectraST.
Software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents.
MATLAB-based package which simulates 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database.
Well-balanced Secondary Structure predictor.
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies.
Employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher’s exact test.
Metastudent predicts Gene Ontology (GO) terms from the Molecular Function Ontology (MFO) and Biological Process Ontology (BPO) for input protein sequences by homology-based inference from already annotated proteins.
Accurate method-aware merging algorithm for structural variations.
MetaTASSER is a protein tertiary prediction method that employs the 3D-Jury approach to select threading templates from SPARKS, SP3 and PROSPECTOR_3, which provides aligned fragments and tertiary restraints as an input to TASSER (Threading/ASSEmbly/Refinement) procedure to generate full-length models.
Meta-components of the Tumor Immune Microenvironment. Data driven framework to overcome the limitations in resolution and consistency that result from manual labelling using known gene markers. Using millions of TME single cells, MetaTiME learns meta-components that encode independent components of gene expression observed across cancer types. The meta-components are biologically interpretable as cell types, cell states, and signaling activities. By projecting onto the MetaTiME space, we provide a tool to annotate cell states and signature continuums for TME scRNA-seq data.
Estimating the biological activity spectra of drug-like compounds taking into account probable biotransformations.
MetaTrass is abbreviation to Metagenomics Taxonomic Reads For Assembly Single Species. MetaTrass is based on high-quality referencess with taxonomic tree and long-range information encoded within co-barcoded short-read sequences. The comprehensive use of co-barcoding information and references in our approach can reduce the false negative effects of genome taxonomy to assembly high-quality metagenomes from the sequencing data.
Visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.
STATA program for estimating trends in cumulative meta-analysis. The author propose a simple and formal regression-based approach for detecting trends in cumulative meta-analysis.
Advancing biomedical annotation empowering relation annotation and collaboration.
Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequences predicted from genomes and metagenomes. METATRYP allows users to investigate the occurrance of tryptic peptides within the protein coding sequences predicted from genomes. Testing for the Corona-2 (COVID-19) virus has utilized RNA and antibody analytical methodologies to date. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequences predicted from genomes and metagenomes.
Deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. The MetaTX is aimed for plotting the transcriptomic distribution of RNA-related genomic features.
Introducing metavariant species models for reference-free metagenomic-based population genomics. metaVaR: MetaVariant Species (MVS) for reference-free and metagenomic-based population genomic analysis. metaVaR is a R package developed for population genomic analyses based on variants generated directly from metagenomic data without reference genomes or transcriptomes.
MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
A MetaVelvet deep learning extension for de novo metagenome assembly.
metaviralSPAdes - tool for assembling plasmids from metagenomic data sets
Software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets.
Interactive visualization and exploration of metagenomic sequencing data. Provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots. It supports a flexible plugin framework so users can add new d3 visualizations.
Websocket communication to the metaviz web app for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported, while providing an easy mechanism to support other data structures.
A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments. MetaWorks consists of a Conda environment and Snakemake pipeline that is meant to be run at the command line to bioinformatically processes Illumina paired-end metabarcodes from raw reads through to taxonomic assignments. MetaWorks currently supports a number of popular marker gene amplicons and metabarcodes: COI (eukaryotes), rbcL (eukaryotes, diatoms), ITS (fungi), 16S (prokaryotes), 18S (eukaryotes, diatoms), 12S (fish), and 28S (fungi). Taxonomic assignments are made using the RDP classifier that uses a naive Bayesian method to produce taxonomic assignments with a measure of statistical support at each rank.
MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.
An Automatic and Comprehensive Pipeline for Processing Untargeted Metabolomics Data.
Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets
Software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
metaXplor is an interactive viral and microbial metagenomic data manager. It aims at storing large volumes of user-defined sample, sequence and assignment information while providing a user-friendly fine-filtering web-interface. This online GUI also offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. metaXplor is available as a set of Docker containers that make it simple to deploy on various infrastructures.
A database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.
A Software Tool for Detection of Interaction between Metal Ion-RNA Base Pairs.
Web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics.
Screening for inborn errors of metabolism using untargeted metabolomics and out-of-batch controls. This repository contains code and datasets used for the article Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism published in MDPI Metabolites:.
Pipeline to explore structural similarity across metabolite modules.
This tool comprises a workflow to interactively explore metabolomics data by creating MSP or calculating m/z values and the similarity between precursors.
METdb is a genomic reference database dedicated to micro-eukaryotic marine species transcriptomes. Most datasets were from Marine Microbial Eukaryote Transcriptome Sequencing Project and others from Roscoff marine station and Tara research projects. All datasets were assembled and analyzed using two workflows dedicated to de novo assembly and functional annotation both developed with the CWL workflow management system. The assembly compartment includes evaluation, filtering and trimming of raw data and the de novo assembly and evaluation of assembled transcripts. The annotation compartment defines the presence of coding regions and functional annotation is performed. The resource includes transcriptome assemblies and associated data (metrics and annotations) of 463 distinct marine micro-eukaryotic taxa.
App for Cytoscape, the bioinformatics network visualization tool. The app is used to annotate a metabolic network with MeSH disease terms, explore related diseases within a network, and link to PubMed references corresponding to any network node and selection of MeSH terms.
Transforming and analyzing clinical metabolomics data with convolutional neural networks.
Creates visualizations of genome-scale, metabolic models. These “reaction maps” can be used to visualize high-throughput expression data using the companion program MetColor.
An R package and web application for metabolomics enrichment and pathway analysis in Metabolomics Workbench. Metabolite enrichment analysis and their associated enriched pathways. MetENP is a R package that enables detection of significant metabolites from metabolite information (names or names and concentration along with metadata information) and provides.
An operational online three-dimensional forecasting platform for lake hydrodynamics. The online platform for monitoring and forecasting the bio-physical state of Swiss lakes. This product is developed, managed and maintained by Theo Baracchini and part of his PhD thesis. The application shares with the public some results of 3D hydrodynamic-biological simulations performed daily with the Delft3D modelling framework on a compute server. Additionally, it displays measurements from a field station with data connexion and remote sensing images downloaded from satellites in real-time.
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.
Metabolomics Explorer Application for Natural Product Discovery.
Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation.
Web application designed for the identification of regulated metabolite families. This is possible on the basis of metabolite profiles for a set of MS¹ features as well as one MS/MS spectrum for each MS¹ feature. Group-discriminating MS¹ features are identified using a PCA of metabolite profiles and metabolite families are identified using a HCA of MS/MS spectra. Regulated metabolite families are identified by considering group-discriminating MS¹ features from corporate metabolite families.
Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.
It combines compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. It supports candidate structure retrieval from the compound databases PubChem, ChemSpider and KEGG or user defined structure data file(SDF). After in silico fragmentation in a combinatorial manner, candidates get filtered and scored on criteria like: occurrence of certain elements/substructures, retention time information and reference information.
Approach to combine the knowledge from spectral databases like MassBank with the multitude of candidates generated by fragmenters such as MetFrag. The functionality of the original MetFusion application has been integrated into MetFrag, MetFusion itself has been deactivated.
Gene-centric metabolomics information retrieval tool.
An updated database of DNA methylation across a variety of species.
A DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder. methCancer-gen is a deep neural network-based tool for generating DNA methylome dataset based on a user-specified cancer-type.
Tracing and tracking epiallele families in complex DNA populations.
The database contains information about the occurrence of methylated cytosines in the DNA.
Compute DNA methylation heterogeneity levels from Bismark-aligned bisulfite sequencing data.
Beb-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. A web-based bioinformatics software for correlating DNA methylation and gene expression. The web user-interface can be accessed through https://paoyang.ipmb.sinica.edu.tw/Software.html . Correlation analyses of genome-wide DNA methylation and gene expression. Ordinal association analyses with genes ranked by gene expression level.
Simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).
Combining allele-specific DNA methylation and SNPs for haplotype region identification. DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms.
Information repository of DNA methylation and gene expression in human cancer. Demonstration of searching results in MethHC. More Clinical and Experimentally Validated Data.
This package implements functions for calling methylation for all cytosines in the genome.
Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.
Web server for identifying methylated lysines on histones and non-histone proteins.
Design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.
A software tool to capture metadata and generate comprehensive microscopy methods text.
A parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection. MethPanel is a computational pipeline in Linux operating system with an interactive graphical interface for rapid analysis of multiplex bisulphite PCR sequencing data. The tool covers a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. Moreover MethPanel offers important and unique features, such as a epipolymorphism score and a bisulphite PCR bias correction. MethPanel can be run in parallel by samples on either a personal computer or a high performance computer. The outputs are automatically forwarded to a shinyApp for convenient display, visualisation and sharing of data with collaborators and clinicians.
Summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.
Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. We developed a diagnostic classifier based on DNA methylation profiles. This tool is a toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version can classify the following: DIPG, Ependymoma, ETMR, GBM, MB3 and 4, MB_WNT, MB_SHH, and PiloAstro.
The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).
Analysis of modified nucleotides from nanopore sequencing. Plotting tools for nanopore methylation data. This script generates a browser view on a window using data from. i) nanopolish, either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
Estimating the regulatory potential of DNA methylation in gene transcription. Assessing the regulatory potential of DNA methylation regions or sites on gene transcription. Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions.
An R/bioconductor package for systematic aggregation and analysis of bisulfite sequencing data. Fast and efficient summarization of generic bedGraph files from Bisufite sequencing. Bedgraph files generated by BS pipelines often come in various flavors. Critical downstream step requires aggregation of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.
Perform step by step methylation analysis of Next Generation Sequencing data.
This package allows the visualization of DNA methylation data after bisulfite sequencing.
This package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.
Methylation-eQTL analysis in cancer research
Technology-independent estimation of cell type composition using differentially methylated regions. R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms. Estimate the cell composition of whole blood in DNA methylation samples. A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing). For help with the methylCC R-package, there is a vignette available in the /vignettes folder. Hicks SC, Irizarry RA. (2019). Genome Biology (accepted and in press). This is a package to estimate the cell composition of whole blood in DNA methylation measured on any platform technology (e.g. Illumina 450K microarray, whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)). DNAMethylation, MethylSeq, MethylationArray, Microarray, Sequencing, Software, WholeGenome
Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.
R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide.
A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
R package for preprocessing and initial QC of Illumina DNA methylation microarray data. (450K, EPIC v1.0, EPIC v2.0) Two-step preprocessing of raw array data (.idat files): 1) for each methylation bead chip (containing several arrays/samples) 2) Combine information from individual bead chips
A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors. Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present MethylationToActivity (M2A), a machine learning framework that uses convolutional neural networks to infer promoter activities based on H3K4me3 and H3K27ac enrichment, from DNA methylation patterns for individual genes. Using publicly available datasets in real-world test scenarios, we demonstrate that M2A is highly accurate and robust in revealing promoter activity landscapes in various pediatric and adult cancers, including both solid and hematologic malignant neoplasms
Comprehensive downstream pipeline for the analysis of genome-wide DNA methylation.
Estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks
Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions)
A (mostly) universal methylation extractor for BS-seq experiments.
User friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.
Software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
These models estimate several properties, such as the level of processivity and preference for hemimethylated CpG dyads over unmethylated ones, of DNA methyltransferases from double-stranded binary methylation data. The inference is done by Markov chain Monte Carlo methods under a Bayesian framework.
Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.
R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.
Algorithm implemented to identify hyper/hypomethylated genes for a disease. Based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. It uses the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression.
To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.
Database of DNA methylation profiles of human and mouse brains.
Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.
Modular and reproducible pipelines for multi-omics predictors of complex traits.
Graphical interface for comprehensive DNA methylation array data analysis.
An R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. methylscaper is a Shiny app for visualizing methylation data. Install the package with.
This is a package for the discovery of regulatory regions from Bis-seq data.
R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments.
methylSpectrum is a software for deconvolution of DNA methylation array data into source contributions from distinct cell types. The major application of this software is to determine the composition of white blood cells (WBCs) from DNA methylation array data assayed in whole blood
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data. A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data. To process a large number of WGBS samples in a consistent, documented and reproducible manner it is advisable to use a pipeline system. MethylStar is a fast, stable and flexible pre-processing pipeline for bulk or single-cell (de-multiplexed) WGBS data.
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control are also included.
This tool was developed from CpGviewer such that the program can now analyse up to four different methylation sites such as CpG, GpC, CpNpG or any four user defined sites. If a non-native DNA methylase is used to modify chromatin-bound DNA, the methylation pattern can be used to identify the binding sites of DNA-binding proteins.
This package provides facilities for differential methylation analysis based on variable importance measures (VIMs), a class of statistical target parameters that arise in causal inference. The estimation and inference procedures provided are nonparametric, relying on ensemble machine learning to flexibly assess functional relationships among covariates and the outcome of interest.
metID is a R packge which is used for metabolite identification based on in-house database and public database based on accurate mass (m/z), rentention time (RT) and/or MS2 spectra.
Open-Source R Package to Decipher Small-Molecule Drugs Metabolism Through High Resolution Mass Spectrometry. MetIDfyR is an open-source, cross-platform and versatile R script to predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest.
Repository, in a prototype stage, of mass spectra of small chemical compounds for life science (<2000 Da). The database will contain MSn data acquired on different platforms by different research groups. MSn data will be annotated with chemical information about the fragments.
MetLab is aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes.
Metabolite mass spectrometry database with multiple searching capabilities, including precursor ion, neutral loss, accurate mass, and product ions.
A MATLAB package for metabolical modeling, analysis and optimization.
MetMatch is a software tool for the semi-automated comparison of different LC-HRMS chromatograms of untargeted metabolomics experiments. It provides methods to correct the raw-LC-HRMS data for m/z and retention time shifts relative to one or several preprocessed reference chromatograms.
MetMiner is a user-friendly pipeline designed for large-scale plant metabolomics data analysis. It's built on R Shiny and integrated into TBtools for convenient dependency resolution.
Generalized meta-analysis method for combining information across discovery-oriented datasets and for testing between-study heterogeneity for each biological variable of interest. The method is based on non-parametric Monte Carlo permutation testing.
METRO is a new computational method that leverages expression data collected from multiple genetic ancestries to enhance Transcriptome-wide association studies (TWAS).
An automated method for robust quantification of subcellular fluorescence events at low SNR. METROID (Morphological Extraction of Transmembrane potential from Regions Of Interest Device) is a computational tool to filter cellular transmembrane potential signals obtained from low signal-to-noise ratio (SNR) regions of interest (ROIs) in single cell fluorescence images. Metroid can be executed as a software with a graphical user interface (Windows only, click here to download the installer) or its code can be run in jupyter notebooks (check the Examples folder). A simplified flowchart is shown below:.
Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data.
A diverse collection of metabolomics related statistical tools.
Software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis.
Projecting the Course of COVID-19 in Turkey. COVID 19 Case Projection Model for Turkey. COVID-19 Salgın Yönetimi ve Çalışma Rehberi. To fit data using all observations up to latest known day and project 20 days in the future:. To fit using observations up to a certain date (e.g. May 12th, 2020):. ERİŞKİN YOĞUN BAKIM DOLULUK ORANI.
Visualisation of genomic data, Differential Gene Expression based on DEGseq, DESeq and edgeR
Hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets.
MEYE is a free and open-source tool to perform pupillometry in real-time (or on videos) in different subjects (human and mice) and in different experimental conditions (head-fixation, virtual reality, 2-photon calcium imaging)
Testing an optimally weighted combination of common and rare variants with multiple traits using family data. R program to implement MF-TOWmuT, a new method developed for large-scale genome wide association study with multiple genetic variants and multiple phenotypes using family data.
The tool can be used to download, filter, and assemble the MF-PCBA datasets in a format that is easily usable for machine learning.
MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers.
An MATLAB implementation of the (Mutliple) FAst MEdoid Selection algorithm (MFAMES).
This tool could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction.
Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures. Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.
An automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology.
A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data. A method for detecting CNV using neural networks. There are six directories. 1.program This directory contains three files that have been coded, including code for training the model, for detecting simulation data, for detecting real data, for extracting eigenvalue form simulation data, for extracting eigenvalue form real data and for transforming .txt to .mat. 2.test This directory contains two subdirectories including RealData_mat and SimulationData_mat, OriginalData_bam and Reference.
Designed to reliably detect recent positive selection in a varying size population, even if you only have polymorphism data from a single locus (i.e. a very short piece of DNA).
Combines per-residue disorder probabilities predicted by MFDp with per-sequence disorder content predicted by DisCon, and applies novel post-processing filters to provide disorder predictions with improved predictive quality.
The Male Fertility Gene Atlas – A web tool for collecting and integrating data about epi-/genetic causes of male infertility. The Male Fertility Gene Atlas (MFGA) is a public platform for providing a fast, simple and straightforward access to OMICS data in the context of male infertility and germ cells. It is developed in the context of the DFG Clinical Research Unit "Male Germ Cells: From Genes to Function" (CRU 326) under the supervision of an interdisciplinary team of physicians, biologists and computer scientists. The MFGA aims to.
MFIB is a database and resource classifying protein complexes formed by intrinsically disordered proteins that fold upon binding. It provides annotations, clustering, and evidence levels for these complexes, with a major update introducing hundreds of new entries and features.
An Efficient Lightweight Multi-Scale Feature Learning CNN for COVID-19 Diagnosis from CT Images.
Simple program which automates setting up likelihood calculations for linkage analysis using a variety of different transmission models, and then collating the results in order to produce a (nearly) model free lod score.
Web-based platform that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms.
Taking Advantage from Founder Mutations in Genetics Diagnosis, Genetic Diversity and Migration History of the Mediterranean Population.
Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.
Mascot file parsing and quantitation using ICAT and SILAC.
FASTA/FASTQ extractor for multiple sets of read names
RESTful web service for high-throughput prediction of elemental compositions from accurate mass values detected by high-resolution mass spectrometers.
Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc.
MIPS mouse functional genome database (MfunGD)
Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).
Comprehensive analysis of ncRNA involvement in brain microglia immunology.
Multi-level global-aware network for thymoma segmentation.
MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison
Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.
Multiple Genome Aligner computes multiple genome alignments of large, closely related DNA sequences. MGA is a software tool for efficiently aligning two or more sufficiently similar genomic sized sequences [HKO02]. It belongs to the category of anchor-based multiple alignment methods. mga uses multiMEMs (or MEMs, MUMs as special cases) to anchor the alignment. In essence, they are (hopefully long) stretches or regions of identical bases occuring in all input sequences.
For rapidly visualizing and aligning the most highly conserved regions in multiple genomes. It is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.
New algorithm designed to detect modules with a strongly interconnected neighborhood in large scale biological interaction networks.
Gene prediction in phage genomes with multiple genetic codes.
A total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.
MGCPdb is a database providing genome size, chromosome number, and ploidy data for mulberry germplasm resources. The database includes raw data and is valuable for research in mulberry genome evolution, breeding, and genetic diversity.
Community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. It includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information.
A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics. MGDrivE2: Mosquito Gene Drive Explorer 2. MGDrivE 2 is a new simulation platform which extends capabilities from the MGDrivE simulation package in a new mathematical and computational framework. For more information about MGDrivE, see our publication. Some of the notable capabilities of MGDrivE 2 include incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations.
Designed to find the optimal trees for multiple genome rearrangement by signed reversals. The problem is modeled as: For a given collection of genomes represented by signed permutations on genes, find a tree to connect the given genomes by reversal paths such that the number of all signed reversals is minimized.
mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.
A web application for microglia gene list enrichment analysis.
De novo computational method identifies new LTR (long terminal repeat) retrotransposons without relying on a library of known elements. Specifically, the method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis.
Classification of multigene families of African swine fever viruses. MGFC: a web server for classifying multigene family proteins in ASFV. MGF proteins are classified into 31 groups based on sequence homology. Three, nine, three, eleven and five protein groups were obtained in MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505 families, respectively. This server provides a user-friendly interface for classifying MGF proteins into groups based on MGF protein sequences.
The package is designed to detect marker genes from Microarray gene expression data sets.
The package is designed to detect marker genes from RNA-seq data.
It has shown that infections, psychosocial, nutritional, hygiene, and socioeconomic factors may be related in such an intricate way, that could be hardly detected using traditional regression based epidemiological techniques.
Integrated genetic, genomic, and biological data for mouse.
A powerful tool to analyze plant multivariate data.
mgikit is a demultiplexing toolkit for MGI FASTQ files, designed to overcome limitations of the standard MGI demultiplexer and achieve high performance. It provides tools for efficient data demultiplexing, reformatting, and quality reporting.
Suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.
The Musa Germplasm Information System (MGIS) is a database containing information on Musa (banana) germplasm diversity, including passport data, morphology, and molecular information. It has been expanded to incorporate in situ observations sourced from iNaturalist, GBIF, and other resources.
Musa Germplasm Information System (MGIS)
Reference based mapping and taxonomy annotation of metagenomics sequence reads.
Membrane glycolipid mass spectrum simulator for polymicrobial samples. 'MGMS2' for Polymicrobial Samples. A glycolipid mass spectrometry technology has the potential to accurately identify individual bacterial species from polymicrobial samples.
MGraph is a probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray.
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships.
Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.
Mapping-based Genome Size Estimation (MGSE) predicts the size of a genome based on a (short) read mapping to an existing genome assembly. Low complexity sequences are often collapsed in a genome assembly thus the assembly size is smaller than the genome size. The actual copy number of sequences in the assembly is identified based on the coverage (sequencing depth) which allows the calculation of a genome size.
MGSurvE is a computational framework that optimizes trap placement for genetic surveillance of mosquito populations, aiming to minimize the time to detect an allele of interest. It accounts for mosquito resource requirements, movement patterns, and trap attractiveness profiles.
Gene set analysis method based on GSZ (Gene Set Z-score) statistics and asymptotic p-value. It is different from the standard GSZ method in that it assigns asymptotic p-values to the gene set scores instead of empirical p-values.
This website contains implementations of the MGT for various species. The MGT and metadata is searchable to allow identification of GTs associated with spatial, temporal or clinical characteristics.
A web service and database for studying the global and local genomic epidemiology of bacterial pathogens.
A number of tools and meta-tools developed at CNB/CSIC for the analysis of metagenomics data (some rely on QIIME).
The Multiple Genome Viewer (MGV) supports comparative, simultaneous browsing of multiple genomes.
Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights.
MGWT is a tool for identification of protein coding regions using the ModifiedGabor-wavelet transform.
Open source client/server framework for the analysis of shotgun metagenome data. Flexible analysis workflows based on the Conveyor workflow engine provide the user with a wide range of recent algorithms for taxonomic, functional and statistical analysis. The ability to integrate own datasources and custom analysis pipelines enables researchers to address highly specific study aims and generate high-quality charts as well as interactive visualizations.
Interactive website for scRNA-seq data of male genitourinary development and disease.
Predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms.
Comprehensive database for visualization and analysis of DNA methylation haplotypes.
A simple DNA methylation haplotype format for storing DNA methylation BS-seq data. It reduces the size of a BAM file by 40 to 140-fold while keeps all read-level CpG methylation information. It’s also compatible with the Tabix tool for fast and random access. We implemented a command-line tool mHapTools for converting BAM/SAM files from existing platforms to mHap files as well as postprocessing DNA methylation in mHap format. With this tool, we pro-cessed all publicly available human reduced representation bisulfite sequencing (RRBS) data and provided as a comprehensive mHap database.
Python tool to identify peptides that are naturally processed by the MHC-I pathway.
Assigning alleles to different loci in amplifications of duplicated loci.
A machine-learning approach to estimate affinity of MHC class II peptides based on structural interaction fingerprints.
SVM based method for prediction of promiscuous MHC class II binding peptides. The average accuracy of SVM based method for 42 alleles is ~80%. The performence of the method was poorer for few allele due to smaller size of dataset. The performence of the method was tested through 5-fold cross-validation.
A database of MHC binding specificities and ligands.
Predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model. MHCAttnNet uses a Bi-directional Long Short Term Memory (Bi-LSTM) styled encoder to deal with variable-length peptide sequences. This permits the model to handle a large variety of peptides, and hence makes it more general.
The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding, Non-binding peptides and T-cell epitopes. The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases.
Functional cluster of MHC class I molecules (MHCI) based on their predicted binding specificity.
A software package that can predict peptide binding affinity to major histocompatability complex I. The software implements allele-specific neural networks that use a novel architecture and peptide encoding scheme.
NetMHCIIpan-4.1 is a web tool and standalone package that predicts MHC class II binding affinities and T-cell antigen presentation. It is used for epitope discovery and vaccine design.
MHCII3D-Robust Structure Based Prediction of MHC II Binding Peptides. MHC II Automated Server Benchmarks. The knowledge of MHC II binding peptides is highly desired in immunological research, particularly in the context of cancer, autoimmune diseases, or allergies. MHCII3D is a prediction tool based on structural scaffolds of MHC II-peptide complexes and statistical scoring functions (SSFs). Its prediction performance is among machine learning tools.
MHConstructor is a containerized pipeline for high-throughput, haplotype-informed, reproducible assembly of MHC sequences from short read data, facilitating alignment-free MHC sequence analysis.
An interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes.
Uses the additive method to predict the binding affinity of major histocompatibility complex (MHC) class I and II molecules and also to the Transporter associated with Processing (TAP).
MHCquant2 is a Nextflow-based pipeline for identifying and quantifying HLA-presented peptides from immunopeptidomics mass spectrometry data. It leverages OpenMS tools and peptide property predictors to improve peptide identifications and facilitate tumor antigen discovery.
Pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences.
The tool for global and local false discovery rate (FDR) estimation for MHC-peptide binding prediction
Detailed Experimental Protocols and Rapid, User-Friendly Visualization of MHC I and II Ligand Datasets with MhcVizPipe. A reporting pipeline for visualization of immunopeptidomics MS data. Welcome to the MhcVizPipe (MVP) wiki!. MhcVizPipe connects the bioinformatic tools NetMHCpan, NetMHCIIpan and GibbsCluster and generates organized and easy-to-understand reports in HTML format. The reports are fully portable and can be viewed on any computer with a modern web browser. Here are some of the features of MhcVizPipe:.
Integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data. This documentation has three sections:. This documentation has two sections:. In order to have an integrated tool, we developed a Graphical User Interface for MHiC. This graphical User Interface enables the user to set parameters and generate significant interactions and also visualize a Hi-C contact map. We developed this part as an HTML page.
Prediction of lncRNA-disease associations based on multiple heterogeneous networks. Package: MHRWR Type: Package Title: MHRWR Prediction of lncRNA-disease associations based on multiple heterogeneous networks.
Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. Multiple instance learning based classification for MSI data.
marker informativeness for multi-ancestry admixed populations.
Mathematical analysis software specifically for use with mechanistically described microbial interactions described in terms of reactions, substrates/reactants and products. It provides a user-friendly environment in which microbiologists, microbial ecologists and biological mathematicians can rapidly and robustly characterize the dynamics of ecological motifs of up to three microbial species, without the requirement to develop their own code, programme models or rely on a detailed knowledge of the mathematics of dynamical systems analysis.
Weighted quality evaluation of assembled microbial genomes | SUMMARY:Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons. AVAILABILITY AND IMPLEMENTATION:miComplete is written in Python 3 and released under GPLv3
A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. miR2Diabetes aims to provide a comprehensive resource of miRNA dysregulation in diabetic microvascular complications (DMC). Each entry in the miR2Diabetes contains detailed information on a miRNA-DMC relationship, including miRNA symbol, DMC name, experiment subjects, miRNA dysregulation pattern in a specific experimental design, and literature reference. microRNAs (miRNAs) have been established as critical regulators of the pathogenesis of diabetes mellitus (DM), and diabetes microvascular complications (DMCs). The annotations in the database cover 14 DM and DMC phenotypes, involving 156 miRNAs, by browsing diverse sample origins (e.g., blood, kidney, liver, and other tissues).
An online database for prediction of functional microRNA targets | MicroRNA Target Prediction Database | An Online Database for MicroRNA Target Prediction and Functional Studies | miRDB is an online database for miRNA target prediction and functional annotations | Choose one of the following search options: | HumanMouseRatDogChicken GenBank Accession NCBI Gene ID Gene Symbol
miRDRN (miRNA Disease Regulatory Network) is a useful platform for discovering potential novel disease networks and comorbidity genes by disease-associated miRNAs targeting pathways.
Tool for the Prediction of Pre-miRNA⁻Protein Interactions.
A novel release of the miRNA Pathway Dictionary Database. Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https: mpd.bioinf.uni-sb.de. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data.
Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. the experimentally validated microRNA-target interactions database. As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.
Web application for the analysis of miRNA-target interactions in human tissues.
Translational Bioinformatics Laboratory at CNR-ICAR
> Slight manual curation of an auto-generated entry. Authors please revise and amend. (Matus Kalas @matuskalas) > MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'mirtop', 'isomiR', 'mirtop API', 'mirGFF3 mirtop' | Unification of miRNA and isomiR research | GFF3 format with miRNA and isomiR information from sequencing data | A proxy for miRNA/isomiR data analysis where all tools meet with the idea to create an ecosystem of data analysis promoting community collaboration | As discussed here: https://github.com/miRTop/incubator/issues/10 we've defined a GFF3 format for output of small RNA pipelines focused on miRNA data currently. We is an open community project (read more) and joint us! | This output is based on the current GFF3 definition: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
Tool for quality control and tracing taxonomic origins of microRNA sequencing data.
Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and disease. Despite much effort, microRNA annotations still contain errors and are incomplete due especially to challenges related to identifying valid miRs that have small numbers of reads, to properly locating hairpin precursors and to balancing precision and recall. Here, we present miRWoods, which solves these challenges using a duplex-focused precursor detection method and stacked random forests with specialized layers to detect mature and precursor microRNAs, and has been tuned to optimize the harmonic mean of precision and recall. We trained and tuned our discovery pipeline on data sets from the well-annotated human genome, and evaluated its performance on data from mouse.
Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma. transcriptome-wide microRNA target prediction including lncRNAs. miRcode 11 (June 2012) based on: UCSC GRCh37/hg19, GENCODE 11 transcripts, Multiz 46 species, TargetScan6 families. MiRcode provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation, including >10,000 long non-coding RNA genes.
Confident detection of microRNA editing | Confident detection of A-to-I miRNA editing events in small-RNA seq data | miRmedon it's a python3 code which takes fastq file of trimmed small-RNA reads, and reports on A-to-I editing events detected in the data. In addition, miRmedon reports on read counts and sequence of both edited and non-edited miRNAs. miRmedon require several extrenal softwares and python libraries, as descirbed below
R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules.
Identifying miRNA synergism using multiple-intervention causal inference. Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. A novel method for identifying miRNA synergism using multiple-intervention causal inference.
Web-based tool for microRNA Truncation and Tailing Analysis.
A genotype imputation server for high-dimensional data.
An Open Source Standalone Deep Learning Application for Microscopic Image Analysis.
Compliant microarray data submission tool.
Mutual Information-based Analysis of Multiplex Imaging data.
Human microbiome affect the host epigenome.
miARma-Seq is a suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism.
Microscopy image browser (MIB) is a software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data.
Microscopy Image Browser 2 (MIB2) is an update package for segmentation of multi-dimensional (2D-4D) microscopy datasets
Metal ion-binding site prediction and modeling server.
MiBiAnTo is a web server for efficient compositional analysis of metagenomic sequencing data, utilizing k-mer based methods to expedite analysis and offering functionality beyond quantification, including community composition estimation.
An interactive web application for multi-omics data exploration and integration. A web application for multi-omics analysis.
Multimodal joint deconvolution and integrative signature selection in proteomics.
Microsatellite Characterization in Genome Assemblies | analysis of genome microsatellite content | micRocounter is currently in beta version please do not publish results without consultation or running with the postpublication released version | Characterization of microsatellite sequences in R
New short-read aligner that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core.
A pipeline for multimodal neuroimaging and connectome analysis.
R package which provides methods to detect chromatin interactions from ChIA-PET data.
Software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference. The pipeline can be applied to a range of highly conserved genes/spacers, such as 16S rRNA gene, Internal Transcribed Spacer (ITS) and 28S rRNA. It is an open-source, GPLv3-licensed software.
Mice-N-Mates is a software resource providing tools for studying mouse behaviour in home-cage environments, including automated classification using the Activity Labelling Module (ALM) and modeling using a Global Behaviour Model (GBM). The resource also provides training datasets (ABODe and IMADGE).
Annotate microscopy time series of complex cell surfaces with 3D virtual reality (VR). It allows the annotation of colour surfaces segmented from microscopy movies using either a VR headset and controllers, or computer screen with mouse and keyboard.
Online tool for the generation of micelle models as input for molecular dynamics simulations.
A next-generation pipeline to enable the FAIRification of drug screening experiments. MICHA (Minimal Information for CHemosensitivity Assay) is a protocol for the annotation and reporting of Chemosensensitivity assays by FAIRifying drug sensitivity screening data. MICHA (Minimal Information for CHemosensitivity Assay) is a web-based platform to facilitate the annotation of major components of common chemosensensitivity (drug sensitivity) assays
Verify gene annotations in previously published microbial genomes.
Sculpting protein views on web pages without coding. Michelaɴɢʟo is a web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site. Convert PyMOL files, upload PDB files or submit PDB codes and create a webpage to edit, share or implement standalone on your site.
Simple script to recover and plot Neurolucida files and outputs from "Michi Tracer".
Very basic Neurolucida-like system without microscope and for 2D cultured cells.
This package takes the miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.
Identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis.
Visualizing and unraveling a microbial network.
Visualizing and deconstructing a microbial network.
Meta-tool for automatically querying and collecting related information from multiple biology/bioinformatics enabled web servers with prediction capabilities.
Inferring microbial co-occurrence networks from amplicon data.
Interactive database to predict mutagenicity, genotoxicity, and carcinogenicity of mycotoxins.
An interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications.
Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers.
This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis.
Automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data by invoking TM4 platform.
Web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.
Web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5 software packages is also displayed.
A user-friendly, comprehensive microbial genome annotation pipeline. Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes. MicrobeAnnotator uses an iterative approach to annotate microbial genomes (Bacteria, Archaea and Virus) starting from proteins predicted using your favorite ORF prediction tool, e.g. Prodigal. The iterative approach is composed of three or five main steps (depending on the flavor of MicrobeAnnotator you run).
Bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner.
Microbench is a small Python package for benchmarking Python functions, and optionally capturing extra runtime/environment information. It is most useful in clustered/distributed environments, where the same function runs under different environments, and is designed to be extensible with new functionality. In addition to benchmarking, this can help reproducibility by e.g. logging the versions of key Python packages, or even all packages loaded into the global environment. Other captured metadata can include CPU and RAM usage, environment variables, and hardware specifications.
Accurate Cell Segmentation with OMERO Data Management.Wan-Microbi is used.
Over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. It includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, it can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. It also includes fast phylogenetic profile searches and more.
Centers for Disease Control and Prevention
MicrobeTrace is a web-based tool to visually render networks from surveillance, epidemiologic investigations, and genetic analyses. Using simple point-and-click interfaces, data can be readily imported, integrated and visualized...no coding required!
Microbial genome and functional analysis of Bacillus subtilis.
Microbial advanced database organisation (Micado)
Tool for visualization of microbial genomes. Chromosome wheels and linear genome maps with user specified features/color coding can be generated interactively. Graphics are created in SVG format.
Tools for the analysis of microbial community profiling data. Extends the phyloseq class.
MicrobiomeDASim: Simulating longitudinal differential abundance for microbiome data. Tools to simulate longitudinal differential abundance for microbiome data. Microbiome Differential Abundance Simulation. A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance. Microbiome, Software, Visualization. After installing Jupyter and the appopriate kernel you can access an interactive simulation session of microbiomeDASim using mvrnorm_demo.ipynb.
Methodological approaches to derive and visualize microbiome trajectories.
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Note - MicrobiomeAnalystR is still under development - we cannot guarantee full functionality.
Current challenges and best-practice protocols for microbiome analysis. Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing. This review paper (https://doi.org/10.1093/bib/bbz155) aims to provide a comprehensive workflow to perform amplicon and shotgun metagenomics analysis. There are two workflows provided. First workflow for amplicon, using the standard mothur and dada2, and along with it some standard visualization are provided for the processed data. Second workflow for metagenomics, using a variety of tools openly available which have been stitched together to form a usable pipeline. Both the workflows are controlled by bash scripts: amplicon_analysis.sh and metagenomics_analysis.sh.
MicrobiomeGWAS is a software package for identifying host genetic variants associated with micorbiome distance matrix or beta-diversity. For each SNP, microbiome GWAS tests the main effect or the SNP-environment interaction.
An R/Bioconductor package for microbiome marker identification and visualization.
MicrobiomeNet is a database integrating microbial associations with their metabolic profiles to facilitate mechanistic insights. It contains microbial associations and genome-scale metabolic models (GEMs) covering thousands of species, enabling users to explore interactions and compare metabolic profiles.
MicroBundleCompute is a computational framework for automated segmentation, tracking, and analysis of subdomain deformation in cardiac microbundles. The tool offers tools for tissue segmentation and tracking, enabling the quantification of morphology-based mechanical metrics from beating cardiac microbundles.
MicroBundlePillarTrack is a Python package for automated segmentation, tracking, and analysis of pillar deflection in cardiac microbundles. It provides tools for quantifying contractility metrics and enables reproducible cross-platform comparisons.
Dirichlet-tree multinomial regression models with Bayesian variable selection. In this folder you'll find code for the R package MicroBVS found in:. “MicroBVS: Dirichlet-Tree Multinomial Regression Models with Bayesian Variable Selection - an R Package” (Accepted by BMC Bioinformatics 2020), by MD Koslovsky and M Vannucci.
Methods for Taxonomic Classification of Prokaryotes.
Online machine learning algorithm based on SVM (support vector machine) to predict Human miRNA-mediated gene silencing: mRNA degradation or translational repression, and it can also determine whether a mRNA is a target of a miRNA according to Pictar and PITA.
Program that estimates allelic dropout rates from nonreplicated microsatellite genotype data. MicroDrop uses the estimated dropout rates to provide imputed data sets that sample missing genotypes (and replace some homozygous genotypes) using an allele frequency model with or without Hardy-Weinberg equilibrium.
Computer program for analysing the genotyping errors of microsatellites in parentage exclusion analysis.
Extending Association Rule Mining to Microbiome Pattern Analysis.'
Identify the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.
A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences. MicroGMT: Microbial Genomics Mutation Tracker. MicroGMT is a python based package, which takes either raw sequence reads or assembled genome sequence as input and compares against database sequences to identify and characterize small indels and point mutations in the microbial genoems. Although our default setting is optimized for SARS-CoV-2 virus, the package can be also applied to any other microbial genomes.
A python package for cryo-EM micrograph cleaning using deep learning. MicrographCleaner (micrograph_cleaner_em) is a python package designed to segment cryo-EM micrographs into:.
R package for topological pathway analysis integrating gene and miRNA expression profiles using validated and/or predicted miRNA-target interactions. It is based on updated versions of graphite and CliPPER Bioconductor packages dedicated to pathway analyses recently proposed by our group.
microGWAS is a computational pipeline for performing large-scale bacterial genome-wide association studies. It integrates state-of-the-art tools into a user-friendly and reproducible workflow, allowing for the identification of genetic variants associated with bacterial phenotypes.
A portable and extensible database of all published microhaplotype marker and frequency data. MicroHapDB is a portable database intended for scientists and researchers interested in microhaplotypes for forensic analysis.
Tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.
Database of proteins that localize in midbody, centrosome and/or kinetochore. The database contains experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification.
ImageJ Plugin for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. It works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging.
MicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.
U.S. Department of Agriculture | Agricultural Research Service (ARS)
MicroMPN estimates most probable number (MPN) from lab microplates (how many viable bacteria are in a sample). It has been develeped for high-throughput screening of microbe suppression (e.g. of a pathogen of interest) in mixed populations, where we need to accurately distinguish viable pathogen cells from non-viable and non-target microbes. In-vitro dilutions are made with replication, and the number of tubes or wells with bacterial growth is recorded. This presence/absence, and dilution information are used to estimate the number of bacteria in the starting sample. With liquid-handling robots and plate reader, it can be faster than conventional plate counting or spotting on agar. 2 inputs from a plate reader: A plate layout file in Wellmap TOML format, and a CSV plate reader file with columns for the plate, the well or row+column, and the optical value used for determining growth. MicroMPN's MPN estimation function is usable for MPN calculation for other applications in Python.
Specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.
A new feature selection method called Biological Pathway-based Feature Selection (BPFS) for microarray data. Unlike most of the existing methods, the method integrates signaling and gene regulatory pathways with gene expression data to minimize the chance of overfitting of the method and to improve the test accuracy.
R package for the study of prokaryotic pan-genomes. A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species.
Microbe set enrichment analysis and disease similarity calculation based on a list of microbes.
Microphaser is a tool for phasing small tumor DNA sequences - e.g. coding for small peptides - in linear time. It can be used in tumor neoantigen prediction to generate the neo-peptidome.
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.
Microbial Phenomics Information Extractor (MicroPIE) is a natural language processing application that uses a robust supervised classification algorithm (Support Vector Machine) to identify characters from sentences in prokaryotic taxonomic descriptions, followed by a combination of algorithms applying linguistic rules with groups of known terms to extract characters as well as character states.
The Micropilot software from EMBL is a computer program that can rapidly learn what a scientist is looking for in an experiment and then take over the laborious and time-consuming task, automatically performing complex microscopy experiments when it detects cells with interesting features.
An end-to-end solution for high-quality complete bacterial genome construction. microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing. microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.
Selects samples from abundance tables based on various selection schemes.
Package designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).
MicroRazerS is a tool optimized for mapping short RNAs onto a reference genome.
Different data resources for miRNAs and some functions for manipulating them.
MicroRNA prediction model based only on plant small RNA sequencing data.
A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome.
MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data and includes integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis.
Python-based bespoke microscopy for bio-medical science. Cockpit is a microscope graphical user interface. It is a flexible and easy to extend platform aimed at life scientists using bespoke microscopes. More detailed information is available:. Micron Advanced Imaging Consortium. Micron Advanced Imaging ConsortiumMicron Advanced Imaging ConsortiumMicron Advanced Imaging Consortium.
Read Digital Micrograph files for electron microscopy
Web-based application which predicts the impact of a SNP on putative microRNA targets.
+microstate is a MATLAB toolbox for performing microstate analysis in sensor- or source-reconstructed EEG or MEG data. +microstate can be used for individual- or group-level analyses, and applied to both resting-state or task-evoked data. As well as microstate analysis, +microstate includes functions for calculating microstate statistics and microstate-segmented functional connectivity, visualisation, and simulation of data.
A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.).
Uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.
microTSS is a machine-learning algorithm that provides highly accurate, single-nucleotide resolution predictions for intergenic miRNA transcription start sites (TSSs). MicroTSS integrates high-resolution RNA-sequencing data with active transcription marks derived from chromatin immunoprecipitation and DNase-sequencing to enable the characterization of tissue-specific promoters
A low-cost platform for indoor marine swarm robotics research.
Automatic segmentation and morphological analysis of microvessels in histological tumour sections
Combines positional information with information on motif occurrences to better predict binding sites of transcription factors (TFs)
MID (Micro-Inversion Detector) is a tool to detect microinversions (MIs) by mapping initially unmapped short reads back onto reference genome sequence (i.e. human genome assebly hg19).
Software designed to compute the theoretical isotopic distribution for molecules of known elemental composition. It computes for a molecule simultaneously two isotopic distributions: the coarse-grained isotopic distribution and the fine-grained isotopic distribution.
Metagenomic Intra-species Diversity Analysis System.
R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions.
Meaningful Immunogenetic Data at Scale. Human immunogenetic variation in the form of HLA and KIR types has been shown to be strongly associated with a multitude of immune-related phenotypes. We present MiDAS, an R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions. MiDAS closes the gap between inference of immunogenetic variation and its efficient utilization to make meaningful discoveries.
Data normalization and analysis tool for microarray data.
Identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns | Welcome to the minor intron database (MIDB)! | Minor introns, or U12-type introns, were initially identified based on their divergent terminal dinucleotide sequences (Jackson, 1991) | MIDB contains the most recent information on minor introns and the genes they are found in, also called MIGs (minor intron-containing genes) | Species: Mus musculus Homo sapiens All
Measures the concentration of specific infections (SIN) in a virus sample based on a TCID50 endpoint dilution assay.
MicroRNA enrichment analysis and annotation.
Method aims to characterize the energetic patterns of proteins binding to their partners.
Matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment It computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information.
Analysis and visualization of miRNA sequencing data in neurological disorders.
Pattern discovery for microsatellite genome analysis. MiGA is a user friendly programme for the detection of all microsatellite loci in genomic data.
Classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts.
Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure meta-tools as a pipeline of individual tools and intermediate filters.
An Evidence-based Database of Genes and Phenotypes of Male Infertility.
MIGNON (Mechanistic InteGrative aNalysis Of rNa-seq data) is a versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently handled are allelic counts but sequences will be handled in the forthcoming version.
The toolbox for microbial and individualized GEMs, reactobiome and community network modelling.
Massive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis.
Learn a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data.
Interactive exploration of a global clinical network from a large breast cancer cohort.
MIIND is a simulator that allows the creation, simulation and analysis of large-scale neural networks. It does not model individual neurons, but models populations directly, similarly to a neural mass models, except that we use population density techniques.
MIIT is a Python framework for integrating spatially resolved multi-omics data. The main spatial-omics technologies that we focus on are Spatial Transcriptomics (through Visium) and MSI (ImzML). There is additional_data support for various types of annotations (pointset valued data, geojson data, and masks).
A lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.
Integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding.
A manually curated and comprehensive knowledge base for myocardial infarction.
Visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. Millefy is a tool for visualizing read coverage of single-cell RNA sequensing (scRNA-seq) datasets in genomic contexts. By dynamically and automatically reorder single cells based on 'locus-specific' pseudotime, Millefy highlights cell-to-cell heterogeneity in read covreage of scRNA-seq data.
Multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.
Method that outperforms a leading recent method, centipede, marginally in human but dramatically in yeast (average auROC across 20 TFs increases from 74% to 94%). The sofware is based on logistic regression and thus benefits from supervision, but we show that partially and completely unsupervised variants perform nearly as well.
Differential abundance testing on single-cell data using k-NN graphs. Milo is a method for differential abundance analysis on KNN graph from single-cell datasets. For more details, read our preprint.
Mixed Logistic Regression in Genome-Wide Association Studies. milorGWAS: MIxed LOgistic Regression in GWAS. This package is for Genome Wide Association Studies using a logistic mixed model, using fast approximate methods as described in (Milet and Perdry, 2020). One of these methods extends the GMMAT method by Chen et al. (Chen et al., 2016). A similar method was described in (Zhou et al., 2020).
Calculates a measure of sequence specificity called Motif Independent Metric.
Easily visualize and inspect microarrays for spatial artifacts.
The Multi-Omic Integration by Machine Learning (MIMaL) method can be found as scripts and a web page.
Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using this herein developed user-friendly, cross-platform software.
Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces. A new version of ShinyProxy is available Switch to new version!.
The Microbial Metabolites Database (MiMeDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human microbiome. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain and link metabolite data, microbe data, host data, health and bioactivity data, and exposure data. Many data fields in the database are hyperlinked to other databases (FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank). The Microbial Metabolites Database supports extensive text, sequence, spectral, chemical structure and relational query searches.
Exploring Microbiome-Metabolome Relationships using Neural Networks. MiMeNet predicts the metabolomic profile from microbiome data and learns undelrying relationships between the two. MiMeNet uses microbial features to predict metabolite output features. To do so, neural network hyper-parameters are first tuned. Then models are evaluated in a cross-validated fashion resulting in Spearman correlation coefficients (SCC) for each metabolite representing how well they could be predicted.
Minimal Microbial Consortia creation tool is a bioinformatic approach for generation of synthetic communities from metagenomes
MIMIC-III is a freely-available database containing de-identified clinical and physiological data from patients admitted to intensive care units. This resource is used to develop and evaluate machine learning models for predicting patient outcomes, such as 30-day mortality.
MIMIC-IV is a freely available, retrospective database of critically ill patients. This resource allows researchers to develop and validate predictive models, exemplified by the study presented, which focuses on predicting in-hospital mortality in patients with sepsis-associated kidney injury receiving renal replacement therapy.
MimickNet, Mimicking Clinical Image Post- Processing Under Black-Box Constraints. The above is a cineloop of cardiac data with conventional delay-and-sum beamforming and ReFoCUS beamforming. We apply clinical-grade post-processing, MimickNet post-processing, and show the unscaled difference between the two.
An Efficient Toolkit for MiMiC-Based QM/MM Simulations. MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection
R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR Metabolomics data.
Accelerating bioactive peptide discovery via mutual information-based meta-learning.
MIMO addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information.
Medical informatics and digital health multilingual ontology (MIMO): A tool to improve international collaborations which is hosted by HeTOP (Health Terminology/Ontology Portal)
A mimotope database. The MimoDB database also provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly.
Comprehensive software package for mapping-by-sequencing, i.e. for the mapping, identification and annotation of phenotypic mutations in model organisms from whole-genome sequencing (WGS) data.
Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.
MIMOSA2 is a tool for metabolic model-based evaluation of paired microbiome and metabolomics datasets. MIMOSA2 1) constructs community metabolic models, 2) assesses whether metabolite measurements are consistent with estimated community metabolic potential, and 3) identifies specific taxa and reactions that can explain metabolite variation.
A deep multiple instance learning framework improves microsatellite instability detection from tumor next-generation sequencing. A deep, multiple instance learning based classifier for identifying Microsatellite Instability in Next-Generation Sequencing Results.
MinActionPath calculates the most-probable trajectory between two known structural states of a protein.
A database of metal ions in DNA and RNA. Complies info on innersphere, outsphere, and larger coordination environment of >70,000 metal ions of 36 elements fround in >2000 structures of nucleic acids.
MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes.
MIND4OLIGOS is a Shiny application that predicts the monoisotopic mass of oligonucleotides observed in high-resolution mass spectrometry. It adapts the MIND algorithm for use with oligonucleotide data, enabling more accurate annotation of complex spectra.
An open source brain morphometry platform for analyzing human brain image data.
Next-generation variant caller specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable.
MinDrug is a method for predicting anti-cancer drug response by finding an optimal subset of drugs that have the most similarity with other drugs. This method predicts IC50 for a new cell-line.
Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.
A new information theoretic method to identify multivariate statistical dependencies between a transcription factor and one or more of its targets, conditional on the presence (or absence) of a candidate modulator gene.
Enhanced biochemical coverage for peak identification in untargeted metabolomics.
mineXpert is a graphical user interface software piece that allows the user to: - load mass spectrometry data files [ (x,y) text files or mzML standard format ] - visualize the TIC chromatogram and the intensity=(mz, dt) colormap in case of ion mobility mass spectrometry - integrate the mass data in many different ways and display them, effectively permitting the exploration of the mass data in their full depth - many other features
The goal of this tool is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.
A pathway analysis tool. MinePath identifies of differentially expressed functional paths or sub-paths within a gene regulatory network (GRN) using gene expression data analysis. The analysis takes advantage of interactions among genes (e.g. activation/expression, inhibition) as nodes of a graph network, which are derived from expression data.
AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics.
Tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).
This package implements various algorithms for inferring mutual information networks from data.
Tools to analyze & visualize Illumina Infinium methylation arrays.
Mini-COVIDNet is a efficient lightweight deep neural network for ultrasound-based point-of-care detection of COVID-19.
We developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type-specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy.
This pipeline was developed to detect and quantify isoforms from the expression of minigenes, whose cDNA was sequenced using Oxford Nanopore Technologies (ONT).
Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.
Improved design and analysis of practical minimizers. This repo contains reference implementation and analysis codes for the manuscript "Improved Design and Analysis for Practical Minimizers".
Minicore is a fast, generic library for constructing and clustering coresets on graphs, in metric spaces and under non-metric dissimilarity measures. It includes methods for constant-factor and bicriteria approximation solutions, as well as coreset sampling algorithms. These methods allow for fast and accurate summarization of and clustering of datasets with strong theoretical guarantees. Minicore both stands for "mini" and "core", as it builds concise representations via core-sets, and as a portmanteau of Manticore and Minotaur.
Minicule provides researchers with a streamlined way to explore and organize biomedical knowledge by using knowledge graphs and dendrograms to map connections between concepts and findings. It connects directly to trusted data sources like PubMed, OpenAlex, and the USPTO, giving users immediate access to high-quality, up-to-date scientific publications and patent records. This approach helps researchers trace relationships, discover patterns, and verify evidence efficiently, supporting better-informed decisions without adding unnecessary technical complexity.
Designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes.
It is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. It accomplishes this by identifying repeat haplotype patterns and using these to simplify the underlying calculations, with no loss of accuracy. It uses M3VCF files to store reference panel information in a compact form. M3VCF files can also store pre-calculated estimates of recombination fraction and error, which speeds up later rounds of imputation.
Minimac4 is a genotype imputation software.
Pairwise aligner for genomic and spliced nucleotide sequences
The source codes of minimum redundancy feature selection
Minimum-redundancy maximum-relevance feature selection
Implementation of Prim algorithm to solve Minimum Spanning Tree (MST).
Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
MinION™ nanopore sequencing of environmental metagenomes.
A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
Minirmd is a tool to fast remove duplicate reads.
Machine-learning for optimization of bacterial strain typing. Machine-learning based minimal MLST scheme for bacterial strain typing. minMLST is a machine-learning based methodology for identifying a minimal subset of genes that preserves high discrimination among bacterial strains. It combines well known machine-learning algorithms and approaches such as XGBoost, distance-based hierarchical clustering, and SHAP. minMLST quantifies the importance level of each gene in an MLST scheme and allows the user to investigate the trade-off between minimizing the number of genes in the scheme vs preserving a high resolution among strains.
Analyzes protein queries for the presence of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs), its functions include posttranslational modification of the minimotifs (PTM), binding to a target protein or molecule, and protein trafficking. MnM 3.0 uses a rich semantic model and trained algorithm to reduce false positive predictions.
Effective drug-target interaction prediction with mutual interaction neural network.
An Efficient and Easy-to-Use Network-Based Integrative Method of Multi-Omics Data for Cancer Genes Discovery.
An open-source software for refining metabolic networks and investigating complex network activity using empirical metabolomics data.
A principled framework for rapid simulation of dscRNA-seq data at the read level | Minnow ( read level simulator for dscRNA-seq data) | Most analysis pipelines validate their results using known marker genes (which are not widely available for all types of analysis) and by using simulated data from gene-count-level simulators
Variant adjudication and joint genotyping of cohorts of bacterial genomes.
MinoTour, real-time monitoring and analysis for Nanopore Sequencers.
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. Licensed under GNU GPL.
Comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments.
Molecular interaction Database (MINT) - public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The web interface allows the users to search, visualize and download interactions data
Dept. of Molecular Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome
A metagenomic INserT integrated assembly and annotation tool.
MINTIE is a tool for identifying novel, rare cryptic variants in cancer RNA-seq data. Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease. MINTIE is a method for the identification of rare, novel RNA variants in cancer and rare disease.
Generate tRF profiles from short RNA-Seq datasets.
A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.
An outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads. MINTyper is a tools designed to quickly a distance matrix from a set of input sequencing reads. It can take both short read from Illumina's sequencing platforms and long reads from Oxford Nanopore's platform.
MicroRNA target analysis system for Immuno-Oncology.
Vertical and horizontal integration of multi-omics data with miodin. R software package for integration of multi-omics data
The MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Biology Laboratory, Greece, appropriately filtered GOLM database peak information and Human Metabolome database information.
MIOM (Mixed Integer Optimization for Metabolism) is a python library for creating and solving complex optimization problems using genome-scale metabolic networks, in just a few lines. It offers a high-level API that leverages the power of modern Mixed Integer Optimization (MIO) solvers to easily define steady-state metabolic optimization problems, from simple Flux Balance Analysis (FBA) simulations, to more complex problems, such as sparse FBA or context-specific reconstruction algorithms, and solve them the required level of optimality.
Program for scaffolding contigs produced by fragment assemblers using mate pair data.
Application that enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using it’s standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.
Fast, simple way to generate designs for MIP (Molecular Inversion Probes) assays targeting hundreds or thousands of genomic loci in parallel.
A database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. Users can derive structure-based sequence alignment for sets of MIPs. Sequences and structures of MIPs can be downloaded.
This package finds optimal sets of genes that seperate samples into two or more classes.
the mouse integrated protein-protein interaction reference. » Mouse Integrated Protein-Protein Interaction rEference. Welcome to MIPPIE, a web tool to generate reliable and meaningful mouse protein-protein interaction networks.
This tool can distinguish between real and pseudo microRNA precursors.
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. MIPRIP: The Mixed Integer linear Programming based Regulatory Interaction Predictor.
miQC is an adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. It gives flexible, probablistic metrics for quality control of scRNA-seq data.
Fitting admixture graphs using mixed-integer quadratic optimization. Abstract Admixture graphs represent the genetic relationship between a set of populations through splits, drift and admixture. In this paper we present the Julia package miqoGraph , which uses mixed-integer quadratic optimization to fit topology, drift lengths, and admixture proportions simultaneously. Inference of topology is particularly powerful, with integer optimization automating what is usually an arduous manual process. Availability https: github.com juliayyan PhylogeneticTrees.jl Contact jyyan@mit.edu.
Computational tool for the identification of all transcripts that are targets of a list of input miRNAs.
An ultrafast and memory-efficient tool for plant miRNA annotation and expression analysis.
Uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
An interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies. MicroRNAs (miRNAs) have been found in many organisms and play essential roles in gene expression regulation of many critical cellular processes, including human cancers.
For gene pattern discovery by enrichment analysis of their microRNA regulators is a web-accessible program, which is used to mine potential patterns for one single gene, multiple genes, and KEGG pathway genes based on miRNA set enrichment analysis of the miRNAs regulating given genes.
Web based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO (Functional analysis of genetic and somatic mutations in microRNAs) and miRpair2GO (Comparative functional analysis for microRNA pairs).
Identification of Condition-Specific Targets of MicroRNA in Time-series Transcript Data using Gaussian Process Model and Spherical Vector Clustering.
Software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches.
MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler
New tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations.
Multimodal models for Integrated Regulatory Analysis, or MIRA, is a python package for analyzing the dynamic processes of gene regulation using single-cell multiomics datasets.
Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation. A simple and efficient miRNA target prediction tool.
A Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. It can currently check pathways models written either in CSML or SBML.
Web-application for handling reverse phase protein array chips.
miRACLe is an individual-specific approach to improve microRNA-target prediction based on a random contact model. The strength of miRNA-mRNA interactions (MMIs) in a biological system depends on both the sequence characteristics and expression patterns of RNAs.
Tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.
Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction. miraculix is a C/CUDA library for mathematical operations on compressed genotype data. It provides highly efficient routines that can be used in statistical analyses of genomic information, e.g. genome-wide association studies, genomic breeding value estimation and population summary statistics. As such, it offers interfaces to allow integration into existing C utilities as well as interoperability with higher-level programming languages such as R, Julia or Fortran.
An adaptable pipeline for next-generation sequencing analysis, reporting, and visualization for clinical decision making.
The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.
A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model. Mirage is ancestral genome estimation software with high accuracy based on a phylogenetic mixture model and a RER model.
Web-server for identifying and analyzing miRNA in NGS sequencing experiments.
miRAnno-network-based functional microRNA annotation.
Repository for all microRNA sequences and annotation. It has mapped reads from short RNA deep-sequencing experiments to microRNAs and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression.
A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.
A Deep Learning Method for miRNA Binding Classification.
Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.
Predicts mature miRNAs and their precursors from an sRNA dataset and a genome.
Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Part of the UEA small RNA Workbench.
Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers.
Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.
Interactive assessment of qPCR-based microRNA quantification and quality control algorithms. Read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.
Innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.
Web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. It combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse.
Identifying Cooperating miRNAs via Kernel Based Interaction Tests. Although miRNAs can cause widespread changes in expression programs, single miRNAs typically induce mild repression on their targets. Cooperativity among miRNAs is reported as one strategy to overcome this constraint. Expanding the catalog of synergistic miRNAs is critical for understanding gene regulation and for developing miRNA-based therapeutics. In this study, we develop miRCoop to identify synergistic miRNA pairs that have weak or no repression on the target mRNA individually, but when act together induce strong repression. miRCoop uses kernel-based statistical interaction tests, together with miRNA and mRNA target information. We apply our approach to patient data of two different cancer types. In kidney cancer, we identify 66 putative triplets
miRcorrNet is a machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking. This tool allows you to make an integrated mRNA - miRNA profiles analysis. Via using this document you can easily execute the steps and you can obtain the results. Using this document you can easily repeat the experiments. miRcorrNet uses 2 different data sheets with same control-case column. It means you should have same samples in one column which should be both in mRNA and miRNA data sheet. In this study we used KNIME analytics platform. Therefore, the data is stored in ".table" extension files.
A tool for quality control, filter and curation of microRNAs of animals and plants. MirCure: A tool for quality control, filter, and curation of microRNAs of animals and plants. Given a list of miRNA candidates, MirCure evaluates a number of miRNA-specific features based on gene expression, biogenesis, and conservation data, and generates a score that can be used to discard poorly supported miRNA annotations. MirCure can also curate and adjust the annotation of the 5p and 3p arms based on user-provided small RNA-seq data. We evaluated MirCure on a set of manually curated animal and plant microRNAs and demonstrated great accuracy. Moreover, we show that MirCure can be used to revisit previous bona fide miRNAs annotations to improve microRNA databases.
Discovering known and novel miRNAs from deep sequencing data.
miRDeep2 discovers active known or novel miRNAs from deep sequencing data.
High stringency miRNA predictor identifies several novel animal miRNAs.
Tissue context annotation and novel microRNA curation.
MirDNN is a novel deep learning method specifically designed for pre-miRNA prediction in genome-wide data. The model is a convolutional deep residual neural network that can automatically learn suitable features from the raw data, without manual feature engineering. This model is capable of successfully learn the intrinsic structural characteristics of precursors of miRNAs, as well as their context in a sequence. The proposal has been tested with several genomes of animals and plants and compared with state-of-the-art algorithms.
A full end-to-end deep model based on Transformers for prediction of pre-miRNAs.
A manually curated database of validated and putative editing events in microRNAs. MiREDiBase (miRNA Editing Database) is a catalog of validated and putative miRNA editing sites (Adenosine-to-Inosine and Cytosine-to-Uracil) and an online resource for functional prediction of miRNA editing.
This tool correlates the logarithm of expression fold changes of a set of genes with the motif content of the regulatory sequences of these genes. In particular, it correlates the genome wide mRNA log fold changes in experiments involving the knockout/knockdown/overexpression of one or more miRNAs with the motif content of the 3'UTRs. The model is based on linear regression, and is intended for genome-wide studies.
R package and web application for miRNA text mining.
miREV is an online database and tool to uncover potential reference RNAs and biomarkers in small-RNA sequencing data sets from Extracellular Vesicles enriched samples. miREV was developed as an easy to use online tool with a graphical user interface. Main goal is to uncover potential reference RNAs from EV studies in relation to different experimental conditions. Because suitable reference RNAs, for instance to validate findings from NGS experiments or to perform meaningful expression analyses by RT-qPCR, can vary from study to study because the RNA fingerprint strongly depends on the kind of experimental methods used. miREV also serves as a database. Interested parties can download the raw read counts and the associated metadata for further analyzes.
MIREyA (MIRnas functioning through Enhancer Activation) is a computational approach to detect miRNA-directed gene activation. It is a pipeline for detection of miRNAs and their gene targets up-regulated through triggering their enhancer in the provided expression
An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. Defence Institute of Physiology and Allied Science. miRNA and Transcription Factors (TFs) are fundamental transcriptional and post-transcriptional regulators of the gene expression respectively, controlling important biological processes.
MIRfix automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.
Searches for a good miRNA-like folding in the sequence surrounding a putative miRNA. It was optimized on plant miRNAs.
Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data.
A comprehensive microRNA and tRF sequencing analysis pipeline. An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. Enables building small-RNA libraries for the organism of choice to use in the miRge pipeline.
MirGeneDB is a database of manually curated microRNA genes that have been validated and annotated as initially described in Fromm et al. 2015 , Fromm et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 ) includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. All microRNAs can be browsed, searched and downloaded.
integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator. microRNA-target binding site prediction tool.
miRGTF-net is a tool for construction of miRNA-gene-TF regulatory networks using both database-level and transcriptomics/miRNomics data. miRGTF-net uses graphml format to export networks and their weakly/strongly connected components.
Retrieve the list of all available MIRIAM datatypes; retrieve information about a given datatype; resolve a given MIRIAM URN.
A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images.
Web Services which provide generation and resolving facilities for MIRIAM Annotations.
Online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). It integrates microRNA regulations and PPIs with microRNA/mRNA expression data to identify the perturbed microRNA regulatory modules and reveals their functional roles in specific biological conditions.
Prediction of biological processes indirectly targeted by human microRNAs. miRinGO: Prediction of GO terms indirectly targeted by human microRNAs. This R Shiny application can be used to predict Gene Ontology (GO) terms indirectly targeted by human microRNAs. In contrast to direct targets which are predicted to have binding sites, indirect targets are regulated transcriptionally through transcription factors (TFs).
Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.
A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes.MiRKAT-MC
miRkit is an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, can perform the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and is specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.
Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.
Novel method which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.
Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.
Provides comprehensive prediction of microRNA target repression strength. MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. Our resource enables to search precompiled and predict online miRNA targets with miRmap.
Site-level and UTR-level classifier for miRNA target prediction.
miRMaster 2 is a comprehensive analysis framework for sncRNA-seq data. Samples are directly preprocessed in the browser before being uploaded to our server.
MiRmat is a software designed to predict mature microRNA from pri-microRNA. This tool can be divided into two parts, one is for predicting Drosha processing site, which is based on energy distribution pattern along primary microRNA’s secondary structure; the other is for predicting Dicer processing site, which is based on precursor microRNA’s structure feature
Chenfeng He (suggestions on online tool)
miRmine database is a collection of expression profiles from different publicly available miRNA-seq datasets, Panwar et al (2017) miRmine: A Database of Human miRNA Expression, prepared with this data package as RangedSummarizedExperiment.
Binary classification of microsatellite instability using methylation and mutations.
miRMOD is a tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data.
Software tool for systematic discovery of miRNA modules from a set of predefined miRNA target sites. Given a sets of miRNA binding sites, miRModule efficiently identifies groups of miRNAs, whose binding sites significantly co-occur in the same set of target mRNAs, as putative miRNA modules.
Detecting miRNA-mRNA Regulatory Modules.
MicroRNA precursor identification based on distance structure status pairs.
Pipeline for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.
A Comprehensive Web Resource for Plant Pre-microRNA Classification.
Fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.
A software pipeline for the analysis of microRNA Deep Sequencing data
Adaptive Lasso based method that integrates full spectrum of sequence features for microRNA target prediction.
Package containing an S4 class for translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names.
This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.
A webserver for comparative quality control of miRNA-seq data. mirnaQC will try to automatically detect protocol and species from your data but if you provide these, your job will run faster. mirnaQC provides several quality features that can help researchers identify issues in their samples. These features are provided as absolute values and ranked with a percentile calculated from a corpus of more than 36,000 samples.
A comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Welcome to the miRNASNP -v3 database. microRNAs (miRNAs) are endogenous and regulatory non-coding RNAs by targeting mRNAs for cleavage or translational repression. SNPs in pre-miRNAs or target sites will affect miRNA expression or function. miRNASNP is a comprehensive resource of human miRNA-related SNPs, including their effects on target gain and loss.
Machine learning method specifically designed for pre-miRNA prediction. It takes advantage of unlabeled sequences to improve the prediction rates even when there are just a few positive examples, when the negative examples are unreliable or are not good representatives of its class.
The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).
Updates to the experimentally validated microRNA-target interaction database. the experimentally validated microRNA-target interactions database. As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.
A SOM-based miRNA-target interactions predictor.
A small noncoding RNA tissue atlas by determining the RNA expression for nine different types of sncRNAs. For the human atlas, the expression data is determined in 21 organs using 188 samples from six humans. For the mouse atlas, the expression data is determined in 7 organs using 59 samples from 37 mice.
miRNEST: a comprehensive database of animal, plant and virus microRNAs.
Tool with comprehensive support for statistical analysis and functional interpretation of data generated in miRNAs studies.
miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.
Enables rapid and simple browser-based miRNA homology detection and quantification.
It extends miRDeep to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants.
Tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.
A partial linear structure identifier method for cancer subtyping using microRNAs. The R package for ‘mirPLS: a partial linear structure identifier method for cancer subtyping using MicroRNAs’. Run cv_mirPLS to determine the regularization parameters: lambda1 and lambda2. We suggest to search lambda1 and lambda2 in the ranges of (0, 1) and (0, 10), respectively. With lambda1 and lambda2, run mirPLS to select miRNAs linearly or non-linearly associated with disease outcomes. Finally, run sp_clustering to conduct spectral clustering on patients using the selected non-linearly associated miRNAs. In the whole process, cv_mirPLS are time consuming. It may take hours to run the whole process for a typical miRNA data from TCGA.
Determines normalised expression levels of sRNAs matching known miRNAs in miRBase.
Database and a related web application which provides a powerful and intuitive interface to the researchers that want to search for publications related to particular microRNA molecules. It also provides useful information about the correlation of these microRNAs to any diseases, tissues and genes. It facilitates publication search by considering microRNA families and the history of the microRNA nomenclature.
A pipeline for automated analyses of small RNAs in non-model plants
A Modular and Cost-Effective Microclimate Monitoring System for Real-Time Remote Applications.
Database and Tool for Metataxonomics with Long-Read Sequence.
Computational procedure to identify miRNA genes conserved in more than one genome.
miRSCAPE -- to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy separately in 10 tissues comprising ~10,000 tumor and normal bulk samples and demonstrate that miRSCAPE accurately infers cell type-specific miRNA activities (predicted vs observed fold-difference correlation ~ 0.81) in two independent datasets where miRNA profiles of specific cell types are available (HEK-GBM, Kidney-Breast-Skin).
miRSM is an R package to infer and analyse miRNA sponge modules in heterogeneous data.
This package provides several functions to study miRNA sponge, including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.
The product of this pipeline creates a miRspring document, which essentiallyis a small HTML javascript file. Each miRspring document has been developed in such a way that it reproduces miRNA sequencing data from a BAM file. Additionally it provides unique analysis tools, and does not need internet connectivity for these processes.
miRStart 2.0 is a tool for annotating miRNA transcription start sites (TSSs) and identifying tissue-specific TF-miRNA interactions using a deep learning-based model. It integrates over 4500 high-throughput datasets and provides network visualizations to facilitate miRNA regulatory insights.
Detecting microRNA arm shift and switch events. This website uses Matomo Analytics and cookies. For more information, please refer to the privacy notice for our websites. Learn more I agree.
Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.
MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. miRSystem integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan.
Novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA–target interaction data.
miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.
The experimentally validated microRNA-target interactions database
miRTARGET is an integrated web tool for the identification of microRNA targets with potential therapeutic or prognostic value in cancer. The target prediction is based on four dataset categories: mRNA profiling in cells or mice after (1) ectopic miRNA expression or (2) miRNA inactivation by knock-out or knock-down, (3) correlation analyses of mRNA and miRNA expression profiles, and (4) ten computational miRNA target prediction algorithms.
Visual analysis tool for miRNA-mRNA expression profile data.
Text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature.
Imputation via Rank-Transformation and Harmonization (MIRTH), a method to impute unmeasured metabolite abundances by jointly modeling metabolite covariation across datasets which have heterogeneous coverage of metabolite features.
Machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRanda, PicTar and TargetScanS.
A miRNA Target Prediction Method Based on Matrix Completion Algorithm. miRNA target prediction based on matrix completion algorithm. This project includes the dataset and excuteable programs (both on Windows and Linux platform) of the paper "miRTMC: A miRNA target prediction method based on matrix completion algorithm", which is submitted to the Journal of Biomedical and Health Informatics.
Web server for microRNA data analysis, profiling and discovery based on high-throughput sequencing.
Web-based application to analyse the interactions between miRNAs and predicated target genes via their transcripts (mRNAs).
Web server to accurately detect de novo mutations (DNMs) based on Expectation-maximization (EM) model. mirTrios also surports identification of rare inherited mutations, known diagnostic variants, as well as the prioritisation of novel and promising candidate genes.
miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.
Performs digital 24-loci MIRU-VNTR typing for Mycobacterium tuberculosis.
Allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.
MIRUMIR is an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets.
a tool to predict the impact of genetic variants on miRNAs. miRVaS is a program designed to predict the impact of genetic variants on miRNAs. Upload variant file (tab separated or vcf). or paste data in the field below (complete including header and with tabs). Cammaerts, S., Strazisar, M., Dierckx, J., Del Favero, J., De Rijk, P. (2015) miRVaS: a tool to predict the impact of genetic variants on miRNAs. Nucl. Acids Res., 10.1093/nar/gkv921.
miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).
Robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs.
A novel webserver application to visualize and interpret microRNA datasets. miRViz – visualizing microRNA data on networks. Overlay microRNA data (miR expression, differential expression, phenotypic score, etc.) on various microRNA networks (position on the genome, shared targets, shared seed). Compare different datasets on the same networks and/or compare the same datasets on different microRNA networks.
Web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.
Allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
MISCAN is an online modelling-based tool for informing breast, cervical, and colorectal cancer screening decisions in Europe.
MIssense variant to protein StruCture Analysis web SuiTe. MISCAST (MIssense variant to protein StruCture Analysis web SuiTe; http://miscast.broadinstitute.org/) is a web server to interactively visualize and analyze missense variants in protein sequence and structure space.
MiscMetabar aims to facilitate the description, transformation, exploration and reproducibility of metabarcoding analysis using R. The development of MiscMetabar relies heavily on the R packages dada2 (Callahan et al. 2016), phyloseq (McMurdie and Holmes 2013) and targets (Landau 2021).
A framework for medical image segmentation with convolutional neural networks and deep learning. The open-source Python library MIScnn is an intuitive API allowing fast setup of medical image segmentation pipelines with state-of-the-art convolutional neural network and deep learning models in just a few lines of code.
Microbiome data simulator for power analysis
A Metric Library for Medical Image Segmentation Evaluation.
Tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis.
MISHIMA is a program for multiple DNA sequence alignment. It takes input in FASTA format and outputs the alignment in MISHIMA or CLUSTALW format.
Tool to view and analyze sRNA maps of genomic loci and viruses which spawn multiple sRNAs.
A tool for the computation of the similarity matrix among a set of sequences. The tool uses an alignment-free approach to compute sequence similarity measures based on shared maximal words allowing mismatches.
An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.
A knowledgebase and transparency tool for minimum information in spheroid identity.
An atom-based analysis and repository of 4M human protein-coding genetic variants. Welcome to the Missense3D suite of resources, developed by Professor Michael Sternberg's Group. The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates. Missense3D predicts the structural changes introduced by an amino acid substitution. It is applicable for the analyse both experimental coordinates and predicted structures. Missense3D-DB is a database of precomputed structural predictions for ~4M human missense variants.
Software that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data.
Addressing False Assumptions Improves Ligand-Based Virtual Screening | Data and analysis scripts for Missing Label Problem paper | Data and analysis scripts for the paper "The missing label problem: Addressing false assumptions improves ligand-based virtual screening" by Martin LJ and Bowen MT, 2019 link
Normalisation and testing for differential variability and differential methylation for data from Illumina's Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN). The test for differential variability is based on an empirical Bayes version of Levene's test. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.
The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.
Identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. It contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; among others.
MISTIC (Mutual Information Server to Infer Coevolution) is a web server for graphical representation of the information contained in a multiple sequence alignment and a complete analysis tool for mutual information networks in proteins.
Integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets.
Update to the previous server (MISTIC: calculate covariation in protein families and visualize the results.), that allows to calculate four covariation methods (MIp, mfDCA, plmDCA and gaussianDCA).
MISTIC (MISsense deleTeriousness predICtor), a prediction tool to reveal disease-relevant deleterious missense variants based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids.
An open-source multiplexed image t-SNE viewer.
Bringing spectral library predictions to metaproteomics with an efficient search index.
The advancement of technologies for measurement of highly multiplexed spatial data require the development of scalable methods that can leverage the availability of the spatial context. Multiview Intercellular SpaTial modeling framework (MISTy) is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data.
Integrative web cloud platform for user-friendly microbiome data analysis with survival responses.
A tool for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.
A hybrid deep learning-based approach for predicting miRNA targets.
Multi-contrast pathway enrichment for multi-omics and single-cell profiling data. This repo contains code to reproduce analysis presented in the mitch paper. The Mitch R package can be found at https://github.com/markziemann/Mitch. Multi-Contrast Gene Set Enrichment Analysis. mitch is an R package for multi-contrast enrichment analysis.
MITE Digger is designed for the de novo retrieval of miniature inverted repeat transposable elements (MITEs) at genomic scales with high accuracy, specificity and efficiency.
Tool for identifying and visualizing enriched miRNA targets in ranked lists of genes.
An automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data. MITGARD (Mitochondrial Genome Assembly from RNA-seq Data) is a computational tool designed to recover the mitochondrial genome from RNA-seq data of any Eukaryote species.
Modeling the residue interaction network of the Respiratory Chain subunits. MitImpact is a collection of pre-computed pathogenicity predictions for all possible nucleotide changes that cause non-synonymous substitutions in human mitochondrial protein coding genes.
The Medical Imaging Interaction Toolkit (MITK) is a free open-source software for the development of interactive medical image processing software. Based on MITK, there is the MITK Workbench, a powerful and free application to view, process, and segment medical images.
Visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.
MitoAnnotator is a pipeline for annotating fish mitogenomic sequence fully automatically and accurately just in 30 seconds.
MitoBank is a simple perl script to obtain from GeneBank mitochondrial genomes, parse them, and store the different genes in separate files. It can be used to retrieve both coding genes and RNA genes. Coding genes might be obtained in their amino acid or nucleotide sequence.
Comprehensive on-line resource with curated datasets of mitochondrial DNA (mtDNA) rearrangements. MitoBreak provides a complete, quality checked and regularly updated list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially-duplicated (duplications) and linear mtDNAs.
An updated mitochondrial proteome now with sub-organelle localization and pathway annotations. An Inventory of Mammalian Mitochondrial Proteins and Pathways. MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,.
Tool for counting mitochondrial DNA reads from Whole Genome Sequence,
A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations.
Mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
An efficient, high-performance toolkit for animal mitogenome assembly, annotation, and visualization. MitoFlex is a Python3 based toolkit designated for mitochondrial genome assembling, it's inspired from MitoZ, but with improved performance and result quality. And also it implemented a both easy and flexible mechanism to extend the program feature. It accepts both single-end and pair-end data, and follows an already set workflow to output results. Working mechanism is highly flexible and can be easily reconfigured here.
Developed to assist in the annotation of genes and tRNAs in seed plant mitochondrial genomes.
Dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability. It integrates and establishes cross-comparisons between these data.
Find, circularise and annotate mitogenome from PacBio assemblies
A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases.
MitoMiner integrates mitochondrial proteomics data for a range of organisms. You can run flexible queries, export results and analyse lists of data.
The package contains the methods to fit a cell-cycle model on cell count data.
MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito). It is a logically-framed tool for visualizing multiple mitochondrial pathways.
New automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes.
The MitoPhen database is a human phenotype ontology-based approach to identify mitochondrial DNA diseases.
A human phenotype ontology-based approach to identify mitochondrial DNA diseases.
Uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.
Calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site.
De novo metazoan mitochondrial genome annotation.
MitoSAlt is a pipeline for identifying large deletions and duplications in mitochondrial genomes from next-generation sequencing data. It’s designed to analyze circular genomes and was recently used to investigate mtDNA rearrangements in patients with intellectual disability.
A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.
Open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. It evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.
Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology. MitoSegNet_AccuracyTesting_Manuscript. Scripts used to generate quantitative figures shown in MitoSegNet manuscript. All scripts used to generate statistical and visual data shown in the MitoSegNet manuscript can be found here.
A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq.
An algorithm for predicting the impact of novel mitochondrial tRNA mutations. The algorithm is available through MITOMAP
Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.
Web-based bioinformatics platform, provides a convenient, user-friendly interface for handling human mtDNA sequence data.
Designed for data analysis of mitochondrial DNA of eight domestic animals, including cattle, chicken, dog, horse, goat, pig, sheep and yak.
MitoTouch is a computerized method for analyzing mitochondrial shape and network architecture from confocal fluorescence images, providing more than thirty features to quantify changes in mitochondrial organization. It enables the identification of subtle differences in morphology and has potential applications in cell biology, medicine, and environmental toxicology.
A comprehensive mitochondrial toxicity database.
Computational framework for analyzing mitochondrial variation in single-cell RNA sequencing data.
MitoVisualize is a tool for analysis of variants in human mitochondrial RNAs and DNA.
A curated mitochondrial genome database of metazoans for comparative genomics studies.
Web-server specifically trained to predict the proteins which are destined to localized in mitochondria in yeast and animals particularly.
Clustering algorithm based on a straightforward geometric principle. Initially it was designed to be a binary hierarchical clustering algorithm for gene expression analysis.
Stand-alone tool for methylation-based discrimination of mitochondrial DNA ONT reads
Command line application for the discovery of transcription factor binding site (TFBS) motifs.
A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data. Technically you can run mity call and mity normalise separately, but since mity report requires a normalised vcf file, we recommend running mity call --normalise
Tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.
CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France
CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France
NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
Designed for breeding value estimation. The aim is to offer a general and effective program for many kinds of data sets. One of the most important application is to solve large random regression test-day models for national dairy cattle evaluations. Nevertheless, the software is designed to be a general tool that is suited to fit many models.
Efficient Detection and Classification of Epigenomic Changes Under Multiple Conditions. Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions. mixNBHMM is an R package for the detection of genomic regions exhibiting short and broad differential enrichment under multi-replicate, multi-condition settings. It is applicable to data from ChIP-seq, ATAC-seq, DNase-seq, and related experiments. mixNBHMM detects these regions using a three-state hidden Markov model (HMM) with a finite mixture of negative binomials as emission distribution in the HMM’s differential state. The HMM framework is particularly suitable for the detection of differential broad peaks and the mixture model allows the classification of differential combinatorial patterns of enrichment across conditions. Code to replicate the results from the mixNBHMM paper is available at https://github.com/plbaldoni/mixNBHMMPaper
Modern genetic evaluation system for all breeding organizations. It estimates genetic merit of individuals using observations and family relationships, given the components of variance.
Probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data.
Comprehensive software package to study the subclonal structures of tumor genomes, including subclonal cellular prevalences estimation, allelic configuration estimation, absolute copy number estimation and a few visualization tools.
MixDB is a database search tool that able to identify mixture MS/MS spectra from more than one peptide.
The R package mixedCCA implements sparse canonical correlation analysis for data of mixed types: continuous, binary or zero-inflated (truncated continuous).
Computes the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%.
A R package for statistical independence testing of loci in database of multi-locus genotypes. Genetics and Independence Testing of Mixed Genetic Panels. Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package. The goal of mixIndependR is to test the mutual independence of mixed genetic markers.
Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package.
MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.
A tool for calculating required masses and volumes for laboratory solutions. Simple calculator for weighing out components of media/buffers/etc. Mixology is a tool that makes it easy to calculate the ingredients needed for media, buffers, etc. First you enter the final volume of buffer at the top. Then on the left hand side you enter the concentrations desired, in any units (mg/ul, uM, % v/v, etc.). The amounts you need to measure out will appear on the right hand side, in the units that you enter there. Mixology automatically extracts molecular weights from ChEBI to make these calculations as smooth as possible.
The tool offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection.
Software for the Dereplication of Mixtures Based on 13C NMR Spectroscopy. 13C-NMR based dereplication software. MixONat allows the dereplication of natural products mixtures using 13C-NMR and DEPT data.
Programmatic Detection of Diploid-Triploid Mixoploidy via Whole Genome Sequencing. Detection and visualization of 2n/3n mixoploidy from a VCF. This repo contains the scripts used to calculate ratios of diploid-triploid mixoploidy within a Whole Genome Sequencing (WGS) sample. The only input requirement is a tabix-indexed VCF file containing a trio (child, mother, father) with alleles depths (AD tag) and call quality (GQ tag). We have tested the scripts using VCF files from GATK3 on human samples.
MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms.
Software for disease scoring (combining case-only admixture and case-control SNP association signals) in Admixed Populations such as African Americans.
Probabilistic model for solving the single individual haplotyping (SIH) or haplotype assembly problem.
Mixture of Trees using Expectation Maximization is a species tree reconstruction method.
MixTwice is an R package for large-scale hypothesis testing for peptide arrays by variance mixing. Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local false discovery rate statistics and local false sign rate statistics when provided with data on estimated effects and estimated standard errors from all the measured peptides. As the name suggests, the MixTwice tool involves the estimation of two mixing distributions, one on underlying effects and one on underlying variance parameters
Multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene.
Automatic Polyp Segmentation with Multiple Kernel Dilated Convolution Network.
Program we use routinely to build each new release of ProDom, Protein domain families automatically generated from protein databases. It relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains.
Algorithm used to build each new release of ProDom. It can be run on any set of protein sequences in a fasta file.
Open source program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on our implementation of Manzini's lightweight Deep-Shallow algorithm [1], which can also utilize multiple CPUs/cores for some extra speed-up. The generated output is compatible with the output of mkvtree from the Vmatch package written by Stefan Kurtz.
Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.
A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations. Derives Gromacs virtual site parameters (angle constraint, dummy constraints) for an itp/rtp file based on force field data.
Automatic detection of nanoparticles using hyperspectral microscopy and machine learning
Machine learning assisted hypersperal imaging
A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories
Predicting the multi-label protein subcellular localization through multi-information fusion and MLSI dimensionality reduction based on MLFE classifier.
Universal reconstruction of structured illumination microscopy images using transfer learning
Implements regulatory module identification through multi-level support vector regression.
ML-wPBE is a machine learned range separated hybrid functional for use in density functional theory (DFT) calculations.
An approachable, flexible and practical machine learning workshop for biologists.
A web-based interactive browser of a survey on ML4VIS studies
A tool based on artificial intelligence that is able to perform a categorisation of MRI series by using standardized DICOM tags. The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).
ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
A web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions.
MLA is a software resource for label-guided seed-chain-extend alignment on annotated De Bruijn graphs, designed to improve taxonomic classification accuracy and handle long reads by leveraging multi-label alignment scoring.
Machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling.
A LASSO-based interpretable human-protein subcellular localization predictor.
Generic Lattice Constant Prediction of Crystal Materials Using Machine Learning.
R package to correct for machine learning bias when many classifiers are compared and the best is selected.
Identifying multi-functional bioactive peptide functions using multi-label deep learning.
Tools for analyzing and quantifying effects of confounder variables on machine learning model predictions.
MLDA is a tool for the exploration and analysis of multi-label datasets with both simple and multiple views. MLDA comprises a GUI and a Java API, providing the user with a wide set of charts, metrics, methods for transforming and preprocessing data, as well as comparison of several datasets.
Machine Learning-Assisted Directed Evolution Navigates a Combinatorial Epistatic Fitness Landscape with Minimal Screening Burden. A machine-learning package for navigating combinatorial protein fitness landscapes. This repository accompanies our work "Machine Learning-Assisted Directed Evolution Navigates a Combinatorial Epistatic Fitness Landscape with Minimal Screening Burden".
R package for machine learning (ML)-based differential network analysis of transcriptimic data.
Multilevel Edge Features Guided Network for Image Denoising. This repository is an official PyTorch implementation of the paper ''Multi-level Edge Features Guided Network for Image Denoising''. (TNNLS 2020). The paper can be downloaded from MLEFGN. Image denoising is a challenging inverse problem due to the complex scenes and information loss.
An R package to analyze computer models of complex systems.
Machine Learning-Based Analysis of Gaze Error Patterns in Consumer Eye Tracking Systems. A machine learning repository for pattern recognition of gaze errors in consumer eye trackers. The MLGaze repository contains python coding resources for gaze data processing such as data augmentation, outlier removal , creation of gaze features for training and machine learning algorithms for classification and modelling of gaze error patterns. The data used for implementing and testing the methods may be found in the Mendeley repository (link below).
A Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction.
Processing and analysis of high throughput, long-read (e.g. Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.
A maximum likelihood ratio test of natural selection, using polymorphism and divergence data.
MLHO (pronounced as melo) is an end-to-end Machine Learning pipeline that implements iterative sequential representation mining, and feature and model selection to predict health outcomes.
Database search engine developed to assist the user in the detection and identification of small compounds, such as anabolic androgenic steroids, using the soft ionisation technique Matrix Assisted Laser Desorption/Ionisation (MALDI) coupled with mass spectrometry. It compares the results of the experimental data with theoretic values included in the database. It simplifies the interpretation of the mass spectrometry data and reduces the amount of time required to analyze the results manually.
SeSAMe is an R package for analyzing Illumina Infinium DNA methylation arrays, providing utilities for preprocessing, quality control, and inference. It facilitates data integration across different Infinium platforms and is actively maintained.
This package provides uniform interfaces to machine learning code for data in R and BioConductor containers.
ML-LPA (Machine Learning-assisted Lipid Phase Analysis) is a Python 3 library developed to analyse lipid membranes generated during molecular dynamics (MD) simulation runs in order to predict the phase of each lipid and map the local environment of the lipids in the bilayer.
Drug repositioning based on multi-view learning with matrix completion.
A web server for predicting multiple sub-cellular localization of mRNA
A manually curated database of the relations between membraneless organelles and diseases. Membraneless organelles (MLOs) play important roles in the temporal and spatial regulation of various biological processes, and emerging evidence supports that liquid-liquid phase separation (LLPS) is underlying the assembly of MLOs. Dysfunction of MLOs and LLPS are associated with various pathological processes. MloDisDB aims to gather MLOs and LLPS related diseases from the dispersed literature. Each entry was assigned with one of the three evidence levels based on original publication: Direct experiment, Indirect experiment, Clinical Investigation. The functional factors, changes of MLOs and changes of the factors were recorded, the components of MLOs and LLPS related predictions were integrated (go to About for detail).
mlPhaser is an R package for phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.
mlplasmids consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived. It currently classifies short-read contigs as chromosomes and plasmids for Enterococcus faecium, Escherichia coli and Klebsiella pneumoniae.
MLpronto is a tool for rapid, robust, and reproducible machine learning. No ML background is needed whatsoever.
An R Package for Machine Learning in Survival Analysis. mlr3proba is a machine learning toolkit for making probabilistic predictions within the mlr3 ecosystem. It currently supports the following tasks:. Probabilistic Supervised Learning for mlr3. Core learners are implemented in mlr3proba, recommended common learners are implemented in mlr3learners, and many more are implemented in mlr3extralearners. Use the interactive search table to search for available learners and see the learner status page for their live status.
Model-based optimization of subgroup weights for survival analysis | Toolbox for Bayesian Optimization and Model-Based Optimization in R | Model-based optimization with mlr | Issues, Requests and Bug Tracker
Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate.
mlscluster is a phylogenetic clustering algorithm designed to identify mutations under transient/multilevel selection in SARS-CoV-2 time-scaled phylogenies. It was used to analyze a large dataset from England to characterize transmission fitness polymorphisms and guide experimental investigations.
This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data.
Multi Locus Sequence Typing from an assembled genome or from a set of reads.
Chlamydia trachomatis multilocus sequence typing (MLST) database.
Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework. Deconvoluting the Diversity of Within-host Pathogen Strain in a MLST Framework.
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability.
MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known.
Tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments.
Graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites.
Ultrafast and accurate scoring function for protein-protein and protein-ligand docking.
mm2-gb is a GPU-accelerated version of Minimap2 designed to speed up long-read DNA mapping without compromising accuracy. It leverages GPU parallelism to significantly improve the chaining step, a performance bottleneck in the standard Minimap2 workflow.
Genomic Resource for the Improvement of the Family Musaceae.
Welcome to the mmannot Web page. For instance, suppose that you have sequenced your organism of interest with sRNA-Seq (RNA-Seq works too), and you want to know how many times you have sequenced miRNAs, rRNAs, tRNAs, etc. This is what mmannot does.
An analysis pipeline for mapping mutations using RNA-seq. It works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome.
User-friendly and free software to view MS data in a range of formats.
Previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient.
REST API to access MMB-IRB data repo (PDB, Uniprot, Protein Variants, NA Features)
Method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.
Server of prediction of of MHC class I binders which can bind to wide range of MHC alleles with high affinity. This server has potential to develop sub-unit vaccine for large population.
MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects
R package for consensus molecular subtyping of mouse colorectal cancer models.
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data. It is distributed as a R package. .
Accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity.
mmCSM-PPI is a tool for predicting the effects of multiple point mutations on protein-protein interactions.
Database of molecular modelling of 3-D structures; experimentally determined structures only.
A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated metadata. Identify frequently found bacterial species in the gastrointestinal tract of healthy laboratory mice.
This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).
Mitochondrial mixture database and interpretation tool (MMDIT) is an open-source, interactive software for the probabilistic genotyping of mitochondrial DNA mixtures based on complete mitochondrial genomes (mtGenomes). MMDIT can perform both 'Mixture Deconvolution' and 'Mixture Analysis'.
Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis.
mmeta is a program to produce and to align the TF-maps of multiple promoter regions. mmeta is very powerful to characterize promoter regions from multiple orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites.
Adaptive multi-marker meta-analysis (aMeta) is an R package provides facilities for multi-marker meta analysis (mMeta) and adaptive multi-marker meta-analysis (aMeta) which conduct meta-analyses to combine multiple studies throughout multiple related markers. The R package includes two core functions, mMeta.aMeta and mMeta.aMeta.plot, and one summary data set, HIV.Sum.Data.
A database for human metagenomic extrachromosomal mobile genetic elements. Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below)
an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality
Database for the mulberry metabolome. The Mulberry Metabolome Database. Comprehensively, freely, and User-friendly.
Web server that integrates miRNA and mRNA expression data with predicted miRNA target information. It incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).
A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm.
MMIR is an open-source, cloud-based software for multimodal histological image registration designed to simplify the process with a user-friendly approach. It facilitates algorithm management and supports the conversion of segmented annotations between different modalities.
A mind mapping knowledgebase prototyping tool for precision medicine.
Is a software to analyze haplotype polymorphisms in a real human population.
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors | Minimum Message Length (MML) based aligner of protein (amino acid) sequences | Dependencies: GNUMake or equivalent. A modern C++ compiler. seqMMLigner is known to build with g++ (GCC) >= 4.1.2. If these dependencies are met, follow these instructions:
Mouse Multiple Tissue Metabolome Database: metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway.
mmmvi is a tool to identify potential SARS-CoV-2 Variants of Concern (VoC) in metagenomic samples.
MMMx is a toolbox for protein ensemble modeling and analysis, supporting the design of experiments to characterize the distributed structure of proteins with disordered domains. It leverages AlphaFold2 predictions and offers various analysis and visualization tools for conformational ensembles.
This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.
A workflow framework to accelerate the development of experimental simulations.
The Marine Metagenomics Portal (MMP) hosts the marine databases MarRef, MarDB, MarFun, and SalDB. These databases provide the marine scientific community with openly accessible, comprehensive microbial genomics and metagenomics resources, including high-quality, manually curated sequences. The user-friendly web interface allows visitors to easily navigate and refine searches within the contextual databases and offers additional BLAST searches, visualizations, downloads, and workflows (via META-pipe).
R package compendium for the analysis of murine palate miRNA two-color expression data.
MMPatho: Interpretable Model with Multilevel Consensus and Evolutionary Information for Missense Mutation Pathogenic Prediction and Annotation.
A distance-assisted multimodal conformation sampling for de novo protein structure prediction. Distance-assisted multimodal conformation sampling for de novo protein structure prediction.
Tool for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes.
Infers optimal mapping locations from the coverage densities of other mapped reads in vicinity.
MMRFBiolinks isn R package that extends TCGABiolink package for integrative analysis with MMRF-COMMPASS data. IMMRFBiolinks extends TCGABiolink package for searching, downloading and analyzing MMRF-COMMPASS data available at the NCI’s Genomic Data Commons (GDC) Data Portal.
The NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA.
An R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides. The package mms2plot visualizes multiple tandem mass spectrometry (MS/MS or MS2) for modificated and/or non-modified peptides identified from the same raw MS files, annotated by peptide identification algorithms. It will output a mirror-style plots for two peptide-spectrum matches (PSMs) and an aligned plot for more than two PSMs. MMS2plot features a batch mode and generates the output images in vector graphics file format (i.e. PDF) that facilitate evaluation and publication of the PSM assignment.The output file width is recommended as 3.35 inch (single column) or 7 inch (double column).
Alternative web-oriented InChI-based normalization tool developed with the specific aim to efficiently analyze and remove chemical redundancy, minimizing all problems that might affect the performance and the usability of any chemical database.
Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data.
Software suite for very fast protein sequence searches and clustering of huge protein sequence data sets.
mmsig is a tool for flexible and easily interpretable mutational signature analysis. mmsig was developed for hematological malignancies, but can be extended to any cancer with a well-known mutational signature landscape. mmsig is based on an expectation maximization algorithm for mutational signature fitting and applies cosine similarities for dynamic error suppression as well as bootstrapping-based confidence intervals and assessment of transcriptional strand bias.
An open toolbox for accessible structured illumination microscopy. Parent repository for the MMSIM framework which currently includes MMSIMPlugin and MMLiveFFT which are plugins for MicroManager. MMSIMPlugin modifies MicroManager to produce multiple frames per MicroManager "frame" for microscopy systems like SIM. MMLiveFFT provides a live Power frequency spectrum of the live image which is useful for system alignment and quality control.
Web-oriented database of commercially-available compounds for virtual screening and chemoinformatics applications. It contains over 4 million non-redundant chemical compounds in 3D formats.
Web-oriented tool developed with the specific aim to calculate chemical similarity indexes between a query structure and a chemical database.
Can be used for replica exchange calculations with sander. This package also facilitates other Amber tasks, such as dealing in a consistent way with an ensemble of conformations, massaging PDB files, and carrying out some common types of structural analysis.
MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.
MMV_Im2Im is an open-source Python package for image-to-image transformation in bioimaging applications. MMV_Im2Im is designed with a generic image-to-image transformation framework that can be used for a wide range of tasks, including semantic segmentation, instance segmentation, image restoration, and image generation, etc.. Our implementation takes advantage of state-of-the-art machine learning engineering techniques, allowing researchers to focus on their research without worrying about engineering details.
Vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses.
Neural networks for estimating microbe-metabolite interactions through their co-occurence probabilities.
MMX-I is a data-processing software for multimodal X-ray imaging and tomography.
Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA and disease. Here, we have updated the MNDR to version 3.1 by integrating experimentally supported and predicted ncRNA-disease associations curated from manual literatures and other resources. MNDR v3.1 currently contains more than one million ncRNA-disease entries, including 6,301 miRNAs, 39,880 lncRNAs, 20,256 circRNAs, 10,894 piRNAs and 521 snoRNAs with over 1,600 diseases, and an increase of species coverage to 11 mammals.
Organizing electrophysiological data into the BIDS format and facilitating their analysis.
The Mnemiopsis Genome Project Portal provides access to computationally predicted protein structures for the ctenophore Mnemiopsis leidyi, generated using AlphaFold. It allows users to explore and compare these structures, facilitating research into early animal evolution and human health.
MNHN Tree Tools are a set of programs to investigate a database of sequences, and its "evolution", with a plethora of options.
Algorithm to identify the gene targets of a drug treatment based on gene-expression data. In a typical use of the algorithm, a single expression profile, say obtained as a result of a treatment under study, is used as the test profile while a set of hundreds of expression profiles is used as the training set.
An Open-Source Tool for Computing Subtraction Ictal Single-Photon Emission CT Coregistered to MRI. MNI SISCOM is a Windows/Mac/Linux desktop and command line application for computing Subtraction ictal single-photon emission CT coregistered to MRI (SISCOM). The underlying Python library that implements the functionality of MNI SISCOM is also available on PyPi. Please cite the following paper if you use MNI SISCOM in a paper: [reference to come]. A simple command line tool and GUI for computing subtraction ictal SPECT coregistered to MRI (SISCOM). mnisiscom is exclusively intended for research use!.
Predicting human microbe-disease association via a method to minimize matrix nuclear norm.
MntJULiP is a method for comprehensively and accurately quantifying splicing differences at intron level from collections of RNA-seq data.
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding.
A multi-outcome interaction identification approach
Efficient software for detection of enriched regions of MeRIP-Seq. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species.
Discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined.
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies The MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location.
Web server to detect and visualise flexible regions in NMR solved structures.
Database of protein disorder and mobility annotations.
MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions
Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data.
A Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.
A free user-friendly application for collecting experience sampling data. mobileQ is a free, open-source web dashboard and Android smartphone application developed by the research group of quantitative psychology and individual differences at KU Leuven to enable researchers to perform experience sampling or ecological momentary assessment (ESM/EMA) studies and interventions in an easy, intuitive, and accessible way.
Extremely Efficient RGB-D Salient Object Detection.
An R package for effective mobility transformation of CE-MS data.
Tool for high-throughput genomic island discovery.
A unifying concept of animal breeding programs. Simulation Study on the Integration of Health Traits in Horse Breeding Programs. Developed and optimized in Google Chrome. Added Sharing of projects between users (03/11/20). More convenient input for Manuel Select (selection of cohorts for BVE - 03/11/20).
Used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method.
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. Model-based tumour subclonal deconvolution.
MobyWat is a program that analyzes and predicts the hydration structure of molecular surfaces and interfaces, using frames sampled from molecular simulations. It calculates hydration structure and classifies the role of water molecules during ligand binding, utilizing Gromacs, Mopac, and open source packages.
A comprehensive Python library for simulating cancer development with Phase Field Models.
Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM.
MOCAT is a modular and scalable software pipeline for analyzing shotgun metagenomics datasets generated with Illumina technology. Starting from raw fastQ files, it can quality-filter and remove contaminants from them, assemble metagenomic reads into contigs, predict prokaryotic genes on these, identify phylogenetic marker genes and generate taxonomic abundance profiles by mapping reads to these marker genes.
MOCCA (Motif Occurrence Combinatorics Classification Algorithms) is a suite for modelling DNA cis-regulatory element (CRE) sequences.
Designed to convert certain basic forms of ODE simulation models written in MATLAB or Octave and translate them into SBML format.
Method for for clarifying DNA-binding motif ambiguity.
Hybrid genome browser and motif visualization/analysis/management desktop software.
Haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Suite of gene set enrichment analysis tools for model organisms.
Set of Apache modules for Bioinformatics based on the htslib C library.
Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes, WeederH, a tool for detecting TFBS and regulatory regions from homologous genes, and RNA profile, a tool for secondary structure motif discovery in RNA sequences.
This tool can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.
MODalyseR is a software for identifying disease module regulators and reducing modules to the most disease associated genes.
A comprehensive mitochondrial genome database for Mollusca.
Three-dimensional protein models calculated by comparative modelling.
PCA and normal mode analysis of protein.
Database of protein Molecular Dynamics simulations, with 1800 trajectories representing different structural clusters of the PDB.
The Model Debugger for SimBiology lets you analyze model responses, model structure, and expressions during simulations.
Model-M is an agent-based epidemic model of a middle-sized municipality. Model M is an agent-based epidemic model for COVID-19 computational experiments on realistic multi-graph social networks. It allows to simulate projections of main epidemic indicators with respect to various interventions. These include lockdowns, closures of different contact layers (leisure, schools, etc.), social distancing, testing and quarantine, contact tracing, and vaccination.
Statistical modeling and removal of vesicles from cryo-EM images
Model annotation and discovery with the Physiome Model Repository | A web-based epithelial transport discovery, exploration and recommendation tool | Model discovery with the Physiome Model Repository | Model discovery tool is a web-based epithelial transport discovery, exploration and recommendation tool. It allows users to discover, explore and recommend CellML models of interest. This tool is deployed at this address: http://model-discovery-tool.nectar.auckland.ac.nz; as a demonstration of the capabilities described is the paper: https://doi.org/10.1186/s12859-019-2987-y
ModelArchive is the archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB-Dev for integrative structures. Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive. This includes single chains or complexes consisting of proteins, RNA, DNA, or carbohydrates including small molecules bound to them. The modelling methods can be pure in silico predictions as found in de novo models or based on experimental structures such as homology models or modified structures including docked ligands, modelled variants, post-translational modifications (e.g. glycosylated structures), etc. The main purpose of a deposited model is to supplement a manuscript for which the model was generated and to make the model accessible to the interested reader.
An R package for statistical analysis of fixel-wise data.
modelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.
an R package for model building and feature selection with erroneous classifications.
ModelCIF provides the data representation for describing structural models of macromolecules derived from computational methods.
ModelDB is a platform for storing and retrieving computational neuroscience models, providing a searchable repository with standardized metadata. The resource facilitates model discovery and contributes to a more comprehensive framework for establishing domain-specific resources.
Estimates amino acid replacement rates from an input of aligned sequences.
Amino acid and nucleotide substitution model selection
Pearl's message passing algorithm implementation and application to lung cancer diagnosis
Modeling Lung Cancer Diagnosis Using Bayesian Network Inference
Used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
ModelMatcher is a scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research.
Generic Autodidactic Models for 3D Medical Image Analysis. We have built a set of pre-trained models called Generic Autodidactic Models, nicknamed Models Genesis, because they are created ex nihilo (with no manual labeling), self-taught (learned by self-supervision), and generic (served as source models for generating application-specific target models). We envision that Models Genesis may serve as a primary source of transfer learning for 3D medical imaging applications, in particular, with limited annotated data.
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes. The ModelSEED is a resource for the reconstruction, exploration, comparison, and analysis of metabolic models.
Program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.
Computational tool that reconstructs gene regulatory networks from high throughput experimental data.
First-order Markov modeling and discovery of monomeric and dimeric binding motifs. MODER2 is implemented in C++ and has been tested in Linux platform. As the only external dependency, the MODER2 requires the Boost library, which is normally installed on Linux machines. Relatively recent version should be used.
Program for comparative modeling of RNA 3D structures.
MODEST: A web-based tool for rapid and effective design of optimal multiplex automated genome engineering (MAGE) oligos based on simple input, to achieve any mutation possible with MAGE. The tool is useful in oligonucleotide-mediated genome engineering and recombineering.
MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general.
The ModFlex server provides an interface with multiple options and tools, which make it possible to explore structural diversity in the available modeling templates and make an optimal choice. The server uses information from the previously developed PDBFlex database which is focused on structural flexibility and conformational diversity of proteins. The PDBFlex database contains structures that were extracted from the PDB and clustered based on sequence identity, such that each cluster represents an individual protein. The structures in each cluster were further grouped into subclusters based on structural similarity, such that each subcluster represents a distinct conformation of the protein. Thus, each cluster represents a protein, while each subcluster represents a specific conformation of that protein.
Global and local quality estimation of 3D protein models. It integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores.
Webserver for the estimation of both global and local (per-residue) quality of 3D protein models. It produces both machine readable and graphical output.
ModFOLDdock is a web server that assesses the quality of protein quaternary structure models, improving upon TM-score for ranking AF2-Multimer models. It is available at https://www.reading.ac.uk/bioinf/ModFOLDdock/ and https://www.reading.ac.uk/bioinf/ModFOLD/.
Tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.
An Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. R package for robust disease module identification.
Extend or shrink a list of genomic coordinates.
MODIG is a GAT-based model designed for generating gene repre-sentation from a multi-dimensional gene network for the identifica-tion of cancer driver genes, which mainly performed three steps to integrate multi-omics data and multiple gene associations.
Mixture of Distributions Indel Locator, a novel method for finding medium sized indels from high throughput sequencing datasets.
An automated online software for modeling epidemics.
Package for the design, classification and visual representation of peptide data.
MoDLE is a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes.
A tool predicts protein fold domain and family by means of sequence similarity and a relevant number of similar interactions (the same partners or is potential homologs).
Tool for advanced analysis of biological networks. Given two biological networks, it seeks a set of modules, each representing strongly connected nodes in the first network, that are also strongly interconnected in the second network.
MODMatcher is a multi-omics data matcher for integrative genomic analysis.
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes.
At MODORAMA two applications can be run: MODexplorer, an integrated tool for exploring protein sequence, structure and function relationships, and MODalign, a rich alignment editor to improve target-template alignments
Fast ab initio structure prediction of protein-bound peptides.
New, easy-to-use webserver for the prediction of binding partners for modular protein domains. The server comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.
ModPhred is an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. modPhred is a pipeline for detection, annotation and visualisation of DNA/RNA modifications from raw ONT data. The pipeline consists of four steps / modules: modEncode (Encoding modification probabilities in FastQ), modAlign (Build alignments keeping modification information in BAMs), modReport (Extraction of RNA modification information and QC reports), and modAnalysis (Plotting venn diagrams (mod_plot.py), co-occurrence of modifications and per-read clustering based on modification profiles).
Software package and web tool that predicts up to 23 types of post-translational modifications.
Server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
An algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field.
Program using modified screening and ranking algorithm to detect chromosome copy number variations. It is an optimal and accurate approach solving practical issues regarding CNV detection.
modSaRa is an R package designed to perform copy number variants identification.
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. A method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. These modular biomarkers are applied to assign novel aging-related functions to poorly characterized longevity genes.
Modular Subnetwork Biomarker Identification
ModTect is a tool for identifying sites of RNA modifications that disrupts base-pairing using typical RNA-sequencing datasets
ModularBoost is an efficient network inference algorithm based on module decomposition.
An itemset mining framework for the detection of cis-regulatory modules.
Novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs.
Software package proposing a synthetic view of a set of DNA sequences by providing both a segmentation of them into domains and a classification on the basis of these domains.
Software for finding cliques and near-cliques in a protein-protein interaction network.
A web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.
MOFA is a Multi-Objective Flux Analysis for the COBRA Toolbox.
A modest Feature Finder to extract features in MS1 Data.
MoFi annotates glycoprotein mass spectra by integrating hybrid data from the intact protein and glycopeptide level.
A workbench for interactive exploratory data analysis of large expression datasets. MetaOmGraph (MOG) is a Java software to interactively explore and visualize large datasets. MOG overcomes the challenges posed by big size and complexity of big datasets by efficient handling of data files by using a combination of data indexing and buffering schemes. By incorporating metadata, MOG adds another dimension to the analyses and provides flexibility in data exploration. MOG allows users to explore their own data on their local machines.
A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks. MOGAMUN is a Multi Objective Genetic Algorithm to find active modules (i.e., highly connected subnetworks with an overall deregulation) in MUltiplex biological Networks. For a detailed description of MOGAMUN check out the preprint https://www.biorxiv.org/content/10.1101/2020.05.25.114215v1. All the expression datasets and networks that we used to obtain the results reported in our preprint are available in the GitHub repository https://github.com/elvanov/MOGAMUN-data.
Useful tool for converting chromosomal contact data into 3D genome models to provide a better view into the spatial organization of genomes.
This package provide a method for doing gene set analysis based on multiple omics data.
Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues. Moiety Modeling implemented in Python. moiety_modeling package provides facilities for moiety model representation, model optimization and model selection. Welcome to moiety_modeling’s documentation! — moiety_modeling 1.0.3.2 documentation. The model selection results produced by moiety_modeling framework using the UDP-GlcNAc isotopologue datasets. ‘moiety_modeling’ runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following depencies and you are ready to go!. Welcome to moiety_modeling’s documentation!¶. 'moiety_modeling' runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following depencies and you are ready to go!.
MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems.
moire is an R package for estimating allele frequencies and effective multiplicity of infection (MOI) from polyallelic data, particularly useful for malaria parasite genetic data where multiple strains may be present.
MoiRNAiFold is a tool for complex in silico RNA design.
Automated computational tool for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.).
A fast and universal method for integration of multimodal single-cell data.
Fast and Flexible Semisupervised Learning for Peptide Detection
Mol2Context-vec provides a deep context aware molecular representation to drive the boundaries for drug discovery. It can integrate different levels of internal states to bring abundant molecular structure information.
A soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm. MolAICal is a drug design software combined by artificial intelligence and classical programming. MolAICal is freely for education, academic and other non-profit purposes. If you want to use MolAICal for any commercial purpose, you should contact with licensors (Email: molaical@yeah.net).
MolAR is a memory-safe library for analyzing MD simulations written in Rust, aiming to explore benefits of modern memory-safe languages for molecular analysis. It demonstrates excellent performance and is freely available under the Artistic License 2.0.
The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.
A VMD Graphical User Interface Featuring Molecule Manipulation. Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks. For instance, translation or rotation of a selected molecule(s) or part(s) of a molecule, which are currently only can be achieved using tcl scripts. Here, we use tcl script develop a user-friendly GUI for VMD, named Molcontroller, which is featured by allowing users to quickly and conveniently perform various molecular manipulations. This GUI might be helpful for improving the modeling efficiency of VMD users.
Molecular Benchmark for Disease and Target Based Machine Learning.
Package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.
Learning Mass Spectrometry Fragmentation of Small Molecules. MolDiscovery is a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by (i) utilizing an efficient algorithm to generate mass spectrometry fragmentations, and (ii) learning a probabilistic model to match small molecules with their mass spectra. A search of over six million spectra from global natural product social molecular networking infrastructure shows that our probabilistic model can identify nearly twice more small molecules than previous method.
MolDy is a user-friendly, interactive front-end application for molecular dynamics simulations built upon GROMACS. It simplifies the MD simulation process, making it accessible to researchers without extensive expertise.
Location and basic characterization of channels in molecular structures.
Palacký University, Olomouc, Czech Republic
Plugin for MOLE 2.0 contains extended options for channel starting point automatic detection, for filtering of obtained channels to select only the relevant channels and allows estimation of basic physicochemical properties of channels.
A new multi-dimensional hierarchical scaffold analysis tool.
Calculates molecular masses and isotopic distributions.
Lightweight m-file for drawing simple .pdb files.
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs.
Provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.
Represents each molecule via a 3-dimensional grid of complex numbers and estimates the extent of geometric and chemical surface complementarity by correlating the grids.
A framework for scientific data management, exploration, integration and analysis. It is adaptable to many types of scientific data and data workflows, and there are several pre-configured MOLGENIS systems for specific data types.
Rapid generation of genetic imputation scripts for grid/cluster/local environments.
Workflow tool useful for core facilities to create pipelines that run on PBS or SGE clusters or on GRIDS. It ships with pipelines for alignment and SNP/SV calling of Illumina next generation data and with pipelines for GWAS imputation using impute2, minimach or beagle.
A collaborative effort to integrate the catalogues of diverse EU research projects and networks to accelerate reuse and improve citizens health.
European Health Research Data and Sample Catalogue
Best practice variant interpretation pipeline to shortlist pathogentic variants for rare heritable disease, build in nextflow and including diagnostics ready reporting. Maintained as part of MOLGENIS community project
Fast and accurate prediction of the pKa values of small molecules is important in the drug discovery process since the ionization state of a drug has significant influence on its activity and ADME-Tox properties. MolGpKa is a web server for pKa prediction using graph-convolutional neural network model. The model works by learning pKa related chemical patterns automatically and building reliable predictors with learned features.
A Web Server for Structure-Based Drug Design by Molecular Hybridization.
Database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes. It provides annotated sequence data and analysis for 72 genomes belonging to 51 species. The database provides genome and genetic element pages, homology relationship defined by various methods, pre-computed statistics, metabolic pathways, and a huge collection of tools for exploring and comparing genomes.
Centre de Bioinformatique de Bordeaux (CBiB)
Web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.
MolluscDB is a genome and transcriptome database for molluscs.
A structured database that provides best practice-based protocols for molecular analyses.
PharmaMind®-MolMiner is a rule-free OCSR (Optical Chemical Structure Recognition) learning system. It aims to transform the vectorization problem into object detection tasks. That means it is able to extract chemical elements in an object detection manner by training well-labelled datasets with atom and bond annotations.
MolModa is a web-based suite for computer-aided drug discovery allowing users to perform molecular docking directly in their web browsers, providing a secure and accessible environment for early-stage drug discovery.
The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.
A lightweight self-attention-based method focused on spatial structure of molecular graph for drug-drug interactions prediction.
MoLPC2 is a software resource that predicts the structures of large protein complexes and their stoichiometry using Monte Carlo Tree Search and AlphaFold2. It provides a new approach to predict protein complex structures without requiring prior knowledge of stoichiometry.
MolPhase is a machine-learning algorithm for predicting protein phase separation, utilizing physicochemical features and experimental datasets. It provides a user-friendly interface to compare biophysical features and has been experimentally validated in vitro and in vivo.
PDB to POV file (POV-Ray) converter and molecular visualization tool for MS Windows.The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format.
MolPredictX is a web tool that allows the scientific community to obtain biological activities predictions of molecules. MolPredictX manages predictive models already published in indexed scientific articles and makes predictions of molecules the researcher wishes to investigate. It informs the qualitative prediction of the molecules, as well as a probability quantitative value of activity. MolPredictX also provides the possibility for the researcher to download predictions in the .csv format
MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.
CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. File Upload/Retrieval (more options). CCTBX, which powers this version of MolProbity (4.2), requires stricter adherence to PDB format. If you are having trouble with version 4.2 try using MolProbity4 legacy version 4.02 at http://rutile.biochem.duke.edu. Note that not all features are supported on legacy 4.02 and we suggest repairing your PDB format instead.
One-stop, general purpose, and AI-based platform for the early stages of drug discovery.
A program for automated molecular replacement in the case where a homologous structure has already been identified.
A Deep Representation Learning Library for Molecular Property Prediction. MolRep is a Python package for fairly measuring algorithmic progress on chemical property datasets. It currently provides a complete re-evaluation of 16 state-of-the-art deep representation models over 16 benchmark property datsaets.
MolScore is an open-source platform designed to facilitate generative molecular design and evaluation. It unifies existing benchmarks, provides a platform for sharing new ones, and improves customization and usability for drug design practitioners.
Image-to-graph model that translates a molecular image to its chemical structure.
Search-based multi-objective molecular generation and property optimization.
Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics.
Mol* Viewer is web app for 3D visualization and analysis of large biomolecular structures. Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB)
Graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.
A tool for the rapid generation of favorable tautomer in aqueous solution.
Molecular interaction transformer for drug target interaction prediction. Drug target interaction (DTI) prediction is a foundational task for in-silico drug discovery, which is costly and time-consuming due to the need of experimental search over large drug compound space.
molUP is a free VMD extension that allows you to open and save Gaussian files. This tool can be used to analyze results from Gaussian output files and prepare Gaussian input files. molUP provides also a set of tools to adjust bond lengths, rotate angles and dihedral angles directly on VMD. With molUP, it is possible to add and remove atoms or molecules using VMD.
Chemical sketching and molecular modeling made easy
Streamlining the design and rendering of molecular movies. A Python script to automate the production of molecular movies in VMD. Molywood is there to make cool molecular movies for you. Specifically, molywood automatizes the most tedious steps in generation of these movies, i.e. scripting in TCL, rendering, generating overlays and combining frames, as well as merging frames into the final movie:.
Takes specific advantage of the geometry of the device to accurately segment and track cells using only phase-contrast images, and further provides a curation user interface with leveraged-editing, meaning that a set of related errors are often fixed with a single click.
Web server for simulating protein-ligand unbinding. It computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms. The PDB file provided as input may contain several ligands.
MoMA-LoopSampler is a method to exhaustively sample the conformational space of protein loops. It exploits structural information encoded in a large library of three-residue fragments, and enforces loop-closure using a closed-form inverse kinematics (IK) solver. A novel reinforcement-learning-based approach is applied to accelerate sampling while preserving diversity.
Momba is a Python framework for dealing with quantitative models centered around the JANI-model interchange format. Momba strives to deliver an integrated and intuitive experience to aid the process of model construction, validation, and analysis. It provides convenience functions for the modular construction of models effectively turning Python into a syntax-aware macro language for quantitative models. Momba's built-in exploration engine allows gaining confidence in a model, for instance, by rapidly prototyping a tool for interactive model exploration and visualization, or by connecting it to a testing framework. Finally, thanks to the JANI-model interchange format, several state-of-the-art model checkers and other tools are readily available for model analysis.
Multi-Objective Matrix Normalization for Fine-grained Visual Recognition. Bilinear pooling achieves great success in fine-grained visual recognition (FGVC). Recent methods have shown that the matrix power normalization can stabilize the second-order information in bilinear features, but some problems, e.g., redundant information and over-fitting, remain to be resolved. In this paper, we propose an efficient Multi-Objective Matrix Normalization (MOMN) method that can simultaneously normalize a bilinear representation in terms of square-root, low-rank, and sparsity. These three regularizers can not only stabilize the second-order information, but also compact the bilinear features and promote model generalization. In MOMN, a core challenge is how to jointly optimize three non-smooth regularizers of different convex properties. To this end, MOMN first formulates them into an augmented Lagrange formula with approximated regularizer constraints
Accurate Biological Network Alignment Through Optimal Neighborhood Matching Between Focal Nodes.
A novel Gene Ontology enrichment analysis visualisation system.
MoNaS is a pipeline to genotype mosquito's voltage-gated sodium channel genes using NGS data. (Mosquito Na+ channel mutation Search).
An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces. Note: This repository contains the scRNA-Seq analysis software. For other tools named Monet, see Disambiguation. This repository contains gene lists and the scRNA-Seq datasets using in the analyses presented in Monet paper (Wagner, 2020). Monet is an open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces. Datasets from the Monet paper (Wagner, 2020) can be found in a separate repository.
MoNET is an R package providing network analysis of -omics findings. It is built on top of an integrated network, including metabolite-protein interactions, protein interactions and relationships between genetic variations and transcription factor binding sites.
Web server that can identify the modules, homologous modules (called module family), and MMI networks across multiple species for the query protein(s).
Modular Network Generation and Visualization Platform with Knowledge Integration Environments (MONGKIE) is a software platform that integrates network visualization with omics data analysis tools.
MONGOOSE (MetabOlic Network GrOwth Optimization Solved Exactly) is a package for structural analysis and refinement of constraint-based metabolic networks. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results certifiably accurate
MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.
A Toolbox for Connectivity-Based Parcellation of Monkey Brain. MonkeyCBP (A toolbox for connectivity-based parcellation of monkey brain).
A Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins. Codes for "MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins". The benchmark dataset described in this paper can be found in ./data/, and the creation of this dataset can be reproduced by the protocol in ./create_dataset/.
Finds meaningful partitions using semi-supervised class discovery.
This tool performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. It also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
An automatic method for determing local resolution of 3D elecron microscopy maps. MonoRes is available via the Xmipp and Scipion software packages
Information on the residues used in glycan databases.
single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data. It takes a list of bam files as input and outputs a vcf file containing the detected SNVs.
MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.
A new tool for high-throughput detection of mosaic copy number variation.
MonteCarbo is a software to generate and dock multifunctionalized ring molecules. It is able to construct simple 5-, 6- and 7-membered ring multifunctionalized monosaccharides and nucleobases and to dock them into target glyco- and RNA DNA- active enzymes.
MONTI is a tool for analyzing large multi-omics cancer cohort data in association with clinical featuers
A suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions.
Moonlight2R is a Bioconductor package designed to identify cancer driver genes by integrating gene expression and DNA methylation data, enhancing insights into cancer mechanisms and providing potential therapeutic targets.
The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role. We present an R/bioconductor package which returns a list of candidate driver genes for specific cancer types based on TCGA expression data. First infers gene regulatory networks and then carries out a functional enrichment analysis to score the importance of well-known biological processes with respect to the studied cancer type.
Core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores.
A Python package for metabolic modelling and topological analysis. Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, amongst others, differential equations based modeling of metabolic systems, constraint based modeling and topological analysis of metabolic networks. Most of these methods are well established and are implemented in numerous software packages, but these are scattered between different programming languages, packages and syntaxes. This complicates establishing straight forward pipelines integrating model construction and simulation
R-shiny application for the simulation and power calculation of multi-omics studies.
Identification and characterization of periodic fluctuations in time-series data.
MORA is a metagenomic read re-assignment algorithm that leverages abundance information to improve assignment accuracy, particularly for similar strains. It is freely available as a command-line tool and is modular for incorporation into broader metagenomics workflows.
Multimorbidity networks in adult general population. Analysis of type 2 diabetes mellitus comorbidity.
Mobile client able to integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools.
Descriptor-calculation software application that can calculate more than 1800 two- and three-dimensional descriptors.
MORE (Multi-Omics REgulation) is an R package for the application of Partial Least Squares (PLS) or Multiple Linear Regression (MLR) models with Elastic Net or Iterative Sparse Group Lasso (ISGL) regularizations to multi-omics data. The MORE method applies MLRs or PLS to model a target omic expression as a function of experimental variables, such as diseases or treatments, and the potential regulators of that given target feature. The aim is to obtain specific candidate regulators for the biological system under study.
A user-friendly Shiny/R application for exploring and comparing data with interactive visualization.
A package for molecular recognition feature function prediction based on multi-label learning and ensemble learning
New computational approach for a fast and accurate prediction of MoRFs(Molecular Recognition Features) in protein sequences.
MORFEE (Mutation on Open Reading FramE annotation) is a tool (R package) that, from a VCF file, detects and annotates single nucleotide variants creating premature ATG codons.
Meta-analysis based orthology finder using symmetrical best hits.
MOrgAna (Machine-learning based Organoids Analysis) to segment and analyse 2D multi-channel images of organoids.
Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors. MORLD is a molecule optimization method based on reinforcement learning and docking. This repository provides the source code of the main part of the MORLD software and its usage. Molecule Optimization by Reinforcement Learning and Docking. MORLD is a molecule optimization method based on reinforcement learning and docking.
Algorithm to associate candidate genes with a given target pathway. Unlike any other algorithm in plant sciences, this algorithm tests multiple combinations by learning how to choose among various forms of evidence (large scale data sets) to link genes to a specific target pathway.
An open-source ImageJ plugin that automatizes the data extraction process of morphological features of single microglial cells.
Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants. 1. MORPH bulk run command line interface. Get MORPH candidate gene predictions for your gene(s) of interest. 2. Install morph-bulk using Singularity (recommended). Get MORPH candidate gene predictions for your pathway or GO term of interest for your favourite organism(s). Make a MORPH network for your process of interest. 3. Install morph-bulk the classical way. Perform complex SPARQL queries on MORPH prediction data. rdf Generate RDF graph (for MorphDB).
A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.
Morpheus is an open-source modeling and simulation framework for multi-scale and multicellular biological systems. The GUI allows to construct and simulate models from gene regulation, metabolism and signaling to tissue morphogenesis and their multi-scale feedbacks without the need to program. Morpheus is based on declarative modeling in biological terms and mathematical expressions and internally uses the domain-specific language MorpheusML, allowing for rapid model prototyping without extra code-compilation. Morpheus supports cell-based model formalisms, ODEs, PDEs, rule-based models, SBML models etc. (all freely coupled) as well as image-based modeling. It renders results in customizable 2D and 3D images or movies and offers analysis tools to extract features right during simulation. The plugin architecture makes it extensible. Binary installers are available for all major OS from the Morpheus homepage together with online courses, a public model repository and many more resources.
An automated tool for unbiased and reproducible cell morphometry. A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2. MORPHEUS is a Fiji ImageJ2 plugin for the automated evaluation of cell morphometry from cell cultures images acquired by fluorescence microscopy.
Web-based bioinformatics tool to study human diseases using model organism genes.
An unsupervised machine learning workflow to detect the activation of microglia and astrocytes.
Cross-platform, open-source application for the visualization and processing of 3D biological datasets.
Library that proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.
An R package for long bone landmarking, cortical thickness, and cross-sectional geometry mapping. morphomap at each section extracts two sets of semilandmarks, cortical thickness, cortical area and the parameters useful for cross-sectional Geometry. morphomap returns also 2D and 3D cortical maps. The morphomap package from a single input (an oriented 3D mesh) is capable to produce the output suitable for thickness geometry, shape analysis and cross-sectional geometry. Morphometric Maps, Bone Landmarking and Cross Sectional Geometry. Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils.
MorphoSource is a platform for housing and sharing 3D morphological data of primate specimens, facilitating collaborative research in phenomics. It provides a repository for digitized specimens from various institutions and enables researchers to access and analyze morphological data.
Transport-based interpolation between EM maps with UCSF ChimeraX. MorphOT is a plugin for ChimeraX, which allows users to directly interpolate multiple density maps. It relies on adapting and optimizing for EM maps some recent methods of shape interpolation based on optimal transport (OT), resulting in significant improvement in quality of morphing, compared with the standard command provided withChimeraX. For more details on the method, please see the appendix here and the paper accompanying the software.
The package MorphoTools2 is intended for multivariate analyses of morphological data.
MorphPod: Deep learning phenotyping of Arabidopsis fruit morphology - Deep learning model weights and inference code to detect Arabidopsis thaliana siliques in scans of stem material. Phenotyping code to extract length, diameter area and volume metrics of siliques from model outputs. Associated with the manuscript "Unlocking the Power of AI for Phenotyping Fruit Morphology in Arabidopsis" by Atkins et al.
Simulink realization of Morris-Lecar neuron model.
Software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone.
A unified trait database to complement structured population models.
Will generate candidate vaccine protein cocktails that optimize the coverage, by a small set of mosaic proteins that could be included in a vaccine cocktail, of potential T-cell epitopes in a large diverse set of proteins.
The MOSAIC bioacc application is a turn-key web tool providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances.
MosaicExplorerJ is an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection.
mosaicMPI is a framework for modular data integration across cohorts and -omics modalities, facilitating the discovery of molecular programs and integration within and across datasets to represent biological themes. The framework integrates data from various platforms, yielding a richly characterized landscape of biological themes.
This package provides functions for fitting MOSAiCS-HMM, an statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.
A software suite for analysis of membrane structure and dynamics in simulated trajectories.
Multi-algorithm Ensemble Biclustering Method MoSBi (Molecular Signature Identification using Biclustering)
Program to view atomic structures of protein molecules. Beyond its basic molecular graphics functions, extension modules provides custom functions for research works in structural biology and computational molecular biology.
Meta-Omics Software for Community Analysis
This code executes the Multi-Omic Single-Cell Analysis using TensOr regression (MOSCATO) method which uses multi-omic, single-cell data with two data types, X and G, and a univariate outcome which follows an exponential family distribution. In summary, it will estimate the similarity and perform tensor regression using the similarity as the predictor tensor. The features will be selected by applying an elastic net constraint on the coefficient vectors, and any non-zero coefficients will correspond to the features selected. In addition to applying MOSCATO, code to simulate multi-omic, single-cell data is also provided.
Molecular simulation design framework (MoSDeF) Cassandra is a complete Python interface for the Cassandra Monte Carlo software.
Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC.
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
Contains a lot of sequence analysis algorithms, including methods for motif statistics, exact motif discovery, analysis of pattern matching algorithms, etc.
A Benchmarking Platform for Molecular Generation Models. Deep generative models are rapidly becoming popular for the discovery of new molecules and materials. Such models learn on a large collection of molecular structures and produce novel compounds. In this work, we introduce Molecular Sets (MOSES), a benchmarking platform to support research on machine learning for drug discovery. MOSES implements several popular molecular generation models and provides a set of metrics to evaluate the quality and diversity of generated molecules. With MOSES, we aim to standardize the research on molecular generation and facilitate the sharing and comparison of new models.
Program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.
Modular Open-Source Genome Annotator. The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies.
MOSim (Multi-Omics Simulation) package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.
Multi-omic integration with Sparse Value Decomposition (MOSS), a free and open-source R package for integration and feature selection in multiple large omics datasets.
Able to analyze all the traits jointly. The framework is flexible in that it can handle both continuous and binary traits, or a mixture of them. In addition, it can accommodate family data, can adjust for covariates (such as ancestry variables, age, gender, etc.), and can be combined efficiently across studies with different designs.
Application in Single-shot T2 Mapping with Severe Head Motion Using Overlapping-echo Acquisition.
MOST+ is a fast MOTIF finding tool(MOtif finding by Suffix tree and heterogeneous Tags). It extracts distribution features of nearby epigenomic markers, like histone modification or nucleosome occupancy, to help de novo find motif, thus rendering a higher level of accuracy on characterizing motif (cross-validated by ChIP-seq data) and more co-factors.
Multi-Omic Strategies for Transcriptome-Wide Association Studies.
Detects structural motifs containing β-strands.
Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings. This repository is the backend library of our GUI based app - MOTHe-GUI. Mothe is a PYPI library to detect and track multiple animals in a heterogeneous environment. MOTHe is a python based repository and it uses Convolutional Neural Network (CNN) architecture for the object detection task. It takes a digital image as an input and reads its features to assign a category.
Converting mothur's taxonomy summaries into Krona-compatible XML files.
Open-source, platform-independent, community-supported software for describing and comparing microbial communities
A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators. We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predic-tive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Genome-wide association studies (GWAS) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging.
Software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.
Protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
Fast and exact quantification of motif occurrences in biological sequences.
Tool for finding matches to degenerate sequence motifs in FASTA files.
Allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. It is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources. It can predict effects for novel or previously described variants in public databases.
a MATLAB GUI platform for determination and evaluation of biologically significant motifs
The package is in particular useful for long motifs and/or relaxed choices of score thresholds, because the implemented algorithms efficiently bypass the need for enumerating a (potentially huge) set of DNA words that can give rise to a motif match.
DNA motif-finding algorithm using a Maximum Density Subgraph.
More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.
Designed to find motifs in multiple DNA sequences.The software uses the randomized algorithm to find good seeds and uses the improved EM algorithm to do local search.
An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. This is an R package for motifeR software. Shisheng Wang, Yue Cai, Jingqiu Cheng, Wenxue Li, Yansheng Liu and Hao Yang. "motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs." Proteomics (2019): 201900245. (DOI: 10.1002/pmic.201900245)
MotifGenie is a Python command line tool for searching transcription factor binding motif sequences in merged ChIP-Seq binding sites. First, MotifGenie analyzes multiple ChIP-Seq samples simultaneously to identify shared binding regions for a locus of interest, then, searches the binding motif sequence of a given transcription factor in these shared binding regions.
Norwegian infrastructure for bioinformatics ELIXIR.no
The National Programme for Research in Functional Genomics in Norway
General workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. It can improve performance of binding site predictions by allowing users to integrate several motif discovery tools, as well as different types of data: phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.
Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.
MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions.
Tools for discriminative motif discovery using regression methods.
MotifSampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. In this implementation we focus on the use of higher-order background models to improve the robustness of the motif finding. At the moment the MotifSampler comes with background models for several organisms .
MotifScan is a non-parametric DNA motif scanning algorithm.
Motif Search allows you to specify several different criteria when searching for sites, such as a p-value or an approximate false-positive rate given a set of negative examples.
Detecting similarity in a single or multiple DNA motif datasets.
This package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.
A machine learning framework for automatic prediction of human sperm motility.
A significant discriminative sequence motif discovery algorithm with multiple testing correction. sudo apt-get install libgmp3-dev. Or see this URL. Notice that the build option "--enable-cxx" is necessary for configuration like this:. Execute MotiMul without distinguishing a sequence and its complementary strand if you use it for DNA sequences. -v.
An algorithm for improving resolution of cryo-electron microscopy. It enables to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images
This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.
A web application for validation of annotation of ligands and residues.
An open-source R toolbox for time-domain motor unit analyses. Analyzing Paired Neuron Discharge Times for Time-Domain Synchronization. Using motoRneuron for motor unit synchronization. The temporal relationship between motor neurons can offer explanations for neural strategies. We combined functions to reduce neuron action potential discharge data and analyze it for short-term, time-domain synchronization. Even more so, motoRneuron combines most available methods for the determining cross correlation histogram peaks and most available indices for calculating synchronization into simple functions. See Nordstrom, Fuglevand, and Enoka (1992) <doi:10.1113/jphysiol.1992.sp019244> for a more thorough introduction. The purpose of this document is to get you started using the motoRneuron package for analyzing motor unit data, even if you've never used R before! So we will show you how to install the toolbox through CRAN, access the functions, help files, and sample motor unit data
Temporal dynamics of the multi-omic response to endurance exercise training across tissues.
Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.
Representing Motifs in Consensus Sequences with Minimum Information Loss. Represent motifs in consensus sequences. -- representing motifs in consensus sequences with minimum information loss. git clone https://github.com/MichaelMW/motto.git.
A robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation.
Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.
Metagenomic operational taxonomic units (mOTUs)
The mOTUs database provides web-accessible genomic context to taxonomic profiling of microbial communities, comprising a large collection of metagenome-assembled genomes and isolate genomes from diverse species-level taxonomic units. It allows users to explore and download genomes at various taxonomic levels.
MountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq | Citation: Cass AA and Xiao X. (2019). mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-Seq. Cell Systems | mountainClimber is a tool built for identifying alternative transcription start sites (ATS) and alternative polyadenylation sites (APA) from RNA-Seq by finding significant change points in read coverage. It is made up of three main steps which can be used in isolation:
Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function.
A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries.
MGI (Mouse Genome Informatics) is a knowledgebase providing integrated genetic, genomic, and biological data for the laboratory mouse to facilitate research on human health and disease. It serves as a central resource, integrating data from multiple databases and providing access to FAIR-compliant data.
data about GPCR expression in different organ systems
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal.
The database and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. It portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information.
R package specifically designed to genotype the Mouse Diversity Genotyping Array, an Affymetrix mouse genotyping array similar to the human SNP 6.0. It contains functions which allow you to perform genotyping, identify probe sets potentially harboring a new mutation (Variable INtensity Oligonucleotide or VINO, here we call it a vinotyping) and perform CNV analysis.
In silico candidate variant and gene identification using inbred mouse strains. This repository contains the backend of the MouseFM tool including the scripts of the etl process and the webserver. The MouseFM client is available as an R package on Github (https://github.com/matmu/MouseFM) or on Bioconductor (https://bioconductor.org/packages/devel/bioc/html/MouseFM.html).
Integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database currently includes polymorphisms identified from our alignment of whole-genome shotgun sequence traces from four laboratory mouse strains mapped against the reference C57BL/6J genome using GMAP.
Data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer.
Online search tool to search for variations in all protein-coding gene sequences of 36 sequenced mouse inbred strains, compared to the reference strain C57BL 6J, which could be linked to strain-specific phenotypes and modifier effects.
A user-friendly tool for rapid biological discovery from human or mouse transcriptional data.
Method for evaluating the pathogenicity of missense variants using AlphaFold2.
Modeling and visualization of dynamics of alternative polyadenylation across biological samples. Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically.
MoveApps is a no-code analysis platform for animal tracking data hosted by the Max Planck Institute of Animal Behavior. The aim is to make sophisticated analytical tools accessible to a larger audience.
An R package for multi-omics integration and visualization in cancer subtyping. Multi-Omics integration and VIsualization in Cancer Subtyping. The goal of MOVICS is to provide a unified interface for 10 state-of-the-art multi-omics clustering algorithms, and standardizes the output for each algorithm so as to form a pipeline for downstream analyses. MOVICS incorporates the most commonly used downstream analyses in cancer subtyping researches and enables creating feature rich customizable visualizations with minimal effort.
MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions.
MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.
A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks.
Python library for machine learning with biomedical ontologies.
Versatile web client to access BioMOBY compatible services for interaction with multiple sources of biological data. .
A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates.
Deep learning-based segmentation for fluorescence microscopy images of microplastics isolated from clams.
Standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets.
Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels. Supplementary repository for: https://github.com/AlgoLab/mp3treesim.
MPA-MutPred is a webserver for predicting changes in binding affinity (ΔΔG) of membrane protein-protein complexes upon mutation. It utilizes sequence and structure-based features and is freely accessible online.
Allows user-friendly creation of user-defined pathways and mapping of experimental data on them
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
MPAC is a computational framework for inferring pathway activities from multi-omic data, predicting patient groups and identifying key proteins. It's available as an R package on Bioconductor.
A Database for Binding Affinity of Membrane Protein-protein Complexes and their Mutants.
A package for multi-patients analysis of genomic markers. It is devoted to (i) efficient segmentation and (ii) genomic marker selection from multi-patient copy number and SNP data profiles.
An open source protocol to design modified peptides with improved binding affinity to a target of reference. The protocol generates single-point mutations on the peptide sequence based on a list of parameterized non-natural amino acids (NNAAs). Then, it estimates their binding affinities in complex with the protein in an efficient but accurate manner by combining backrub sampling from Rosetta with a consensus metric using multiple protein-ligand scoring functions.
Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.
Meta-motif based statistical framework and pipeline to predict SELEX derived binding aptamers. Briefly, MPBind calculates four kinds of p-values (1-sided) for each motif, representing different features.
Software that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed.
Demonstration of a novel MPCC-based technique for solving gene circuit design problems.
MPCC Solution of Genetic Regulatory Circuit Design Problems
Mouse Phenome Database: houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease. Data sets are voluntarily contributed by researchers from a variety of institutions. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications.
Multiplex primer design for next-generation targeted sequencing.
An innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.
MPEA is a rapid tool for functional analysis and biological interpretation of metabolic profiling data. In particular, MPEA is designed to be used with data generated by gas chromatography mass spectrometry (GCMS); one of the most prominent analytical methods for metabolic studies and able to quantify hundreds of small molecules from biological extracts in a single run.
Tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles.
Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.
Massively parallel genetic algorithm that predicts RNA secondary structure.
MPH is a C++ program for fast REML estimation of genetic (co)variance components, designed for large-scale genome partitioning of quantitative genetic variation. It offers enhanced computational efficiency compared to existing tools and is available at the provided GitHub repository.
MPH (MINQUE for Partitioning Heritability)
Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.
Filter bam file using mpileup on coverage and SNPs.
On coverage and SNPs and output a vcf file.
Do you have thousands of files that you need to run the same program on? Are xargs, GNU parallel, and any of the million workflow management systems not working out for you? This package may be of assistance. It provides a command line tool for parallel execution of many command line tasks on any architecture that supports MPI. It also includes parallel implementations of the Python :func:`map` and :func:`imap` functions and a few handy bits and pieces for logging.
Web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.
R package for the genetic analysis of multi-parent recombinant inbred lines. It is a computational tool for complex experimental breeding designs.
mpmsim is an R package for simulating matrix population models with defined life history characteristics. It allows for the exploration of sampling error and uses parametric bootstrapping to calculate confidence intervals.
MPNS is a database providing scientific, pharmaceutical, trade, and common names for medicinal plants, drawing from a wide range of publications. It is used in research regarding Chinese herbal medicine for conditions such as diabetic nephropathy.
Tool used to select or evaluate linkage disequilibrium (LD) tag SNPs for multiple populations. The program analyzes patterns of LD–measured by composite linkage disequilibrium (CLD) or r2–between polymorphic sites in a genome region for multiple populations. It also uses an agreedy algorithm to select a single set of near-minimum numbers of LD tag SNPs for multiple populations.
Microarray-to-Phylogeny-Pipeline encompasses both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. It analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. It can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network.
A Database Extension to Visualize Structural Interactome in One-to-many Manner
Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).
Interactive MPRA experimental design encompassing both power analysis and design of constructs.
MPRAdecoder is a tool for processing of the raw MPRA data with a priori unknown sequences of the region of interest and associated barcodes.
R-package for accurately predicting power for comparisons of 16s rRNA microbiome taxa distributions including simulation by Dirichlet mixture modeling.
Curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. Also integrated is a GBrowse genome browser for visualization of ChIP-seq profiles and to display the annotations.
A machine learning (ML) driven web-app for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists.
mPROSS is a web-accessible design algorithm that uses phylogenetic analysis and atomistic potentials to improve the energy of membrane proteins, increasing their functional expression levels. It's freely available for academic use and has been demonstrated to enhance potassium-selective permeation and voltage dependence in voltage-gated potassium channels.
Review and classification of published variants in the ARSB gene. The purpose of this database is to support researchers and clinicians. understand structural changes on alylsulfatase B (ASB) caused by Mucopolysaccharidosis type VI (MPS6) mutations.
MPSBase is a comprehensive repository of differentially expressed genes for Mucopolysaccharidoses studies. It includes all the currently available RNA-Seq and microarray studies with four MPS models. Here, you can look not only for the genes but also for ontology terms and biological pathways enriched in these studies. Also, the samples include not only the clinical features but also compare several tissues and experimental treatments.
Predicting and validating protein degradation in proteomes using deep learning.
MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.
Predicting multi-label protein subcellular localization by wMLDAe dimensionality reduction and ProSVM classifier.
RNA and Genomic Informatics Resources for Plants. About Next-Gen Sequence Databases. The databases and the web pages (with customized web interfaces) were devloped to handle and display 'next-gen' sequencing data for several organisms and related varieties (mainly plants). The database and the web pages that you see were produced by the Meyers lab at the Donald Danforth Plant Science Center. if you use data from this page.
Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol.
Collects a set of Java objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a discrete mathematical theory based on P systems, introduced by Prof. Vincenzo Manca in 2004 for modeling biological dynamics. By means of the library, it is possible to model dynamical systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations.
Database for membrane protein thermodynamics for understanding folding and stability. MPTherm is a thermodynamic database of membrane proteins and their mutants, contains the thermodynamic data of membrane proteins collected from literature and ProThermDB database. Currently, we have data for around 7,000 mutations in more than 300 membrane proteins with several sequence-, structure-based features and membrane topology information. In addition, for each data we provide the exact location of data in the literature and these data cross linked with UniProt and PDB databases.
Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins. The stability of membrane proteins differs from globular proteins due to the presence of nonpolar membrane-spanning regions.
An open-source software for characterizing the transport of particles in biorelevant media.
Java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.
Mutated Pathway Visible Neural Network (MPVNN) architecture, designed using prior signaling pathway knowledge and random replacement of known pathway edges using gene mutation data simulating signal flow disruption.
R package for comparing the performance of mass spectrometry-based proteomic workflows.
Pathway Tools multiprocessing wrapper (for PathoLogic).
Quotient filters for efficient storage of k-mers with their counts and metadata. Benchmarking MQF vs CQF vs Countmin. Welcome to khmer: k-mer counting, filtering, and graph traversal FTW!. .
Program which can be useful for parametric linkage analysis of quantitative traits on the base of large pedigrees without loops.
MQuad (Mixture Model for Mitochondrial Mutation detection in single-cell omics data) is a tool that detects mitochondrial mutations that are informative for clonal substructure inference. MQuad enables clonal substructure discovery using single cell mitochondrial variants. It uses a binomial mixture model to assess the heteroplasmy of mtDNA variants among background noise.
The tool performs an automatic segmentation of the possible DIPG tumours on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W and Flair/T2-weighted magnetic resonance images. The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.
MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
The tool performs an automatic segmentation of the possible glioblastoma tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core), edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region), total (Total tumor including edema and necrosis by a single model) and total-fused (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG. TRAINING & VALIDATION COHORTS: Initial Development (Veiga-Canuto 2022): -Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018). -Internal validation: 26 patients (median DSC 0.918 ± 0.067). -Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy). -Mean age: 37.6 ± 39.3 months. -Median tumor volume: 116,518 mm³. External Validation (Veiga-Canuto 2023): -300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy). -Performance: median DSC 0.997 (0.944–1.000), 94% successful detection. -Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12). -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).
MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
An automated open-source tool for the ISMRM/NIST system phantom.
A two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants.
Medication recommendation by combining knowledge-enhanced pre-training with a deep adversarial network.
MR-link2 is a tool that estimates causal effects and pleiotropy in Mendelian randomization analyses, addressing limitations in traditional methods. It utilizes summary statistics and linkage disequilibrium (LD) information to improve accuracy and power in identifying causal relationships from observational data.
Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.
A MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences.
MR-MSPOLYGRAPH is a MapReduce based implementation for parallelizing peptide identification from mass spectrometry data
Automated MRI Classification in Progressive Supranuclear Palsy. MRPI – Magnetic Resonance Parkinsonism Index – Online Automatic Tool. MRI slices showing brainstem structures involved in the calculation of MRPI. Parasagittal view of middle cerebellar peduncle. Coronal oblique reconstruction of superior cerebellar peduncles.
Automated Head Tissue Modelling Based on Structural Magnetic Resonance Images for Electroencephalographic Source Reconstruction. MR-TIM: MR-based head tissue modelling is open source MATLAB software for head tissue modelling from structural magnetic resonance (MR) images. It performs automated segmentation of whole-head T1-weighted MR images in 12 tissues:.
An updated version of database with increased data of transcriptome and experimental validated interactions.
A web-based toolbox for predicting mixture toxicity of chemical substances in chemical products.
MRAD is a freely accessible online platform developed using the Shiny package that provides Mendelian randomization analysis results for Alzheimer's disease. The platform incorporates data from MRC IEU OpenGWAS and facilitates the identification of potential AD therapeutic targets.
MRAID(Mendelian Randomization with Automated Instrument Determination),is an R package for efficient statistical inference of two-sample Mendelian Randomization. MRAID takes GWAS summary statistics as inputs to estimate causal effects of one trait on another.
MRanalysis is a comprehensive and user-friendly, web-based platform that provides the first integrated and standardized Mendelian randomization (MR) analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Built using the R shiny framework, MRanalysis enables users to conduct common MR methods, including univariable, multivariable, and mediation MR analyses through an intuitive, no-code interface .
A multi-resolution attention network for sleep stage classification using single-channel EEG.
Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
Dept. of Biodiversity Informatics at the Swedish Museum of Natural History
A set of scripts for molecular replacement. It searches for homologous structures, creates a set of suitable search models from template structures, does molecular replacement and tests the solutions.
Resource management project that provides a dynamic and interactive view of world wide available mouse resources.
Software for image processing of 2D and 3D crystals.
mrCaNaVaR is a copy number caller that analyzes the next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.
mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.
MRCIP is a robust Mendelian randomization method accounting for correlated and idiosyncratic pleiotropy. MRCIP is a Mendelian randomization approach for the inference of the causal effect of an exposure on an outcome of interest based on summary-level GWAS data, which accounts for the correlated pleiotropy and the idiosyncratic pleiotropy.
MRCLinkdb is a database and web server that aggregates and organizes data related to non-protein metabolite-ligand-receptor interactions in cell-cell communication, providing insights into intercellular communication based on metabolite-related ligand-receptor interactions.
Software package for finding mutation regions where the input individuals are closely related, but the pedigree is not given. It takes the genotype data on a chromosome as well as the disease status for a set of input individuals without any pedigree information and outputs the predicted mutation regions.
A multi-resolution model for predicting the structure and dynamics of nanoscale DNA objects. Fix from Will Kaufhold to add_nick routine when on_fwd_strand==False · 04cbde91. Will Kaufhold authored Jan 07, 2020
A design pattern for networked, data-intensive science. Hello Guest Register Now Sign In : Forgot Password?. BPRC Arctic System Reanalysis (ASR). ECMWF 20th Century Reanalysis (ERA-20C)
Highly accurate method for the identification of bona-fide microRNAs targets within mammalian genes.
mreps is a tool for identifing tandemn repeats in DNA sequences.
Tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus.
mrFAST is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.
MRFSeq is a new efficient algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance the prediction power.
Quantitative Systems Pharmacology and Physiologically-Based Pharmacokinetic Modeling With mrgsolve. Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology. Simulate from ODE-based population PK/PD and QSP models in R. mrgsolve is an R package for simulation from hierarchical, ordinary differential equation (ODE) based models typically employed in drug development. mrgsolve is free and open-source software. mrgsolve is an R package for simulation from hierarchical, ordinary differential equation (ODE) based models typically employed in drug development. This website contains (hopefully) helpful vignettes to help you learn and use mrgsolve to get your simulation work done. We keep the vignettes here rather than in the package so they can be better maintained and kept up to date
Accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond.
Standardizing Human Brain Parcellations. Extending and fusing statistical machine learning to address the most important brain science and mental health questions of our time. M2G: Reliable Human Connectomes At Scale. This page hosts projectomes produced with NeuroData's MRI Graphs pipeline (m2g). A 'projectome' is a large-scale mapping between regions of the brain, created from fMRI or DTI. Data are from a multitude of labs and experiments. The data are run through m2g, and after processing, we provide summary statistics, QA, and the projectomes themselves.
This case study shows how MATLAB can be used for a medical imaging problem. Given an MRI scan, first segment the brain mass from the rest of the head, then determine the brain volume. Also compare portions of gray and white matter present.
Tool for brain tumor detection from MRI images using anisotropic filter and segmentation image processing. This image processing routine can detect tumors presence, location, area, and boundary.
Compute SNR for MRI parallel images using different reconstruction methods. There are three methods we used here to compute the SNR of MR images: ACR, SoS, and OPT.
This code implements the MICO algorithm for MRI tissue segmentation and bias field correction.
MRI segmentation and bias field correction
Brain imaging in a cross-sectional cohort of 1870 university students, in french.
The purpose of this tool is to harmonize the intensity dynamic ranges of MR T2W prostate images through a deep learning model that transforms the input image into an harmonized one closer to a curated reference set of high-quality contrast MR T2W. prostate images.
A Matlab Toolbox for Mapping the Responses to Intracranial Electrical Stimulation.
We introduce a new R package ‘MrIML’ (Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to map multi-locus genomic relationships, to identify loci of interest for future landscape genetics studies and to gain new insights into adaptation across environmental gradients. Relationships between genetic change and environment are often non-linear, interactive and autocorrelated. Our package helps capture this complexity and offers functions that construct, fit and conduct inference on a wide range of highly flexible models that are routinely used for single-locus landscape genetics studies but are rarely extended to estimate response functions for multiple loci
MRIReco is a Julia packet for magnetic resonance imaging. It contains algorithms for the simulation and reconstruction of MRT data and is both easy to use and flexibly expandable.
Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity. Code for analyses in MRLocus paper. MRLocus is a statistical method providing Mendelian Randomization analysis per locus, leveraging eQTL and GWAS summary statistics, for estimation of gene-to-trait effect size and dispersion.
A Comprehensive Resource for Targeted Proteomics Assays in the Community.
Automated Data Processing for Large-Scale Targeted Metabolomics Analysis. MRMkit: automated data processing for large-scale targeted mass spectrometry.
An R Platform for Multi-locus Genome-wide Association Studies. Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface. Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
C program for selecting DNA substitution models using PAUP*
Freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.
Web-based tool to improve the speed of manual calibration for multiple reaction monitoring data analysis by mass spectrometry.
MRMQuant is an automated tool for targeted metabolomic quantitation using high-throughput liquid chromatography-tandem mass spectrometry MRM data. It provides users with an easy-to-use interface for accurate MRM data quantitation, minimizing human intervention and offering features like dynamic signal smoothing and batch-effect correction.
mRMR Feature Selectionis a cross-platform version of mimimum-redundancy maximum-relevancy feature selection. It is using a mutual information computation
Contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with minimum Redundancy, Maximum Relevance (mRMR) and a new ensemble mRMR technique.
Tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength.
mRNAid is an open-source platform for therapeutic mRNA optimization, design, and visualization, offering a variety of strategies for sequence and structural features. Experimental validation demonstrates that transcripts optimized by mRNAid are comparable to commercially available sequences.
A novel machine-learning based in-silico tool to predict mRNA subcellular localization.
mRNALocater is a comprehensive and advanced model to accuracy prtiction of eukaryotic mRNA subcellular localization.Three different machine learning models with relatively stable performance based on the optimal feature subset using algorithms including XGBoost, LightGBM and CatBoost are constructed. The mRNALocater is an integration of these three models, and it has better performance than the state-of-the-art mRNALoc for some subcellular localization predict. The independent testing datasets proves that mRNALocater is a comprehensive and advanced predictor.
mRNArchitect is a web portal and open-source toolkit (MIT License) for designing mRNA sequences. It allows users to rapidly assemble and optimize mRNA sequences based on requirements such as GC content, secondary structure, codon optimization, and uridine depletion.
A Parametrizer of Post-Translationally Modified Residues. This program streamlines the process of post-translationally modified residue parameterization. MRP.py is designed to work with AmberTools and the Gaussian software package to handle molecular modeling and QM calculations, respectively. AmberTools15 or higher should be used in conjuction with this program.
MRPC is an R package for inference of Causal Graphs. MRPC builds on existing PC algorithms and learns a causal network with increased accuracy. The inferred causal network contains directed and undirected edges, with the direction indicating causality. For genomic data, MRPC determines edge direction under the principle of Mendelian randomization when genotype and molecular phenotype (e.g. gene expression) data are both available at the individual level. Nodes in the inferred network may be a genotype or a molecular phenotype.
Automated execution of Pixel calculations via the Mercury interface. MrPIXEL is a program that enables the energetics of crystal packing to be analysed quickly and easy through a user interface, using PIXEL, Python scripts and the widely known visualiser, Mercury.
Server that performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.
mrQA is an open-source tool for automatically assessing protocol compliance in MRI datasets, designed to identify and address inconsistencies in acquisition parameters. It supports standard dataset formats such as DICOM and BIDS, and aims to improve data quality and facilitate data pooling across multiple sites.
An open-source tool for quality control of MR imaging data. This tool takes MRI datasets in the file formats (.dcm, .nii, .nii.gz or .mha) as the input. Two Python scripts (QC.py and QCF.py) are used to generate several tags and noise/information measurements for quality assessment. These scripts save the calculated measures in a .tsv file as well as generate .png thumbnails for all images in a subject volume. These are then fed to .js scripts to create the user interface (index.html) output. A schematic illustrating the framework of the tool is as follows.
mrrobust—a tool for performing two-sample summary Mendelian randomization analyses | Stata package for two-sample Mendelian randomization analyses using summary data | Installing and updating mrrobust | Improved compatibility with the github package, i.e. mrrobust and its dependencies can be installed simply by issuing: gitget mrrobust , assuming that you have the github package installed. See below for instructions
MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.
MRSamePopTest is an R package designed to implement a falsification test for the 'same population' assumption in two-sample Mendelian randomisation studies. The package aims to improve the rigor of MR studies and facilitates designing MR studies with diverse populations.
A cloud-based spectral simulation tool “MRSCloud,” which allows MRS users to simulate a vendor-specific and sequence-specific basis set online in a convenient and time-efficient manner. This tool can simulate basis sets for GE, Philips, and Siemens MR scanners, including conventional acquisitions and spectral editing schemes with PRESS and semi-LASER localization at 3 T.
A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease.
micro-read substitution-only Fast Alignment Search Tool. Short read mapper that optimizes cache usage to get higher performance.
Cache oblivious mapper that is designed to map short reads to reference genome. It maps short reads with respect to user defined error threshold. In this manual, we will show how to choose the parameters and tune the tool with respect to the library settings.
MRSLpred - A tool for mRNA subcellular localization prediction
MRVTEST is a simple program which automates setting up likelihood calculations for combined linkage and association analysis using a variety of different transmission models. It consists of an adaptation of the earlier MFLINK program, which performs likelihood-based model-free linkage analysis.
A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.
Specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra.
A feature-filtering approach to improve annotation rate in untargeted LC-MS based metabolomics. MS-CleanR: A package for cleaning and annotating LC-MS data. The MS-CleanR package provides functions for feature filtering and annotation of LC-MS data. MS-CleanR use as input MS-DIAL peak list processed in data dependent analysis (DDA) or data independent analysis (DIA) using either positive ionization mode (PI) or negative ionization mode (NI) or both.
A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. This repository contains the analytical code necessary to reproduce the results described in the paper: "A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.".
The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources.
A user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides.
MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph.
Peptide mass fingerpriting tool in the ProteinProspector suite.
A tool which performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Peptide identification using a combination of ''de novo'' and database search.
MS-HBM is script for individual-specific areal-level parcellations improve functional connectivity prediction of behavior. A multi-session hierarchical Bayesian model (MS-HBM) for estimating high-quality individual-specific network-level parcellations. Here, we extend the model to estimate individual-specific areal-level parcellations. While network-level parcellations comprise spatially distributed networks spanning the cortex, the consensus is that areal-level parcels should be spatially localized, i.e., should not span multiple lobes. There is disagreement about whether areal-level parcels should be strictly contiguous or comprise multiple non-contiguous components, therefore we considered three areal-level MS-HBM variants spanning these range of possibilities: distributed MS-HBM (dMSHBM), contiguous MS-HBM (cMSHBM) and gradient-infused MS-HBM (gMSHBM).
Calculates the isotopic distribution from a peptide sequence.
Project that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.
Multisource Marginal Distribution Adaptation for Cross-Subject and Cross-Session EEG Emotion Recognition.
Python library for large-cohort metabolomics (MS1) processing.
Function that align peaks from several files and gives a matrix as result.
Multiple Peaks Alignment for Mass Spectrometry
Quantitiave analysis of multiple LC-MS(/MS) analyses in mzXML.
A Tool for the Analysis of Fragment Ions Generated from Intact Proteins.
Variability analysis of proteomics data used for deep learning
MS1Connect is a tool that scores the similarity between a pair of mass spectrometry runs.
DirectMS1 proteomics search engine for LC-MS1 spectra
Automated repurposing of public peptide LC-MS data for machine learning applications.
MS2Compound is a user-friendly compound identification tool for LC-MS/MS-based metabolomics data.
MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.
Updated MS²PIP web server supports cutting-edge proteomics applications.
Optimizing Coverage in Tandem Mass Spectrometry based Metabolomics by Iterative Data Acquisition
MGF and dta fragment spectrum preprocessing.
MS2Quant for concentration estimations of chemicals detected with nontarget LC-HRMS from MS2 data.
Sensitive PSM rescoring with predicted MS² peak intensities using MS²PIP, DeepLC, and Percolator.
Software of comparison of minisatellites.
MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins. It is especially designed for high resolution and high accuracy tandem mass spectra.
MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.
Proteome Discoverer 2.3: MS Annika v1.0.0
Proteome Discoverer 2.4: MS Annika v1.0.0
Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3
Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix
Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7
Proteome Discoverer 3.2: MS Annika 3.0 v3.0.7
MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters)
A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides.
Display multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.
R/Bioconductor package MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calcualtes pairwise IUPAC distances.
Mutational signature attribution with confidence based on simulations
Dynamic and fast visualization of sequence alignments, variations and annotations.
The Molecular Spectrometry Adduct Calculator (MSAC) calculates the m/z of potential adducts from given compound m/z.
Collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.
Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function.
Aligns LC-MS and LC-MS/MS datasets using peptides identified by MS/MS and accurate mass MS.
Aligns 2 CE-MS or LC-MS datasets using accurate mass information.
Reproducible mutational signature attribution with confidence based on simulations. Mutational signature attribution with confidence based on simulations.
Multiple alignment algorithm for protein sequences.
Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI. Parallel and accurate multiple sequence alignment. MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. MSAProbs-MPI is a parallelization of MSAProbs (v0.9.7) using MPI for distributed-memory systems.
Python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).
Large MSAs visualization interactively on the web.
Toolbox for the simulation and detection of coevolution in proteins
Software package and web tool for Bayesian protein inference from tandem mass spectrometry peptide identifications. It uses a set of identified peptides (or peptides with scores in a MS/MS search), peptide detectability, and a protein database to provide probabilities of protein identifications.
Tool for the analysis of gene expression data using a new bi-clustering method. It can find constant bi-clusters and additive bi-clusters.
Computational drug repositioning based on multi-similarities bilinear matrix factorization. Based on multiple similarities of drug and disease, we propose a Multi-Similarities Bilinear Matrix Factorization algorithm to identify potential novel indications for known or novel drugs. The code of MSBMF in this package is implemented in Matlab2014a. An international forum for researchers and educators in the life sciences, covering genetic studies of phenotypes and genotypes, DNA sequencing, expression prof.
Tree-level bootstrap and jackknife resampling for gene-tree datasets in multispecies coalescent analysis.
Multi-scale self- and cross-attention network for RNA methylation site prediction.
mscDPB is a tool that uses Chou's 5-step rule to predict DNA-protein binding with nulti-scale complementary feature.
Algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data.
Inferring circRNA functional similarity based on multiple data sources.
Median-supplement model-based classification tool for automated knowledge discovery. MSclassifier classifies instances using median-supplement machine learning methods.
MSCLtoolbox (The MSCL Analyst’s Toolbox) includes a set of scripts accessible as either a customized menu item (Windows) or as stand alone scripts (Mac) for the analysis of Affymetrix gene chip data. The scripts are run in the JMP statistical package, see below. Also available in the toolbox are GCOS database access scripts specific for Affymetrix.
A Matlab package for Clustering 16S rRNA sequences into OTUs.
A Cytoscape Tool for Multi-Level Clustering of Biological Networks.
Unsupervised Cluster Analysis and Gene Marker Extraction of scRNA-seq Data based on Non-negative Matrix Factorization.
MSColoR is a software tool for modeling multi-stage disease progression and identifying genetic risk factors, specifically designed for Alzheimer’s disease studies using longitudinal neuroimaging and genetic data. It leverages a novel collaborative learning method to jointly model disease progression and associate it with genetic variations.
msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.
Quartet methods for species trees and networks under the multispecies coalescent model in R. Analyzing Gene Tree Quartets under the Multi-Species Coalescent.
Read, display and save data from the original HP MSD based on the HP Pascal Chemstation.
An integrated expression atlas of human musculoskeletal system.
Improving the prediction of DNA-protein binding by integrating multi-scale dense convolutional network with fault-tolerant coding.
MSE FINDR is a Shiny R application that estimates mean square error from treatment means and post hoc test results in ANOVA-type experimental designs. It allows researchers to include studies in meta-analyses that lack explicit variance estimates.
Performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. It uses a library of ~6300 predefined metabolite sets from pathways, disease signatures, genetic traits, and cellular/tissue locations. It also facilitates conversion between metabolite common names, synonyms and other database identifies.
The international Mitochondrial Disease Sequence Data Resource Consortium (MSeqDR) Quick-Mitome (QM) is a web-based platform enabling automated variant interpretation of whole-exome sequencing (WES) datasets for the genetic diagnosis of primary mitochondrial diseases (PMD).
Modulated Scanning Fluorimetry Can Quickly Assess Thermal Protein Unfolding Reversibility in Microvolume Samples.
Python bindings for the (non-free) ThermoFisher Scientific MSFileReader.
A database search tool for performing mass spectometry data similarity comparisons. For that it uses a fragment ion indexing method.
Pipeline for the anaysis of a MS-GBS experiment.
Converter from MS-GFDB output to pepXML.
This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current results to another R session so the user can seamlessly integrate the gui into other workflows.
This package contains function to perform peptide identification using MS-GF+.
This R package (multinomial sparse group lasso) fits multinomial models for e.g. multiclass classification with a sparse group lasso penalty.
An MS-DOS program to visualize LC-MS data in 2D and 3D (converter from mzXML available).
This addition to ms, called msHOT, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region. Crossover hotspots may overlap with gene conver-sion hotspots, but crossover hotspots may not overlap with each other and gene conversion hotspots may not overlap with each other.
Ongoing project aimed at the development of software for the computational simulation of spatial processes in immunity. The software is an open source development project; there are several options for acquiring the program, including the complete source code, or just pre-built binaries.
Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals. Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data. This repository contains the python script performing the recalibration of mass spectrometry images (MSI) from the associated paper Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data.
Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.
MSIFinder is a python package for detecting Microsatellite instability (MSI) status using random forest classifier. Microsatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite lengths owing to the deficiency in the mismatch repair system. Based on the degree, MSI can be classified as microsatellite instability-high (MSI-H) and microsatellite stable (MSS). MSI is a predictive biomarker for immunotherapy efficacy in advanced/metastatic solid tumors, especially in colorectal cancer patients. Several computational approaches based on target panel sequencing data have been used to detect MSI; however, they are considerably affected by the sequencing depth and panel size.
GSVA is a method for performing gene set enrichment analysis. It is used to determine whether a defined set of genes shows statistically significant, concordant differences in expression between two or more biological conditions.
MSIGen is an open-source Python tool for processing and visualizing mass spectrometry imaging (MSI) data, supporting various formats and vendors. It offers both a graphical interface and command-line access, efficiently generating ion images and performing signal processing, suitable for MS1, MS2, and IMS-MSI data analysis.
MSight: An image analysis software for liquid chromatography-mass spectrometry. MSight is a tool specifically developed for the representation of mass spectra along with data from a separation step. It provides simple ways to navigate through very large volumes of data, with the ability to display small regions for closer scrutiny.
Generate images from WIFF data and export to imzML.
A software platform for rapidly creating computational tools for mass spectrometry-based proteomics.
MSI QuickView is a tool for real-time visualization and analysis of mass spectrometry imaging (MSI) data, supporting ion images, peak selection, and PCA.
Vendor-neutral MATLAB program to view analyze mass spectrometry imaging data.
MSIreg is an open-source R package for unsupervised coregistration of mass spectrometry and H&E images, designed for high-dimensional MSI experiments and implementing a landmark-free workflow with quantitative metrics.
C++ program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.
Microsatellite instability detection using cfDNA sequencing data. MSIsensor-ct is a novel method based machine learning, which can accurately determine the MSI status of cfDNA sequencing data with ultra-low ctDNA content. In practice, we recommend aiming for a minimum of 30 valid microsatellites to classify the MSI status using MSIsensor-ct. MSIsensor (https://github.com/niu-lab/msisensor) is a viable option if paired tumor and normal sequencing data are available, and MSIsensor2 (https://github.com/niu-lab/msisensor2) is effective for tumor-only samples.
Fast, accurate and matched-normal-sample-free detection of microsatellite instability. MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples.
Program designed to analyse structural data of liganded and unliganded proteins.
A General Approach to Mass Alignment in Mass Spectrometry Imaging. MSIWarp is a flexible tool to perform mass alignment of Mass Spectrometry Imaging (MSI) spectra. A key feature of MSIWarp is its compatibility with centroid spectra.
Making Omics Data Useful to the Broader Scientific Community. Metabolic Disorders Knowledge Portal. ||| CORRECT NAME OF TOOL COULD ALSO BE 'MSK-KP'
Functions for retrieving data from the Cancer Genomics Data Server (CGDS) at MSKCC cBio.
Mining Scientific Literature. Automatic and physical analysis of published scientific literature in PDF format It allows the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on the different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied OCR.
Microbial synthetic lethal and rescue database.
MSLDOCK is a multi-swarm optimization docking program for flexible ligand docking and virtual screening.
Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics.
Statistical Models for Biomolecular Dynamics.
This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences
Tool for mass spectra metadata annotation.
MSModDetector is a Python module for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data. It uses linear programming to infer potential PTM patterns and was evaluated on p53 data.
Interactive modeling and prediction of individual evolution via multistate models.
MSMS is a coalescent simulator that and permits the full range of demographic models provided by ms, in particular, it allows for multiple demes with arbitrary migration patterns, population growth and decay, and for population splits and merges. Applications include power studies, analytical comparisons, approximated Bayesian computation among others.
Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.
Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.
Basic plotting, data manipulation and processing of MS-based Proteomics data.
Learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.
Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.
De novo structure generation from mass spectra.
It may be used to perform ortholog assignment between two genomes A and B.The assignment of orthologous genes between a pair of genomes is usually done using sequence similarity search. In this framework, homologous gene are identified using sequence similarity search and orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangements and (post-speciation) gene duplications.
An Open Source Toolbox for Modeling Acoustic Wave Propagation in Heterogeneous Media. mSOUND is an open-source toolbox written in MATLAB.
A high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.
mspack is a C++ program for lossless and lossy mass spectrometry data compression, achieving a high compression ratio without sacrificing performance. It includes an example implementation for mzXML and mzML as well as a format-agnostic API.
Given a set of peaks from (biological or technical) replicates, this tool combines the p-values of overlapping enriched regions: users can choose a threshold on the combined significance of overlapping peaks and set a minimum number of replicates where the overlapping peaks should be present.
Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates Normalized Spectral Abundance Factor (NSAF) values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution accurate-mass instruments.
Free tool for managing mass spectral libraries with an additional focus on gas chromatography / mass spectrometry, liquid chromatography / mass spectrometry and related techniques.
A powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks. A powerful software for deciphering proteome profiling of multi-tumour mass spectrometry data using deep neural networks. MSpectraAI is a free, user-friendly and comprehensive software for mining and classifying raw LC-MS2-based proteomics or metabolomics data of different samples using deep learning models. Users can also built your own deep neural network model in this software. It is developed with R and an example is shown here: https://www.omicsolution.org/wukong/MSpectraAI/.
Online application for low molecular weight heparin rapid characterization based on liquid chromatography-tandem mass spectrometry.
MSPIKE performs neural spike pattern analysis on extracellular potentials acquired with TDT's System3.
A pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.
Full featured library for working with mass spectrometry data, particularly proteomic, metabolomic and lipidomic data sets. It aims to be fast, robust, and beautiful.
Simulates peptide retention times and chromatographic profiles.
MS data processing in Ruby, including mzML reader/writer/converter, ''in-silico'' digestion, isotopic pattern calculation etc.
M-SPLIT is a spectral-library search tool for identification of mixture spectra of up to two peptides.
Multiset sparse partial least squares path modeling for high dimensional omics data analysis. Simulation studies for sparse partial least squares path modeling.
Open source hybrid database and spectral library MS/MS search engine.
R package for post processing of metabolomic data. Performs summarization of replicates, filtering, imputation, normalization, generates diagnostic plots and outputs final analytic datasets for downstream analysis.
Msprime is a Python package that simulates ancestral histories and DNA sequence data. Msprime uses backwards-in-time "coalescent" models which allows it to simulate data very efficiently; however, it is not as flexible as forwards-in-time simulators (e.g. SLiM, fwdpy11).
Java program that constructs customized transcript databases for tandem mass spectra search. RNA-Seq data is used to generate transcripts and to resolve shared peptide protein inference in a proteogenomic network.
Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data.
Allows a user to do quantitative protein-level statistical inference on label-free LC-MS proteomics data. Fold changes, p values and false discovery rates are estimated.The app allows for an easy-to-use graphical user interface starting from MaxQuant search results that requires no programming skills.
Agentschap Innoveren en Ondernemen - Flemish Government
MSQT is a SNP Query Tool.It was developed to make polymorphism information readily accessible and to assist researchers in selecting distinct sequence changes and developing SNP detection assays.
Interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.
Protein quantitation combining Mascot results and raw data from stable isotope labeling.
A Multi-scale Deep Neural Network to Basecall Oxford Nanopore Sequences.
MSRdb (Mycobacterial Systems Resource) is a mycobacterial systems resource for the research community. The Mycobacterial Systems Resource (MSR) is a comprehensive, integrated biological and bioinformatic resource for the research community. The MSR uses M. smegmatis as its model organism, while focusing exclusively on genes that are highly conserved across the mycobacterial genus. Thus, functional insights from the MSR will apply to all mycobacterial species.
A comprehensive repetitive sequence database of over 80 000 species.
R program for the analysis of genome-wide association data.
A deep learning classification tool of the peptide precursors quantified by OpenSWATH.
Mean-shift super resolution ImageJ plugin
Statistical tool for quantitative mass spectrometry-based proteomics.
Statistical relative quantification of post-translational modifications in bottom-up mass spectrometry-based proteomics.
It is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.
It is a Shiny app which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.
A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments.
Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
MS²Rescore is a modular and user-friendly platform designed to boost peptide identifications in proteomics workflows. It provides a graphical user interface, a modular Python API, and extensive documentation for seamless integration.
Phylogeny inference under the general Markov model using MST-backbone. Phylogeny inference via maximum likelihood is NP-hard. Current methods make simplifying assumptions such as stationarity, homogeneity, and time-reversibility for computational ease. The stationarity assumption is violated by empirical observations of GC content evolution, and might systematically bias phylogeny inference.
It is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool builds the genetic linkage map by first constructing a Minimum Spanning Tree, and hence the name MSTMap. The algorithm implemented in MSTMap is very efficient and can handle ultra-dense maps of up to 10,000~100,000 markers.
A tool to proteome-widely predict the translatable circRNAs based on mass spectrometry
A Tool for the Visualization of Mass Shifts in Deconvoluted Top-Down Proteomics Data for the Database-Independent Detection of Protein Modifications.
MStractor is an R workflow package for non-targeted processing of LC-MS data.
A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow. MStree: A model-flexible approach for estimating parameters during speciation with gene flow. MStree is an open-source software for estimating ancestral population sizes and species divergence times during speciation with gene flow.
Software for detection of population structure in the presence of admixing and mutations from multi-locus genotype data. It is a mixed membership model (also referred to as an admixture model) which incorporates a mutation process on the observed genetic markers.
MSU-Net is a tool for multi-scale U-net for 2D medical image segmentation. Aiming at the limitation of the convolution kernel with a fixed receptive field and unknown prior to optimal network width in U-Net, multi-scale U-Net (MSU-Net) is proposed by us for medical image segmentation. First, multiple convolution sequence is used to extract more semantic features from the images. Second, the convolution kernel with different receptive fields is used to make features more diverse. The problem of unknown network width is alleviated by efficient integration of convolution kernel with different receptive fields. In addition, the multi-scale block is extended to other variants of the original U-Net to verify its universality. Five different medical image segmentation datasets are used to evaluate MSU-Net. A variety of imaging modalities are included in these datasets, such as electron microscopy, dermoscope, ultrasound, etc
A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit. Msuite: Multi-mode DNA methylation data analysis suite. Msuite is written in Perl and R for Linux/Unix platform. To run Msuite you need a Linux/Unix machine with Bash 4 (or higher), Perl 5.10 (or higher) and R 2.10 (or higher) installed.
A centralized online platform for predicting the m6A methylation degree of mRNA and the SNP-related traits in Maize.
Database of human missense variants mapped to 3D protein structures.
Supports manual validation of post-translational modifications (PTMs) and their relative quantitation in small- and medium-size experiments. Thanks to its interactive interface MsViz can display peptide spectrum matches, sequence coverage information, or tandem mass spectrometry (MS/MS) spectra and extracted ion chromatograms. It allows easy and comprehensive visualization of small and medium bottom-up proteomics datasets.
Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.
Identifying diagnosis-specific genotype-phenotype associations via joint multitask sparse canonical correlation analysis and classification. Multi-task sparse canonical correlation analysis and logistic regression. Identifying diagnosis-specific genotype-phenotype associations via joint multi-task sparse canonical correlation analysis and classification, accepted by ISMB 2020.
Resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.
Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study.
Predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network.
A comparative tool for taxon identification of ultra low coverage ancient genomes.
MTB++ is a machine learning classifier that predicts antibiotic resistance in Mycobacterium tuberculosis using genomic data and a 31-mer feature matrix. The software is designed to screen large datasets and provide accurate predictions for resistance phenotypes.
The MTB-Report tool annotates, filters and sorts genetic variants with information from public databases, providing evidence on actionable variants in both scenarios. A web interface supports medical doctors in the tumor board, and a command line mode allows batch processing of large datasets
The Mycobacterium tuberculosis transposon sequencing database (MtbTnDB) is large-scale guide to genetic conditional essentiality. TnSeq has been used extensively in M. tuberculosis genetic research and identification of gene essentiality (TnSeq) profiles is important for predicting gene function. However, these profiles are buried across dozens of research papers within supplementary materials which makes querying them cumbersome. The MtbTnDB solves this problem by building a central repository of TnSeq screens performed in M. tuberculosis, and allows users easy access to data through an interactive web-app.
MtbVeb is a web-based platform developed for designing vaccines against existing and emerging strains of mycobacterium tuberculosis. This includes drug resistant and extreme drug resistant M.Tb strains. It also allow users to design vaccines against M.tb using all three appraches (strain, antigen and epitope based vaccines).
A database of mitochondrial genome variants in chinese population
Mutation To Cancer Therapy Scan. Systematically analyze mutations affecting cancer drug sensitivity based on individual genomic profiles. It was developed by leveraging the latest knowledge on mutation-cancer drug sensitivity associations and the results from large-scale chemical screening using human cancer cell lines.
A unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data.
A set of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood.
Free mtDNA NGS analysis pipeline including heteroplasmy detection and haplogroup-based contamination deconvolution.
Tools to combine sequences from multiple studies. This vignette describes the mtDNAcombine package, an R library designed to support comparative analyses of Bayesian Skyline Plot (BSP) population histories based on mtDNA sequence data from multiple studies.
Web program which enables users to analyze and compare mtDNA sequences whether they are indicated as FASTA format or as a difference to revised Cambridge Reference Sequence (rCRS).
MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.
Computer program to provide Residual Maximum Likelihood (REML) estimates for genetic and environmental variance and covariance across multiple traits.
Improving cancer driver gene identification using multi-task learning on graph convolutional network.
Integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.
Dataset-aware multi-task learning approaches for biomedical named entity recognition. Named entity recognition is a critical and fundamental task for biomedical text mining. Recently, researchers have focused on exploiting deep neural networks for biomedical named entity recognition (Bio-NER). The performance of deep neural networks on a single dataset mostly depends on data quality and quantity while high-quality data tends to be limited in size. To alleviate task-specific data limitation, some studies explored the multi-task learning (MTL) for Bio-NER and achieved state-of-the-art performance. However, these MTL methods did not make full use of information from various datasets of Bio-NER. The performance of state-of-the-art MTL method was significantly limited by the number of training datasets
Multi-task learning framework to predict individualized tissue gene expression profiles.
Efficient protein structure comparisons, which includes are two related modules. The first is for fast database search with one input structure. The second is for multiple structure alignment with two or more input structures. After the search is done, a multiple structure alignment is performed automatically with the top 10 structure, using the second module. The users are also able to select other structures from the returned list to perform multiple structure alignment.
Facilitates fast and detailed evaluation of mass spectrometry data of limited proteolysis experiments to probe the tertiary structure of proteins and even complex formation with other proteins, ligands, and surfaces.
A webserver for the prediction of metastatic triple negative breast cancer (TNBC) patients. MTNBCPred is a service for the prediction of lymph-node metastatic and non-metastatic TNBC patients.
A highly automated bioinformatics pipeline to reconstruct and analyse human mitochondrial DNA from NGS data, also provides mitochondrial haplogroups predictions.
A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics. Two-stage polytomous logistic regression (TOP): in this package, we developed a two-stage polytomous regression framework to handle cancer data with multivariate tumor characteristics. The 'TOP' vignette will provide a good start point for using TOP package.
A time course analysis with functional near-infrared spectroscopy. In the data analysis of functional near-infrared spectroscopy (fNIRS), linear model frameworks, especially the mass univariate analysis (MUA), are often performed when researchers consider examining the difference between conditions at each sampled time point.
MTPpilot is a software for the visualization and interactive interpretation of NGS results in the field of precision oncology. Data can be uploaded either via a Tab-Separated Value file or a table form.
Metagenomics software for clustering at multiple ranks.
MTR3D is a web application for identifying regions within protein tertiary structures under purifying selection.
A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset.
MTSplice predicts effects of genetic variants on tissue-specific splicing.
Rapid alignment-based taxonomic classification and high-confidence metagenomic analysis.
Database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures.
A Web-Based R/Shiny App for Pulmonary Tuberculosis Screening.
A multi-task transfer learning approach for base-resolution mRNA m6A site prediction based on an improved transformer.
Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases. Multi-task U-Net for the simultaneous segmentation and skull-stripping of mouse brain MRI This convolutional neural network is designed to perform skull-stripping and region segmentation on mouse brain MRI. A jupyter notebook going over the deails of this project and the training procedure is available here.
A deep learning method for prediction of pseudouridine sites. Deep Learning Prediction and Analysis for Pseudouridine Sites. Prediction of Pseudouridine Sites using deep learning. Deep learning model architecture for pseudouridine RNA modification prediction. Deep learning method for Pseudouridine site prediction.
Prediction of protein stability changes upon single-point variant using 3D structure profile.
muCNV is genotyping structural variants for population-level sequencingMulti-sample SV genotyper for large-scale WGS data. muCNV uses multiple steps for multi-sample SV genotyping, to handle large number of samples and to enable efficient parallelization:.
Software to aggregate variant information sourced from multiple VCF files (and some others, see below) into a variety of summary files with varying levels of detail and statistics.
Mucormydb is a web server that enables the scientific community to fight opportunistic fungal infections caused by a group of molds
A server for predicting the affect of missense mutations on protein function using sequence and structural features.
Multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.
Biologically-oriented mud volcano database.
A set of programs implementing the framework to assess MS/MS spectra assignments
The Multi-Domain Genome Recovery v1.0 (MuDoGeR v1.0) framework is a tool developed to help users to recover Metagenome-Assembled Genomes and Uncultivated Viral Genomes from whole-genome sequence (WGS) samples simultaneously. The MuDoGeR v1.0 framework acts as a wrapper for several tools. It was designed to be an easy-to-use tool that outputs ready-to-use comprehensive files.
Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN). MUFFIN is a hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis.
MUFFIN is multi-scale feature fusion for drug-drug interaction prediction.
Comprehensive platform for efficient and consistently accurate protein tertiary structure prediction.
Fast tool for protein structural model clustering, visualization and quality assessment.
Open source pipeline for obtaining gene based results from a given GWA study.
The MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.
Performs local multiple DNA sequence alignments of finished and draft-quality sequences. It identifies transcription factor binding sites evolutionarily conserved across multiple species.
Consensus extension of a multi-task clustering algorithm to infer high-confidence strain-specific host response modules under infections from multiple virus strains.
Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.
mulea is an R package for gene set enrichment analysis utilizing multiple ontologies and a progressive empirical false discovery rate method. It offers a comprehensive toolkit for functional enrichment analysis and includes pre-defined ontologies and gene sets for various model organisms.
Unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning.
A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. MULocDeep is a deep learning model for protein localization prediction at both sub-cellular level and sub-organellar level. It also has the ability to interpret localization mechanism at a amino acid resolution. Users can go to our webserver at xxx.xxx for localiztion prediction and visualization. This repository is for running MuLocDeep locally. A protein localization prediction tool at sub-cellular and sub-organellar levels. MULocDeep: An Interpretable Deep Learning Model for Protein Localization Prediction at the Sub-organelle Resolution (in submission).
An efficient tool for comparison of protein structures based on similarity in the local backbone conformation.
Platform-independent software program designed to infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees.
MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.
Visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed — it is the first tool to support comparisons across multiple such datasets.
Classification of ion channel interacting peptides using parallel convolutional neural networks.
Tool of contig scaffolding using multiple references.
A web server for scaffolding contigs using multiple reference genomes.
Comparative population genomic inference under hierarchical co‐demographic models of independent single‐population size changes.
Extends FindCore Toolbox to cluster a set of structural models and superimpose each cluster
The Multi-Fingerprint Browser for the ZINC Database enables one to rapidly identify close analogs among commercially available compounds in the ZINC database (> 13 million molecules).
Interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.
Multi-parametric response map is a generalized approach towards multi-parametric response mapping using principal component analysis. Parametric response mapping (PRM) has emerged as a powerful image-analysis technique which can be used for early prediction of cancer treatment-response
Tool for multiplexed iTRAQ-based quantitation.
The tool performs an automatic multi-regional segmentation of the prostate into central-transition zone (CZ+TZ), peripheral zone (PZ), and seminal vesicle (SV) using a T2-weighted MRI image. A heterogeneous database of 243 T2-weighted prostate studies was used to train a U-Net based model with deep supervision.
Multi-regional prostate segmentation tool
A residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization.
Online accelerated Monte Carlo simulation of light transport through scattering media. Simulating light propagation in turbid media. Welcome to "Multi-Scattering" a freely accessible online software for the modeling of light propagation in scattering and absorbing media. Possible applications of the model are the prediction of photon transport in tissues, blood samples, clouds, smoke, fog, turbid liquids, spray systems, etc. As the simulations are run from a computer server at the Department of Physics at Lund University, any researcher can log in and use it freely without any programming skills or requirements for any software/hardware installations.
A versatile tool for object-localization in microscopy images. Object-recognition using multiple templates in python. Multi-Template Matching for object-detection.
Bioinformatics pipeline for functional annotation of phage isolates.
A query-driven heatmap visualization tool for multi-omics data. Multi-omics Systems-Level Interactive Data Exploration (multiSLIDE). multiSLIDE is an open-source tool for query-driven visualization of quantitative single- or multi-omics data. Using pathways and networks as the basis for data linkage, multiSLIDE provides an interactive platform for querying the multi-omics data by genes, pathways, and intermolecular relationships
Web based tool for performing co-expression queries over large collections of gene expression experiments. It provides access to several hundreds of publicly available gene expression datasets of different tissues, diseases and conditions, arranged by the species and microarray platform types. The main user input is the name or ID of a query gene (various syononyms are accepted) and the choice of the collection of microarray experiments to be used in the co-expression query.
An Extensible Web Based Tool for the Analysis of Genomic Data. Multi Locus View (MLV) is a web based tool for analysing and visualising Next Generation Sequencing data sets. By allowing intuitive filtering and visualisation of multiple genomic locations, it allows the user to quickly drill down and annotate regions of interest. A Public version can be accessed here.
Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER.
Develop an integrative environment where multiple assays are managed and preprocessed for genomic data analysis.
An R package to remove batch effects in multi-omic experiments.
Optimal volume censoring methods for high-resolution (low TR) simultaneous multi-slice (multiband) RSFC fMRI.
Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsible for protein binding.
Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
A General Framework for Data Integration and Interpretable Classification.
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.
Integrative R-package that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. We identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected.
The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric.
MULTICOM is a protein tertiary structure predictor using multi-template combination
MULTICOM2 is an open-source protein structure prediction system powered by deep learning and distance prediction.
gRNA design for prime editing and parallel targeting of thousands of targets. Multi-locus multi-purpose Crispr/Cas design.
Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) dataset and MethylationSet. It is designed for integrating multi omics data sets and MethylationSet to contain normalized methylation data. These package contains base classes for MEAL and rexposome packages.
Space and time efficient procedure to identify differentially co-expressed gene sets and successfully identify influence of individual factors on differential co-expression.
MULTIDISEQ is multipoint linkage analysis software which allows Marker-Marker LD.
A tool for analysing and visualising multiple sequence alignments (MSAs).
Drug-target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network.
MultifacetedProtDB is an integrated and manually curated database providing a comprehensive collection of multifunctional UniProt/SwissProt human proteins.
Mix Multi-Fasta for each sequence in a multi-fasta file.
MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality-of-fit to the density map.
A Computational Approach to Quantify the Modification Stoichiometries in Label-Free Proteomics Data Sets.
Multifocus image fusion using phase congruency
A multiple sample single nucleotide variant (SNV) caller that works with alignment files of high-throughput sequencing (HTS) data. MultiGeMS calls SNVs based on a statistical model selection procedure and accounts for enzymatic substitution sequencing errors.
Helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition.
A GSEA-based pathway enrichment analysis for multi-omics data. multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020). Combining GSEA-based pathway enrichment with multi omics data integration.
A tool for GWAS analysis on tetraploid organisms by integrating results of four GWAS software.
MultiK is a data-driven tool that objectively assesses the optimal number(s) of clusters based on the concept of consensus clustering via a multi-resolution perspective.
multiLCS is a MATLAB script for finding the longest common subsequence for multiple sequences.
MultiLoc2 predicts animal, plant and fungal protein subcellularlocalizations by integrating phylogeny and Gene Ontology terms to the new version of the software.
Computer program used for automated construction of genetic maps. It has been developed primarily for large-scale linkage mapping of markers genotyped in the CEPH reference pedigrees. It has been adapted for automated construction of radiation hybrid maps.
Dimensionality reduction and integration of multimodal data.
multiMarker is a web application that infers the relationship between biomarker and food quantity data from an intervention study, and allows prediction of food intake when only biomarker data are available. Additionally, multiMarker provides quantification of the uncertainty in intake predictions.
Implements permutation method with joint correction for testing multiple mediators.
This R package provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.
This R package is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.
MultiMM is an open-source software utilizing OpenMM for whole genome 3D structure reconstruction. It employs a multi-scale energy minimization strategy and allows users to input files specifying nucleosome positioning, loops, compartments, or subcompartments.
MultiMolecule is a library of code modules and a collection of pre-trained models for machine learning with nucleotide and amino acid sequences.
Multimorbidity is database of genetically interpretable comorbidities among common diseases in UK Biobank.
Refined grouping method for reducing redundant calculations in nanopolish. Nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish for more details). We present an efficient implementation of Nanopolish, called MultiNanopolish. MultiNanopolish use a different iterative calculation strategy to reduce redundant calculations. We propose an abstract concept, namely independent computing unit(GroupTask) which can be distributed to the thread pool for multi-thread concurrent computing.
a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
MultiNMRFit is an open-source software designed for high-throughput analysis of one-dimensional NMR spectra, offering flexibility and reproducible results through fitting experimental spectra using built-in or user-defined signal models. It's accessible as a Python library and via a graphical user interface, supporting both novice and experienced users.
Multiomics2Targets is a bioinformatics workflow that analyzes transcriptomics, proteomics, and phosphoproteomics data from cancer cohorts to identify potential drug targets and generate research-publication-like reports.
Calculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.
A cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation.
Multioviz is a platform for in silico perturbation and interrogation of gene regulatory networks, designed to bridge the gap between high-dimensional computation and wet-lab experimentation. Users can perform hypothesis testing using a web application and an associated R package.
A Python framework for analyzing multi-layer biological networks using diffusion algorithms. A Python package for analyzing harmonized biological networks through diffusion algorithms. systems-biology knowledge-graph network-analysis diffusion-network network-biology. Results of the MultiPaths publication. A Python package for network analysis through diffusion label propagation algorithms.
Performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model)
High-throughput maximum Llkelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.
Program to do the associate test (TDT type test for nuclear-family data) using several tightly linked markers simultanously.
Multipletesting.com is a user-friendly online tool designed to correct for multiple hypothesis testing, helping researchers minimize false positives when performing numerous statistical tests. It supports five widely used correction methods—Bonferroni, Holm, Hochberg, FDR, and q-value—making it an essential resource for reliable data interpretation in life sciences. Key features include: • Input: simple list of p-values, total number of tests, and significance level (alpha) • Output: adjusted p-values based on selected correction method • Integrated calculators for each method with clear explanations and use-case examples It is particularly valuable for genomic, transcriptomic, or other high-throughput studies where many tests are performed simultaneously.
Discovery of disease- and drug-specific pathways through community structures of a literature network. Literature mining and automated hypothesis-generation with. MeTeOR, or the MeSH Term Objective Reasoning network, is a network representation of genes, drugs, and diseases built on MeSH terms curated by the National Library of Medicine. MeTeOR mines the PubMed literature, revealing knowledge previously hidden in a sea of information
Scriptable framework for access to manufacturers' formats via mzAPI.
Tool that uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples and calculates automatically optimal multiplexing (grouping) solution.
Calculates the power for both joint and replication-based analysis of general multi-stage genetic association studies.
The MultiPower R method performs statistical power studies for multi-omics experiments, and is designed to assist users in experimental design as well as in the evaluation of already-generated multi-omics datasets.
Computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.
Fully automated highly efficient technique which detects the multiple structural alignments of protein structures. It finds the common geometrical cores between the input molecules.
MultiPSQ expedites the analysis and evaluation of multiplex-pyrograms, generated from multiplex pyrosequencing
MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
MultiRNAflow is an R package designed for integrated analysis of temporal RNA-seq data with multiple biological conditions. It provides a unified framework for both unsupervised and supervised analyses, including identifying temporal patterns and differentially expressed genes specific to particular conditions.
Contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold.
Estimates gene expressions from several laser scans of the same microarray.
An open-source multiplex-ELISA platform for measuring antibody responses to infection.
multiSNV is a tool for calling somatic single-nucleotide variants (SNVs) using NGS data from a normal and multiple tumour samples of the same patient.
This tool extracts / finds orthologous microsatellite blocks for >2 species alignments.
multiSyncPy is a Python package for assessing multivariate coordination dynamics. The package supports the burgeoning field of research into synchrony, making accessible a set of methods for studying group-level rather than dyadic constructs of synchrony and/or coordination. We offer a range of metrics for estimating mulivariate synchrony based on a collection of those used in recent literature.
A Python package for multi-variate Thermodynamics-based Flux Analysis. We present multiTFA, a multivariate thermodynamics-based metabolic flux analysis package for Python. The framework takes advantage of the reactions' Gibbs free energy covariance matrix to tightly constrain metabolic models using thermodynamic constraints. It represents an improvement over a previous thermodynamic metabolic flux analysis (tMFA) method.
MultiTrans is an algorithm for path extraction through mixed integer linear programming for transcriptome assembly. MultiTrans is a tool for transcripts assmebly, which formulated the transcripts assembly problem into a mixed integer linear programming.
R package for inferring multi-variate/multi-attribute Gaussian graphical models.
MultiVERSE is a multiplex and multiplex-heterogeneous network embedding approach. Embedding of Monoplex, Multiplex, Heterogeneous, Multiplex-Heterogeneous and full Multiplex-Heterogeneous Networks.
MultiiVI is a part of the scvi-tools framework and carries out integration of paired/unpaired multiome data, missing modality imputation, normalization of other cell- and sample-level confounding factors
Software package for multiview pattern recognition methods.
R package for deep mining gene co-expression networks in multi-trait expression data.
Computer program which builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed.
Fast detection of multiple overlaps of genome regions
Program used to generate the empirical results on the missing data problem for an arbitrary, but fixed (at input) number of states.
This extension includes non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed).
Accurate detection of all SV types through whole-genome alignment. MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v3 and v4) to detect variants. Deletions (novel and mobile), insertions (novel and mobile) and tandem duplications (>50bp).
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences
System for rapidly aligning large DNA sequences to one another.
MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by HTS.
Mathematical modelling of collective behaviour without the maths. Multiscale Modelling Tool - mathematical modelling without the maths. MuMoT: Multiscale Modelling Tool. MuMoT (Multiscale Modelling Tool) is a tool designed to allow sophisticated mathematical modelling and analysis, without writing equations - the class of models that can be represented is broad, ranging from chemical reaction kinetics to demography and collective behaviour - by using a web-based interactive interface with minimal coding, rapid development and exploration of models is facilitated - the tool may also be particularly useful for pedagogical demonstrations
Probabilistically reincorporates multi-mapping tags into mapped short read data.
Rapid standardisation and quality control of summary statistics from GWAS
muon is a Python framework for multimodal omics analysis.
Mouse Ultrasonic Profile ExTraction: A signal processing tool for rapid and unsupervised analysis of ultrasonic vocalizations.
Tool to assist in the design of multiplex PCR assays. It takes a set of DNA sequences and other experimental information as input and provides a set of multiplex PCR assays intended to cover as many of the user-supplied sequences as possible.
Protein secondary structure and solvent accessibility prediction server based on a novel framework.
Set of machine learning programs to predict how single-site amino acid mutation affects protein stability. We developed two machine learning methods: Support Vector Machines and Neural Networks.
A deep learning-based framework for estimating fine-scale germline mutation rates.
A robust and multi-reference approach of RNA-seq transcript normalization.
MUSA (Motif finding using an UnSupervised Approach) is a new algorithm that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders.
a graphical user interface for multi-OMICs data integration in radiogenomic studies.
Multiomics single-cell copy number alterations detection: an R package for CNV profiling in cancer cells, using one to multiple single-cell modalities.
This tool performs multiple sequence alignments of nucleotide or amino acid sequences.
Implementation of an optical flow algorithm to track muscle length changes imaged with ultrasound.
Sequence alignment using the Multiple Sequence Comparison by Log-Expectation (MUSCLE) method
The Human skeletal muscle aging atlas provides a resource mapping cellular changes in human skeletal muscle during aging, integrating single-cell and single-nucleus sequencing data from young and old adults.
A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.
MUSE-XAE is a tool for mutational signature extraction from cancer genomes using an explainable autoencoder. It aims to improve accuracy and interpretability in classifying tumor types.
Multi-query Sequence Blast Output Examination is a program designed for multi-query sequence BLAST output examination. It examines the BLAST output, extracts the informative parameters of BLAST hits, and saves them in tabular form in either text or HTML format. The hit tables are optionally further analyzed with the program to produce subsets of BLAST hits according to user-specified criteria.
MuSERA (Multiple Sample Enriched Region Assessment) is a broadly useful stand-alone tool for both interactive and batch analysis of combined evidence from enriched regions in multiple ChIP-seq or DNase-seq sample replicates, with a user-friendly graphical interface.
Designed to analyze (aligned) gene libraries, in particular in case that codon directed mutagenesis was applied to them. The program generates several tables providing information about trinucleotide characteristics, deletions, substitutions and amino acids distributions.
Tool for uncovering multiple peptides and nucleic acids binding specificities from sequence data. MUSI provides a simple interface for processing short peptides or nucleic acid sequence data. Starting from a set of sequences observed to bind to a given target, it automatically generates an optimal number of motifs based on the different specificity patterns present in the data.
MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another.
Mutational Signatures in Cancer is a shiny-based web application aimed to visualize the somatic mutational profile of a series of provided samples (different formats are allowed) and to extract the contribution of the reported mutational signatures on their variation profile. It is mainly based on the MutationalPatterns R package.
Assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones.
MuSiCal is a computational framework for accurate and sensitive mutational signature analysis. It provides algorithms to improve signature discovery and assignment, outperforming state-of-the-art methods and enabling enhanced understanding of mutational forces in cancer genomes.
The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures.
An R package for detecting multiple signatures with similar predictive performance.
A deep-learning based webserver for protein post-translational modification site prediction and visualization. MusiteDeep is a deep-learning based webserver for protein post-translational modification site (PTM) prediction and visualization. The MusiteDeep web server is available at http://www.musite.net. This repository contains the stand-alone tools in python to run MusiteDeep on a local machine:.
It is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. It is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time.
Database of standardized mouse morphology data for morphometric meta-analyses.
Improved de novo detection program for recently active miniature inverted repeat transposable elements (MITEs).
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation. Mustache (Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation) is a tool by Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi and Ferhat Ay (ferhatay@lji.org).
Softwear for the alignment of multiple protein structures.
Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci. MuStARD - autoMated SmAll Rna Detection.
Multiple structure-guided sequence alignment of protein families.
Minimal Unsatisfiable Subsets Enumeration Tool. MUST is a tool for online enumeration of minimal unsatisfiable subsets (MUSes) of a given unsatisfiable set of constraints. The tool currently implements three online MUS enumeration algorithms: MARCO [9], TOME [2], and ReMUS [3], and supports MUS enumeration in three constraint domains: SAT, SMT, and LTL. A paper [1] describing MUST will be presented at TACAS 2020.
Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.
MUTation AnaLyIS toolKit. Comprehensive analysis of somatic DNA mutations with genome regulation elements and DNA sequence contexts.
Tool that checks, analyzes and corrects descriptions of sequence variants according to the standard human sequence variant nomenclature of the Human Genome Sequence Variation Society (HGVS).
Checks sequence variant nomenclature according to the guidelines of the Human Genome Variation Society.
Online tool for assessing the mutational spectrum of epPCR (error-prone PCR) libraries with poor sampling.
A computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. My Personal Mutanome: A Personalized Cancer Medicine Platform for Searching Network Perturbing Alleles Linking Somatic Genotype to Phenotype. A pharmacogenomics database for prioritizing actionable mutations for personalized cancer treatments.
A Pipeline for Identifying Saccharomyces cerevisiae Mutations. A bioinformatics pipeline for identification and characterization of mutations in Saccharomyces cerevisiae. MutantHuntWGS compares data, input in FASTQ format, from a mutant strain to a wild-type strain to identify high confidence sequence variants present only in the mutant. This pipeline was designed to be as user friendly as possible.
A platform linking gene expression changes and mutation status in solid tumors. connect mutation status to gene expression changes in solid tumours. muTarget is a cancer biomarker / target discovery tool with two major functions.
Analysis and visualization of mutation-induced changes in RNA structure. MutaRNA (Mutational Analysis of RNAs) predicts and visualizes the mutation-induced structure changes of a single-nucleotide polymorphism (SNP) in an RNA sequence. This covers changes in the accessibility (single-strandedness) of the molecule, its intra-molecular base pairing potential and its the base pairing probabilities. Combined with evaluation results of tools like remuRNA and RNAsnp, MutaRNA enables a detailed evaluation of a mutation's effects on RNA structure formation.
Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.
A functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures.
Prediction of Mutation Effects using a Deep Temporal Convolutional Network. This is the code for the paper Prediction of Mutation Effects using a Deep Temporal Convolutional Network. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz873/5634146. The code is compatible with tensorflow-gpu=1.10.0 and python=2.7
Open Source Oligo Design Platform for Protein Engineering. Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins. Mutation Maker, An Open Source Oligo Design Software For Mutagenesis and De Novo Gene Synthesis Experiments.
It evaluates the pathogenic potential of DNA sequence alterations. It is designed to predict the functional consequences of amino acid substitutions as well as intronic and synonymous alterations, short insertion and/or deletion mutations and variants spanning intron-exon borders.
MutationalPatterns is a Bioconductor package that allows users to analyze mutational processes from whole-genome sequencing data. It identifies characteristic mutational signatures and allows comparisons between different tumor types and other datasets.
This enables you to explore mutation hotspots identified in protein domains from more than 5000 patients across 22 cancer types.
An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data.
Make the analysis of Next-Generation Sequencing data simple. Depending on your background and interest, it offers various modes with optimised settings: Clinical (HPO), Clinical (Gene Panels), Gene Function and Basic Search.
The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome. MutationExplorer is a lightweight web application for exploring somatic mutations in cancer datasets. It is based on R and the Shiny framework. MutationExplorer is currently most usable for breast cancer samples, since the relevant biomarkers for patient selection (e.g. clinical status of ER and PgR) are hardcoded.
MutationInfo is a python package to extract the position, the reference and the alternative sequence of a genomic variant. It accepts variants in dbSNP rs format or in HGVS format.
This library provides capabilities for analysis of mutation properties. Two different analysis approaches are supported: (1) log-linear analysis of neighbourhood base influences on mutation coupled with a sequence logo like representation of influences; (2) log-linear analysis of mutation spectra, the relative proportions of different mutation directioons from a starting base. A logo-like visualisation of the latter is also supported.
Identifying potential mutations across target gene sequences.
Employs a Bayes classifier to eventually predict the disease potential of an alteration. The Bayes classifier is fed with the outcome of all tests and the features of the alterations and calculates probabilities for the alteration to be either a disease mutation or a harmless polymorphism.
A tool to identify disease-prone sites in cancer using deep learning.
Identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search. MutCombinator - Combinatorial mutation search. MutCombinator enables us to practically identify mutated peptides from tandem mass spectra allowing combinatorial mutations during the database search. It uses an upgraded version of a variant graph, keeping track of frame information. The variant graph is indexed by nine nucleotides for fast access. Combinations of point mutations are considered, and also it can be practically applied together with a large mutation database such as COSMIC.
A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2.
Database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.
A method for identification of somatic point mutations in next generation sequencing data of cancer genomes.
A flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. Author: Anthony R. Soltis (anthony.soltis.ctr@usuhs.edu, anthonyrsoltis@gmail.com). Institution: Uniformed Services University of the Health Sciences, Bethesda, MD. MutEnricher is a flexible toolset that performs somatic mutation enrichment analysis of both protein-coding and non-coding genomic loci from whole genome sequencing (WGS) data, implemented in Python and usable with Python 2 and 3. License: MIT License, see License.
Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Australia.
Mutated ligand binding site gene DataBase.
MutPred is a web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, it predicts molecular cause of disease.
An R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. Transcriptomic data can uncover complex biological processes in part through the improved understanding of gene coexpression patterns.
Draws a Needle-Plot for mutation data (stacked).
Flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data.
An analytical toolkit for probing the mutational landscape in cancer genomics.
Human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.
An R package to map spectra to mutational signatures based on shot-noise modeling. R package mutSigMapper aims to resolve a critical shortcoming of existing software for mutational signature analysis, namely that of finding parsimonious and biologically plausible exposures. By implementing a shot-noise-based model to generate spectral ensembles, this package addresses this gap and provides a quantitative, non-parametric assessment of statistical significance for the association between mutational signatures and observed spectra.
An R Package for Extraction and Analysis of Cancer Mutational Signatures. mutSignatures R package - dev version - 2.1. Decipher Mutational Signatures from Somatic Mutational Catalogs. Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes.
Cancer mutational signatures representation by large-scale context embedding. MutSpace is a method aiming to address the computational challenge to consider large-scale sequence context for mutational signatures.
Application to next-generation sequencing based RNA structure probing.
MutVis is an automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains. MutVis is an open-source, user-friendly, automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains, regardless the number, origin or species. The current framework integrates various opensource tools and is scripted using Python, R programming and Snakemake workflow management software. MutVis supports variant calling, processing of VCF files, transition and transversion graphical representation, generation of mutational count matrix, graphical visualization of basepair substitution spectrum (BPS) and mutation signatures.
Assigning and summarizing mutation types for analyzing germline mutation spectra. A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs. See documentation for install and usage information. Ancestral \(k\)-mer Mutation Types for SNP Data — mutyper documentation. Pairs well with the package mushi, which performs mutation spectrum history inference. Ancestral k-mer mutation types for SNP data.
An end-to-end workflow for statistical analysis and inference of large-scale biomedical datasets. muvis is a visualization and analysis toolkit for multivariate datasets. To use this package, you will need the R statistical computing environment (version 3.0 or later).
MUVR2 is an R package that adjusts for covariates and assesses modeling fitness in machine learning, allowing for improved variable selection and prediction accuracy in omics research. The package includes elastic net, partial least squares, and random forest modeling approaches, alongside a tutorial to facilitate its use.
Mutant-seq library analysis and annotation.
Multiplexed quantitiave proteomics using differential stable isotope labeling.
This repository contains a software mvBIMBAM, a version of BIMBAM for multivariate association analysis, implementing a Bayesian approach for genetic association analysis of multiple related phenotypes. We adapted source codes in BIMBAM to deal with multiple related phenotypes.
R package for multi-view genomic data simulator. It is a tool in R to generate synthetic datasets from ordinary differential equations (ODE)-based models with known parameters.
R package for multi-view genomic data integration methodology. It is a tool in R that combines different types of measurements (such as mRNA expression, miRNA expression, DNA methylation, clinical data, etc) for a given set of samples (e.g. patients). The aim is to combine dimension reduction, variable selection, clustering (for each available data type) and data integration methods to find patient subtypes.
A novel multi-view graph convolutional network (MVGCN) framework for link prediction in biomedical bipartite networks.
Platform-independent tools to identify GO terms that are differentially active in multiple contrasts of interest. Given a matrix of one-sided p-values, it uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify them as significantly more active, less active, or not significantly differentially active in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile of differential activity.
Microbiome-based disease prediction with multimodal variational information bottlenecks.
Normalization tests for shoulder electromyographic signals
Re-format the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout.
Reformat the results of a sequence database search (BLAST, FASTA) or a multiple alignment adding optional HTML markup to control colouring and web page layout.
MVIP provides a large number of available multi-omics data under viral infection in various species.
mvlearnR is a package and Shiny application designed for integrating data from multiple sources, such as genomics, proteomics, and clinical data. The application provides a user-friendly interface for multiview learning analysis, accessible through a web browser.
Leveraging the genetic correlation between traits to detect epistasis in genome-wide association studies.
Mainly for the illustration and processing of structure-related information which is useful in structure prediction.
An extensible Galaxy plug-In for multi-omics data visualization and exploration. The Galaxy MVP visualization plugin enables viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data.
mvpaShiny is an R Shiny app that implements Multivariate Pattern Analysis (MVPA), a method for revealing and quantifying predictive association patterns in multicollinear data. It facilitates the usage and interpretation of complex association patterns.
A Classification and Regression Toolbox for Multi-Dimensional Data. Matlab toolbox for classification and regression of multi-dimensional data. This is the companion repository of the MVPA-Light paper.
MVPAlab is a MATLAB-based and very flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data. The MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contribution analyses. This toolbox has been designed to include an easy-to-use and very intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for those users with few or no previous coding experience. However, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner.
A highly efficient and sensitive pathogenicity prediction tool for missense variants.
CIM QTL mapping via multivariate statistical method in an outbred full-sib family.
An R-package that estimates a climate-driven mosquito-borne viral suitability index. Estimator of climate-driven, mosquito-borne viral suitability index. Understanding how climate dictates the timing and potential of mosquito-borne viral transmission is essential for preparedness of public health systems and design of control strategies. We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. The package estimates a suitability index based on a climate-driven mathematical expression for the basic reproductive number (R0) of a well established mathematical model for the transmission dynamics of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, suitability can be estimated for specific and viral species, as well as different regions of the globe.
A toolset for quantifying and designing multivalent interactions.
It provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.
Find weights common to multiple molecular weights files.
Filter noisy data from molecular weights file.
An Algorithm for Context-Based Annotation of Liquid Chromatography-Mass Spectrometry Features through Diffusion in Graphs.
Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms | maximum weighted merger method
MWT computes FDR based on a moderated version of the Welch test. It’s particularly suited for small samples comparisons exprecially with unequal variances
mwTab is a Python library for RESTful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository. The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.
Mann-Whitney-Wilcoxon non parametric test for two unpaired groups.
mxfda is an R package for functional data analysis of single-cell spatial data, facilitating spatial analysis using techniques like Ripley’s K and functional regression. It provides end-to-end analysis capabilities and detailed documentation including vignettes.
Mens per Machina. Flexible feature selection, cross-validation and Bayesian Networks for large datasets.
Java program for computing a phylogenetic network from a collection of phylogenetic trees.
Server for identification and characterization of diversity-generating retroelements.
This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new transcriptome of genome assemblies.
MyBrain-Seq is a Compi pipeline for performing full analyses of miRNA-Seq data, with particular interest on neuropsychiatric data. It can automatically identify differentially expressed microRNAs (DE miRNAs) between two conditions using two differential expression analysis software, namely DESeq2 and EdgeR, and is able to offer an integrated result suitable for experimental validation. Additionally, a functional analysis module puts biological meaning behind the list of DE miRNAs and eases the process of biomarker identification.
MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.
MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication
high-throughput analysis of Streptomyces mycelium live cell imaging data | To quickly get a grasp what results can be generated with mycelyso, please take a look at the static demo page of mycelyso Inspector generated with the example dataset
MyCLADE is an accurate multi-source domain annotation server designed for a fast exploration of genomic and metagenomic sets of sequences. MyCLADE performs a multi-source domain annotation strategy based on a library of probabilistic domain models associated to each domain.
Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. mycoCSM: identifying safe potent hits against Mycobacteria. Douglas E. V. Pires & David B. Ascher.
A sequence-based predictor for identifying mycobacterial membrane proteins and their types.
MycoPrint is a web interface for exploration of the interactome of Mycobacterium tuberculosis H37Rv (Mtb) predicted by "Domain Interaction Mapping" (DIM) method.
A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris.
This web-server was used to predict the subcellular localizations of mycobacterial proteins based on optimal tripeptide compositions.
A data-driven platform for investigating masked forms of mycotoxins.
Partial RdRp sequences offer a robust method for Coronavirus subgenus classification. MyCoV is an R package that allows the prediction of coronavirus subgenus based on partial RdRp data. The ‘MyCoV’ package will currently only work in a linux environment. Essentially it is a wrapper script for nucleotide BLAST, and therefore requires a local installation of BLAST+.
MycoWiki is organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae.
A Semi-Automated Software for Myelin g-Ratio Quantification
Online research environment that supports the social sharing of bioinformatics workflows.
This package provides simple-to-use REST web services to query/retrieve gene annotation data.
An interactive and programmatic platform for community-curated and user-created collections of genes.
Web-based environment that provides biologists with a way to build, query and share their genome browsers.
MyGOD is a Web-based visual exploration tool. It has been designed to enable scientists to easily build dynamic and composite graphical representations of biodiversity data supplemented with environmental data (ex.: physico-chemical measurements). Anonymous visitors have access to all data and all types of graphical representations offered by MyGOD. Authenticated users benefit for additional feautures: they can save all the settings of the dashboards they have composed for later reuse, they can promote their dashboards as gallery entries which makes them publicly accessible; and, if they have the appropriate permissions, they can directly import new datasets into MyGOD. Developement of MyGOD has been funded by the BioGenOuest network, and the Institut Français de Bioinformatique, and been carried out by personnel of the ABiMS platform, with contributions from the Service de Bioinformatique de l'IFREMER and the Mediterranean Institute of Oceanography.
MyGOD : Manipulate your Genomic Observatory Data
The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.
RScript to parse the results of mykrobe predictor.
MyMiner is a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems.
An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle.
Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. This repository contains the companion code for recreating the single nucleus analysis figures from the Kim et al.
explore gene co-expression in normal and pathological muscle. MyoMiner doesn't collect any personal information, but does use some cookies (including google analytics to track basic usage) Learn more OK. Co-expression analyses will help muscle researchers to delineate the tissue-, cell-, and pathology-specific elements of muscle protein interactions, cell signaling and gene regulation. Changes in co-expression between pathologic and healthy tissue may suggest new disease mechanisms and therapeutic targets. MyoMiner is a powerful muscle specific database for the discovery of genes that are associated in related functions based on their co-expression.
A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. A Database of miRNAs during Muscular Atrophy. Defence Institute of Physiology and Allied Sciences,.
Myocardial pathology segmentation with flexible combination of multi-sequence CMR images.
An automated muscle histology analysis tool using machine learning algorithm utilizing FIJI/ImageJ software. automated muscle histology analysis using machine learning algorithm utilizing FIJI/Image J software.
Artificial intelligence workflow quantifying muscle features on Hematoxylin-Eosin stained sections reveals dystrophic phenotype amelioration upon treatment.
The Myotube Analyzer is an open source app made specifically for the analysis of microscopic images taken of muscle stem cell cultures.
Open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory’s microbial ecology data.
MyPROSLE was developed with the aim of bringing molecular information from patients to clinical practice. For this, we have created a new methodology to summarize the transcriptome of individual patients in a series of biological functions or gene-modules, which were later used to predict up to a total of 111 different clinical outcomes, including clinical manifestations, laboratory measurements, cytokine levels, autoantibodies, cell percentages, nearby disease flares and response to drugs.
The tool enables to create context-sensitive protein interaction networks for organisms, tissues and user-defined contexts.
Software package for p-value-based multiple testing that also implements a dependence test and p-value simulation (formerly SGoF+).
Software to align short reads produced by a short read genome sequencer to a reference genome. It performs brute force alignment using a variant on the "bitap" algorithm that aligns several thousand reads to a reference in parallel. It uses bit-parallelism, multiple processors, and Cell SPUs if available. It will find alignments with any number of errors up to a user specified cutoff. The emphasis is on doing a 100% accurate search as fast as is possible.
Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.
Identification and Classification of Reverse Transcriptases in Bacterial Genomes and Metagenomes.
A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues. Copyright © 2021 Institute of Information Science, Academia Sinica, TAIWAN.
Program for the simulation of DNA sequence evolution across a phylogenetic tree.
It is an easy-to-use application to build and publish websites for synteny block analyses by using users’ own genome sequences or synteny block definitions.
A wrapper for querying MyVariant.info services.
Desktop application for high-throughput mutations data management.
Converts analysis.baf files from Bruker into mzXML files. This software requires the CDAL library from Bruker.
mzWiff is a command-line program to convert Analyst native acquisition (.wiff) files to mzXML and mzML.
Converts mzXML and mzML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files. Comes with the current version of TPP.
A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry.
MzDOCK is a free, ready-to-use GUI-based pipeline for molecular docking simulations designed to make the process easier for users with varying levels of experience. It integrates various open-source packages to provide a comprehensive docking workflow with practical options and visualizations.
A new algorithm that enables untargeted metabolomics integration of samples that are measured with high resolution LC-MS.
A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.
Variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys.
Peptide identification from tandem mass spectrometry data
Library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments.
Mzkit is an open source raw data file toolkit for mass spectrometry data visualization and analysis, provides by the BioNovoGene. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), MS-imaging, ms-spectrum tree analysis, build molecule network, formula de-novo search and de-novo annotation.
Modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data.
Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.
mzQC is a standard file format for reporting and exchanging data quality information in mass spectrometry. The software provides open-source libraries in Python, R, and Java for processing mzQC data and facilitating data quality control workflows.
XML-based format that captures extensive information from quantitative proteomics experiments.This library project intends to develop a set of easy-to-use post-processing APIs/applications to facilitate utilizing the standard in the field.
Provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
mzRAPP is a tool for reliability assessment of data pre-processing in non-targeted metabolomics. The goal of mzRAPP is to allow reliability assessment of non-targeted data pre-processing (NPP; XCMS, XCMS3, MetaboanalystR 3.0, XCMS-online, MZmine 2, MS-DIAL, OpenMS, El-MAVEN,..) in the realm of liquid chromatography high-resolution mass spectrometry (LC-HRMS). mzRAPPs approach is based on the increasing popularity of merging non-targeted with targeted metabolomics meaning that both types of data evaluation are often performed on the same dataset.
Recalibrate mass spectrometry datasets using peptides identified by MS/MS
Simulation-based comprehensive study of batch effects in metabolomics studies. batch effect simulation and correction for GC/LC-MS based data. The goal of mzrtsim is to make batch effects simulation for LC/GC-MS based peaks list data
GIS Methods and Tools for Seismic Microzonation Mapping.
A python reference implementation of the mzSpecLib spectral library format.
Converts SCIEX/ABI Analyst format (WIFF) to mzXML.
Convert proteomics data files into a SQLite database Extract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database. The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin.
MzVar is a Java tool allowing the compilation of customized variant protein and peptide databases in the FASTA format for database searching of MS/MS data, using a VCF file as variant input and a FASTA file as transcript input. The tool is compatible with transcript sequences retrieved from either Ensembl or the UCSC Table Browser.
MZViewer is a lightweight viewer for mzData mass spec files. It is not designed to be a full analysis application, but rather to provide a quick view of mzData files.
MzXML viewer from Seattle Proteome Center.
Plots mzXML LC-MS data as virtual gels or heat maps.
A Learning Framework for n-Bit Quantized Neural Networks Toward FPGAs. This implementation supports cifar10/cifar100/imagenet.
A MATLAB script for N-Dimensional Trapezoidal integration
Facilitates the study of HIV diversity by tracking gp120 N-linked glycosylation sites in HIV. The web server provides an automated platform for mapping and comparing variable loop N-glycosylation sites across populations of HIV-1 sequences.
HIV N-linked Glycosylation Site Analyzer
Wavelet analysis based model for predicting nucleosome positions from DNA sequence information.
Web-Based Visualization of Electrocorticography Data for Epilepsy Surgery.
The tool is designed to perform image pre-processing to reduce the bias field effect, improving the quality of the image. Two main functionalities are offered: (1) Apply N4 filter to image/images (either with the default parameters values or with parameters values defined by the user) (2) Find the optimal configuration of the N4 filter for specific image/images by measuring the Full Width at Half Maximum (FWHM) of the periprostatic fat distribution.
A script to calculate N50 from one or multiple FASTA/FASTQ files available via BioConda
Protein-Nucleic Acid Binding Energetic Database
Nabo – a framework to define leukemia-initiating cells and differentiation in single-cell RNA-sequencing data. Nabo is a flexible Python package that allows projections of cells from one population to another using single-cell RNA-Seq data. Nabo works by setting one of the populations as a reference and then maps cells from other populations (targets) onto it. Nabo provides data implicit methods of verifying mapping quality, this allows users to clearly infer similarities between sub-populations across samples.
This tool is a Bayesian network diagnostic model designed to aid in the clinical diagnosis of Alzheimer’s Disease. It leverages data from the NACC and provides a visible and auditable justification for its predictions, unlike ‘black box’ AI models.
Nucleic Acid Circular Dichroism Database.
A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors. Database of structural-functional annotations of nicotinic acetylcholine receptors. NAChRDB is a web-accessible database of residue-level structural-functional annotations of nicotinic acetylcholine receptors. NAChRDB is particularly useful for identifying gaps in knowledge and for guiding discovery through structural and molecular biology experiments, especially when exploring the allosteric mechanisms underlying neuromuscular nAChR function and pathology.
NADbinder server discriminate the NAD interacting residues and non-interacting residues from a given sequence. The NADbinder server uses the SVM based method by using the Position Specific Scoring Matrix (PSSM) generated from the query sequence(s).
This Bioconductor package has been developed for bioinformatic analysis of the NAD-seq data, including normalization, smoothing, peak calling, peak trimming and annotation.
Evaluating gene regulatory network activity from dynamic expression data by regularized constraint programming.
Identification of disease-related genes and construction of a gene co-expression database in non-alcoholic fatty liver disease.
Knowledge base and platform for drug development against nonalcoholic fatty liver disease.
Nucleic Acids flexibility analysis portal.
Nucleation-and-growth parameters from the kinetics of protein phase separation.
Performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses. NAguideR is a web-based tool, which integrates 23 common missing value imputation methods and provides two categories of evaluation criteria (4 classic criteria and 4 proteomic criteria) to assess the imputation performance of various methods. We hope this tool could help scientists impute the missing values systematically and present valuable guidance to select one proper method for their own data. In addition, this tool supports both online access and local installation.
Set of tools for solving problems in the life sciences using network (graph) approaches. It includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.
R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods.
Web application NAmech helps 3D structure and mechanical deformability prediction of RNA and DNA duplexes from nucleotide sequence. It is based on a mechanical duplex model parametrized by massive molecular dynamics simulations. It provides datasets with predicted parameters together with visualizations in interactive plots. It can include alternative sequences, such as epigenetically modified or radiation damaged.
Using machine learning to assess the quality of atomic force microscopy-enabled nano-indentation data | Loading, fitting, and rating AFM force-indentation data | Documentation — nanite 1.2.4 documentation | The documentation, including the code reference and examples, is available at nanite.readthedocs.io | Loading, fitting, and rating AFM force-distance data | Free document hosting provided by Read the Docs
This database provide several way to access to the genomic data, as a blast search page, a genome browser and a direct link to download the data.
Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Bespoke script collection for nanopore sequencing-based Isoform Dynamics (nano-ID), a method that detects newly synthesized RNA isoforms and monitors isoform metabolism. nano-ID combines metabolic RNA labeling, long-read nanopore sequencing of native RNA molecules and machine learning.
A framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection.
Transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.
A repository for DNA and RNA nanostructures.
R-package for visualization of RNA isoforms from long-read RNA-sequencing data.
INDI-integrated nanobody database for immunoinformatics.
Nanopore Current Events Magnifier (nanoCEM) is a Python command-line tool designed to facilitate the identification of DNA/RNA modification sites through enhanced visualization and statistical analysis of nanopore sequencing data. It is compatible with multiple preprocessing methods and offers improved visualization of current events.
Nanopore Current Events Magnifier (nanoCEM)
A species-level analysis of 16S rRNA nanopore sequencing data based on de novo clustering and consensus building.
Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
NanoCore is a user-friendly software for Nanopore-based genomic surveillance that enables the calculation and visualization of core-genome multilocus sequence typing (cgMLST) sample distances directly from unassembled Nanopore reads. It supports Illumina data analysis as well and is available as free software via conda.
An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2.
A pipeline that detecting recombinant crossover using ONT sequencing data.
Deep learning framework for nanopore adaptive sampling on microbial sequencing.
nanodisco is a toolbox for de novo discovery of all the three types (6mA, 5mC and 4mC) of DNA methylation from individual bacteria and microbiomes using nanopore sequencing. For microbiomes, nanodisco also supports the use of DNA methylation patterns as natural epigenetic barcodes to facilitate high resolution metagenomic binning. Specifically, nanodisco can be used to De novo discover DNA methylation motifs, identify specific type (6mA, 5mC or 4mC, namely typing) of a methylation motif, and identify which specific position within the motif is methylated (namely fine mapping), performing metagenomic binning based on microbial DNA methylation pattern by constructing and clustering a methylation profile matrix, and to integrate the two functionalities above together for de novo methylation motif discovery from microbiomes, and metagenomic analysis.
RNA modification detection using Nanopore raw reads with Deep One-Class Classification. RNA modification detection using Nanopore raw reads with Deep One Class classification. This software requires In vitro unmodified RNA raw read and Native RNA raw read to process.
An integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology.
Quantitative detecting DNA methylation from nanopore sequencing data without raw signals
A collection of best practice and popular ONT-oriented tools are integrated (and are expanding) in this custom Galaxy instance.
A high-performance open-source super-resolution microscopy toolbox. NanoJ-Core is an open-source ImageJ and Fiji plugin that provide the base high-performance computing engine that other NanoJ plugins need to run: NanoJ-SRRF, NanoJ-SQUIRREL, NanoJ-VirusMapper and NanoJ-Fluidics. Super-Resolution Radial Fluctuations (SRRF) - ImageJ Plugin.
An analytical approach for quantifying image quality in super-resolution microscopy.
Comprehensive nanobody database with data integration, consolidation, and application.
System for benchmarking DNA assembly tools, based on 3rd generation sequencers.
CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.
Nanometa Live is a user-friendly application for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies' MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data.
An R/Bioconductor package for visualizing long-read methylation data. Visualise methlation data from Oxford Nanopore sequencing. NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
A web-based tool for predicting cytotoxicity of TiO2-based multicomponent nanomaterials toward Chinese hamster ovary (CHO-K1) cells.
Accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples. Accurate multilocus sequence typing using Oxford Nanopore MinION with dual-barcode approach to multiplex large numbers of samples.
NanoMnT: An STR Analysis Tool for Oxford Nanopore Sequencing Data Driven by a Comprehensive Analysis of Error Profile in STR regions.
A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution.
Rapid and accurate end-to-end nanobody modeling by deep learning.
A tool for comprehensive analysis of Oxford Nanopore MinION sequence data.
Visualizing and processing long-read sequencing data.
Nanopanel2 (np2) is a somatic variant caller for Nanopore panel sequencing data. Np2 works directly on basecalled FAST5 files and outputs VCF and TSV files containing variant calls and associated statistics. It also produces haplotype map TSV and PDF files that inform about haplotype distributions of called (PASS) variants.
A workflow for characterizing nanoparticle monolayers for biosensors. A persistent challenge in materials science is the characterization of a large ensemble of heterogeneous nanostructures in a set of images. This often leads to practices such as manual particle counting, and sampling bias of a favorable region of the “best” image. Herein, we present the open-source software, imaging criteria and workflow necessary to fully characterize an ensemble of SEM nanoparticle images. Such characterization is critical to nanoparticle biosensors, whose performance and characteristics are determined by the distribution of the underlying nanoparticle film.
workflow characterizing nanoparticle monolayers biosensors
SimBiology model and code to perform CI and NCA analyses, and optimization using parallel computing.
An easy-to-use user interface for nanoparticle dosimetry with the 3DSDD model. The Nano Particle Administration Sedimentation Simulator (NanoPASS) is a package which intends to simulate the sedimentation process of nano particles in a cell culture well. By simulating this process the experimentator can estimate the effective dose over time the cells are exposed to. Also, this gives an idea on at which time point the cells are exposed to the calculated concentration of sedimenting particles.
NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences
A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data.
NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files. It is a companion package for Nanopolish.
Overcoming high nanopore basecaller error rates for DNA storage via basecaller-decoder integration and convolutional codes. DNA storage for nanopore sequencing using convolutional coding and basecaller-decoder integration. In many of the scripts, you need to set the path for the corresponding data directories as well as the encoding parameters. The current paths assume that the data is stored in ../nanopore_dna_storage_data/.
Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era.
User-friendly tool for nanopore-seq real-time transcriptional analysis.
Nanoranger is a long-read sequencing workflow and analysis pipeline for detecting cell lineage-defining features like single-nucleotide variants and fusion genes, particularly suited for cancer and immune phenotype analysis.
An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm. Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. However, the nanopore sequencing reads are susceptible to a fairly high error rate owing to the difficulty in identifying the DNA bases from the complex electrical signals. Here we proposed a DNA basecalling reviser, NanoReviser, based on a deep learning algorithm to correct the basecalling errors introduced by current basecallers provided by default. In our module, we re-segmented the raw electrical signals based on the basecalled sequences provided by the default basecallers. By employing convolution neural networks (CNNs) and bidirectional long short-term memory (Bi-LSTM) networks, we took advantage of the information from the raw electrical signals and the basecalled sequences from the basecallers.
NanoRTax is a taxonomic and diversity analysis pipeline built originally for Nanopore 16S rRNA data with real-time analysis support in mind. It combines state-of-the-art classifiers such as Kraken2, Centrifuge and BLAST with downstream analysis steps to provide a framework for the analysis of in-progress sequencing runs. NanoRTax retrieves the final output files in the same structure/format for every classifier which enables more comprehensive tool/database comparison and better benchmarking capabilities. Additionally, NanoRTax includes a web application (./viz_webapp/) for visualizing complete or partial pipeline outputs. The NanoRTax pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with conda environments and docker containers making installation trivial and results highly reproducible.
A first person exploration of a cancer cell deep in the human body, featuring a highly detailed simulation of cellular anatomy and processes based on the latest scientific research.
Nanopore sequence read simulator based on statistical characterization.
A progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data.
A scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline. Scalable, Portable, and Cloud compatible pipeline analysing Nanopore metagenomic sequencing data. NanoSPC is a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. It can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. It can also detect single nucleotide variants and assemble high quality complete consensus genome sequences.
Accurate identification of splice junctions using Oxford Nanopore sequencing.
Tool for compression of nanopore genomic reads in FASTQ format (gzipped input also supported).
A method for detection of target short tandem repeats based on nanopore sequencing data.
Pipeline for reproducible NanoString nCounter analysis. nf-core/nanostring is a bioinformatics pipeline that can be used to analyze NanoString data. The performed analysis steps include quality control and data normalization.
This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. It incorporates size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.
Set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
This tool provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data, i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.
A tool for enhanced annotation of genomic structural variants. nanotatoR: next generation structural variant annotation and classification. Whole genome sequencing (WGS) has successfully been used to identify single-nucleotide variants (SNV), small insertions and deletions and, more recently, small copy number variants. nanotatoR: structural variant annotation and classification author: "Surajit Bhattacharya,Hayk Barsheghyan, Emmanuele C Delot and Eric Vilain. Short-read sequencing (SRS) is the predominant technique of DNA sequencing used for clinical diagnosis.
Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).
Development of a parsimonious in silico model for toxicity assessment of metal-oxide nanoparticles using physicochemical features. Computational hazard assessment of MeOx nanoparticle toxicity using machine learning.
A software tool to de novo search high-copy tandem repeats in Oxford Nanopore Technologies (ONT) plant DNA sequencing data
NanoTube performs data processing, quality control, normalization and analysis on NanoString gene expression data.
Explore, share, and contribute nanoparticle flow cytometry experiments annotated according to the MIFlowCyt-EV standards.
Zeta-Potential Read-Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform. Nanomaterials Image Analysis Tool Powered by Enalos Cloud Platform. Computation User Guide Download demo image. Statistically processed image end result.
A new modelling tool for estimating HIV epidemic indicators at the district level in sub-Saharan Africa.
Nucleotide Amino Acid Alignment is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology.
Bioinformatic pipeline to predict MHC-I-restricted T cell epitopes in mice. NeoAntigens Prediction @ CNB (NAP-CNB) is a tool for the prediction of neoantigenic peptides from tumoral RNA-seq or peptide sequences. NAP-CNB uses variant calling methods with models trained on recurrent neuronal networks (RNN) to produce a list of putative neoantigens.
mousechd-napari is a Napari plugin for the deep learning-based detection of murine congenital heart defects from µCT scans. It allows users to segment hearts and screen for malformed hearts, and is retrainable on user-provided data.
A plugin to estimate chromosome sizes from karyotype images.
Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.
Web server for the prediction of specific residues involved in nucleic acid-binding proteins binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.
An efficient Python tool providing statistical tests for large-scale heterogeneous data with enhanced support for missing data
The package applies a functional version of principal component analysis to postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks) and to analyse differential variation between multiple ChIP-seq samples with replicates.
Nascent RNA profiling data analysis platform.
Automated program for side-chain resonance assignment and nuclear Overhauser effect (NOE) assignment from NOESY data. It does not require data from TOCSY experiments.NASCA casts the assignment problem into a Markov Random Field (MRF), and extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data.
Completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein interaction network modeling through gene-name mapping, and outputs the resulting network in graphical form and also in computer-readable graph-forms, directly applicable by popular network modeling software.
A web-based platform for high-throughput sequencing data analysis and visualization. NASQAR (Nucleic Acid SeQuence Analysis Resource):. A web-based portal for High-throughput data analysis & visualization. This portal hosts a number of web-based Bioinformatics analysis and visualization apps. https://github.com/nasqar/nasqar.
The NASSAM webserver searches for 3D patterns in nucleic acid structures. Motifs and formations of nucleic acid bases in 3D space within nucleic acid PDB formatted structures. The searches are based on distances between the bases which are represented as pseudoatom vectors. This search is independent of the base sequence order.
Multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.
The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.
To identify cis-NATs using ssRNA-seq, a new computational method was developed based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries.
A Simple Method for Extracting Antimicrobial Resistance Information from metagenomic sequencing data.
A web server for protein-protein interaction network querying.
Identification of pan-cancer Ras pathway activation with deep learning. ##The identification of hidden responders are often the essential challenges in precision oncology.
A relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses
A package to classify occurrence records in levels of confidence in species identification. naturaList package for R. version 0.2.0.
NaViA is a web tool created to augmend the analysis of complex mass spectra obtained from native mass spectrometry.
Developed as an interactive, multi-scale navigation tool for large and complicated biological networks.
A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams.
NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR is a powerful graphing application for 2D and 3D visualization of biological networks. Tools for manual and automated annontation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs.
NaviNIBS is an open-source toolbox for neuronavigated noninvasive brain stimulation, specifically focused on TMS. It provides tools for target planning, head registration, and coil tracking, alongside addons for robotic positioning and data integration.
Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence at once when predicting the functional consequences. This is relevant if (independent) sequence variants compensate each other effects.
Neighborhood-Aware Variant Impact Predictor
User-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface.
Navpa is non-software, deriving its name from nav pa', Klingon for paper town. Paper towns were fictional entities historically used to detect copyright violation of published works such as maps. Navpa itself does nothing, including in genomics. However, It can be used to test that services building on bio.tools can handle the special case of a tool with no inputs, outputs or operations.
Negative binomial additive model for RNA-Seq data analysis. Negative Binomial Additive Model for RNA-Seq Data. High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.
A versatile method for differential analysis of multiple types of RNA-seq data.
Uses a method similar to that used in many email spam filters to score a genetic sample against different genomes, to possibly identify the closest match.
A network-based integrative analysis framework. With the explosion of high-throughput data, effective integrative analyses are needed to decipher the knowledge accumulated in biological databases. Existing meta-analysis approaches in systems biology often focus on hypothesis testing and neglect real expression changes, i.e. effect sizes, across independent studies. In addition, most integrative tools completely ignore the topological order of gene regulatory networks that hold key characteristics in understanding biological processes. Here we introduce a novel meta-analysis framework, Network-Based Integrative Analysis (NBIA), that transforms the challenging meta-analysis problem into a set of standard pathway analysis problems that have been solved efficiently
A dedicated database of non-B cell derived immunoglobulin variable region. Non-B cell derived ImmunoGlobulin Variable region Database. Welcome to NBIGV, a database dedicated to organizing and characterizing non-B cell derived immunoglobulins.
Network-based R-statistics for (unbalanced) longitudinal samples. Index of /web/packages/NBR/vignettes. Here are the scripts and preprocessed data to illustrate the R package NBR using the dataset SWU-SLIM. Network-Based R-Statistics using Mixed Effects Models.
System for collecting, preserving and providing bioresources for use as experimental materials for life science research.
NBS-Predict aims to provide a fast way to identify neuroimaging-based biomarkers with high generalizability by combining machine learning with graph theory in a cross-validation structure.
Support vector machine-based high throughput pipeline for plant resistance protein NBSLRR (nucleotide binding site-leucine-rich repeats) prediction.
New thermostability database for nanobodies.
Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data. NBZIMM: Negative Binomial and Zero-Inflated Mixed Models, with Applications to Microbiome Data Analysis.
A Curated ncRNAomics Knowledgebase for Bridging Basic and Clinical Research in Eye Diseases. Nc2Eye, a literature-mined resource of experimentally validated non-coding RNAs in eye diseases. Eye diseases (EDs) represent the disorders affecting visual system, such as retinoblastoma, diabetic retinopathy, etc. Non-coding RNAs (ncRNAs), as a large category of functional RNA molecules, have been reported to play a crucial role in EDs. Here, we developed the Nc2Eye database, which contains 7088 experimentally validated ncRNA-ED associations. It covers 4363 ncRNAs involved in 104 kinds of EDs across 8 species through a comprehensive review of more than 2400 published papers. Nc2Eye also gathered 91 high-throughput transcriptome datasets in EDs and normal controls.
A database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types | Numerous studies indicate that ncRNAs have critical functions across biological processes, and single nucleotide polymorphisms (SNPs) could contribute to diseases or traits through influencing ncRNA expression
A comprehensive and curated portal for translational research.
Collecting and managing taxonomic data with NCBI-taxonomist. ncbi-taxonomist handles and manages phylogenetic data from NCBI. Its primary use is to use taxonomic data to find and link related metadata from other Entrez databases, e.g. fetching data for metagenomic data-sets for specific or diverse group of org. Toolbox to manage NCBI taxonomical data.
Links publically available assembly information with the NCBI Trace Archive's raw sequence data.
The NCBI BLAST+ tools find regions of similarity between biological sequences. The programs compare nucleotide or protein sequences to sequence databases and calculate the statistical significance.
Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections.
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.
Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
Resource for whole-genome epigenetic data sets. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. This resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes.
The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.
Database of genes from NCBI RefSeq genomes.
An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
Identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.
Database that stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.
Web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.
NCBI Influenza Virus Sequence Annotation Tool
This program will download sequences en masse from several NCBI databases (at the user's choice). After the downloading is finished, the program will check the resulting file for any missing sequences and continuously retry the download until all sequences are present in the local file. NCBI Data Usage Policies and Disclaimers may apply to downloaded data.
The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.
Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.
Predicting nucleic acid binding residues in proteins based on multilabel learning. predicting nucleic acid binding residues in proteins based on multi-label learning. NCBRPred is a new sequence-based computational predictor for identifying DNA-binding residues and RNA-binding residues. In which multi-label learning framework and sequence labeling model were employed. It improved performance of nucleic acid binding residue prediction whlie maintaining a low cross-prediction rate, which is an important complement to existing methods. The framework and working process of NCBRPred are shown in Fig. 1. For more information please refer to our paper.
nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment.
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
A novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet.
A computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network. ncDRMarker is an integrated bioinformatic platform that enable users to prioritize candidate ncRNAs involved in drug resistance. ncDRMarker uses a simple but effective computational technique, random walk with restart (RWR), to identify chemoresistance ncRNA biomarkers. The method fully exploits the heterogeneous biological interactions of the mRNA-miRNA-lncRNA composite network, which was constructed by integrating experimentally validated interactions (protein-protein , miRNA-target and miRNA-lncRNA interactions). The identified ncRNAs may be targeted to overcome drug resistance and help realize individual treatment.
A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. More and more evidences have shown that non-coding RNAs (ncRNAs), such as lncRNAs, circRNAs and primary miRNAs, could encode proteins or peptides. ncEP is a database for collecting ncRNA-encoded proteins or peptides, which have been validated by low-throughput experiments from published papers. ncEP contains features of the proteins or peptides encoded by ncRNAs, including their names, sequences, species, genomic locations, tissues or cell lines, experimental methods, data source and other detailed information.
ncFANs v2.0 is an integrative platform for functional annotation of non-coding RNAs. NcFANs v2.0 is an updated and full-featured platform for the functional annotation of noncoding RNAs (ncRNAs), which comprises three major modules: ncFANs-CHIP, ncFANs-NET and ncFANs-eLnc.
The ncFO database has peculiar innovation in the following aspects: (i) providing the manually curated ncRNA–ferroptosis associations in cancer, (ii) proposing “Prediction tools” based on ncRNA regulation and co-expression analysis in a specific cancer type, (iii) offering an online web server for convenient searching, querying, and analyzing of ferroptosis-associated ncRNAs.
Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection. The purpose of ncGTW is to detect and fix the bad alignments in the LC-MS data. Currently, ncGTW is implemented in a R-package as a plug-in for XCMS. That is, ncGTW can detect the misaligned feature groups from XCMS and realign them. After that, XCMS can use the realigned data from XCMS for more accurate grouping and peak-filling.
The NCI Cancer Research Data Commons (CRDC) provides access to a large collection of cancer research data, analytical tools, and visualization platforms in the cloud. It aims to make existing cancer data more findable and accessible by aggregating descriptive information and providing a single access method.
Provides the means to compare images from different internet sources using a java-enabled web browser. It was originally designed for the comparison of 2D gels.
Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.
NCIS (network-assisted co-clustering for the identification of cancer subtypes) combines molecular interaction network into co-clustering.
A novel method for haplotype reconstruction based on Neutrosophic c-means clustering. This code is related to our recently proposed method called NCMHap. This method can solve single individual haplotype problem for diploid organisms.
A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome.
The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.
A multi-class SVM classification to distinguish between non-coding RNAs in Viridiplantae. Prediction model for non-coding RNA. Computational Structural Biology Lab. NCodR : A multi-class SVM classifier using single sequence repeat signatures to distinguish between ncRNA types.
Prediction of coiled-coil secondary structure elements.
Efficient and reliable identification of miRNA orthologs.
Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV). Information on COVID-19, the infectious disease caused by the most recently discovered coronavirus.
An R package for exploring COVID-19 statistics.
Docking server to predict the binding modes between COVID-19 targets and its potential ligands.
ncPlantDB is a comprehensive database of plant non-coding RNAs (ncRNAs) and ncRNA-encoded peptides (ncPEPs), integrating data from 43 plant species and offering cell-specific interaction networks and translational potential data.
To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences.
An integrated computational tool for identifying non-coding RNA promoters in multiple species. The promoter is located near the transcription start sites and regulates transcription initiation of the gene. Accurate identification of promoters is essential for understanding the mechanism of gene regulation. Since experimental methods are costly and ineffective, developing efficient and accurate computational tools to identify promoters are necessary. Although a series of methods have been proposed for identifying promoters, none of them is able to identify the promoters of non-coding RNA (ncRNA). In the present work, a new method called ncPro-ML was proposed to identify the promoter of ncRNA in Homo sapiens and Mus musculus, in which different kinds of sequence encoding schemes were used to convert DNA sequences into feature vectors. To test the length effect, for each species, datasets including sequences with different lengths were built
Non-coding RNA classification with convolutional neural network. ncRDeep: Non coding RNA classification with convolutional neural network.
A novel computational approach for classification of non-coding RNA family by deep learning.
Noncoding Ribonucleic Acid Prediction Based on a Deep Resident Network of Ribonucleic Acid Sequences. NCResNet: Noncoding RNA Prediction Based on a Deep Resident Network of RNA Sequences. A deep learning-based method to predict noncoding RNAs of RNA sequences.
A novel end-to-end method for non-coding RNAs family prediction based on Deep Learning. ncRNAs family classification.
A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inflammation is considered to be central to the onset, progression, and outcome of infectious and noninfectious diseases, especially believed as a hallmark of cancer. In addition, the inflammatory agents, such as cytokine and chemokines, can regulate the behavior of the immune system and involve in the immunotherapy.
Non-translatable RNA transcripts that appear to work at the RNA level.
Database for validated and predicted ncRNAs associated with drug resistance and targeted by drugs.
A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. Jun 1, 2018: Startup of the ncRNAVar project.... Sep 10, 2019: The variant mapping was developed...
NONCODE database integrates expression and functional long noncoding RNAs (lncRNA) data.
a comprehensive database platform for identification and validation of disease related noncoding RNAs. Mar 26, 2020: ncRPheno was published on the journal of RNA Biology... ncRPheno is a comprehensive database that provides experimentally supported associations between noncoding RNAs (ncRNAs, including miRNA, lncRNA, circRNA, snoRNA and piRNA etc.) and disease phenotypes across 11 species (including Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Sus scrofa, Pan troglodytes, Marmoset, Gallus gallus, Canis familiaris, Zebrafish and Rabbit). ncRNAs have been experimentally validated as a novel class of biomarkers and potential drug targets for disease diagnosis, therapy and prognosis. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/starbase (SYSU.EDU.CN)
ncStem is a database that provides curated and predicted ncRNAs associated with cancer stemness. It includes experimentally verified and computationally predicted ncRNAs, along with tools for functional enrichment analysis, survival analysis, and cell location interrogation.
A method to evaluate circadian clock robustness in population scale data.
A Bidirectional LSTM Network with Attention for Y RNA and short non-coding RNA classification.
NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids.
The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.
A risk factor knowledgebase for personalized prevention of neurodegenerative diseases.
NDEx, the Network Data Exchange, is a collaborative software infrastructure for storing, sharing and publishing biological network knowledge.
Data-dependent visualization of biological networks in the web-browser with NDExEdit.
This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.
A platform-independent data interface and database for neuroscience physiology and imaging experiments. Neuroscience Data Interface - A means of specifying and accessing neuroscience data. Available at https://github.com/VH-Lab/NDI-matlab. It is assumed that the function ndi_Init.m is run at startup. Please add this to your startup.m file. (If you use the http://github.com/VH-Lab/vhlab_vhtools distribution, it will be run automatically.).
Spacewise Multiscale Representation Learning via Neighbor Decoupling for Real-Time Driving Scene Parsing.
A method for the quality assessment of single-cell RNA-Seq preprocessing data. A R package for selecting the best way for RNA-Seq data pretreatment.
Phylogenic tree from reads using nucleotide difference method.
Neonatal EEG Artifact Removal, an automated pipeline for pre-processing.
A flexible pipeline characterizing protein binding to local RNA structure. nearBynding is an R package that discerns RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. Input CLIP protein-binding data can either be in aligned BAM or peak-called BED/bedGraph formats. RNA structure can either be internally calculated via CapR or can be provided by the user as a BED/bedGraph. RNA structure binding profiles can be visually and mathematically compared between proteins across multiple formats.
Performs network enrichment analysis against functional gene sets. Benchmarks networks. Renders raw gene profile matrices of dimensionality "N genes x N samples" into the space of gene set (typically pathway) enrichment scores of dimensionality "N pathways x N samples".
NearTree is a software tool that constructs neartrees and provides a number of different query tools.
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.
Suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.
Efficient network enrichment analysis test.
A fine-grained read simulator. GenReads simulates real-looking data using models learned from specific datasets. There are several supporting utilities for generating models used for simulation.
Framework for building fully automated NGS pipelines and analyses.
Simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells.
a Nonlinear Analysis Toolbox for Neuroimaging. non-linear neuroimage analysis toolbox. This project is maintained by imatge-upc. NeAT (Neuroimaging Analysis Toolbox) is a command-line toolbox written in Python that provides the tools to analyze the linear and nonlinear dynamics of a particular tissue and study the statistical significance of such dynamics at the voxel level.
NeatMS is an open source python package for untargeted LCMS signal labelling and filtering. NeatMS enables automated filtering of false positive MS peaks reported by commonly used LCMS data processing pipelines. NeatMS relies on neural network based classification.
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.
Ultra-efficient mapping-free structural variant genotyper. Nebula is an ultra-efficient mapping-free structural variation genotyper based on kmer counting. Nebula is a mapping-free approach for accurate and efficient genotyping of SVs. Nebula is a two-stage approach and consists of a kmer extraction phase and a genotyping phase. Given as input a set of SV coordinates (BED/VCF), the reference assembly (FASTA), and a set of mapped samples on which the genotype of these SVs is already known, Nebula extracts a collection of kmers that represent the input SVs (kmer extraction phase) and these extracted kmers will then be used to genotype the same set of SVs on any new WGS sample(s) without the need to map the reads to the reference genome (genotyping phase). This is done by counting the kmers in the WGS reads of the new sample(s) and predicting genotypes using a likelihood model.
Nebulosa recovers single cell gene expression signals by kernel density estimation. Due to the sparsity observed in single-cell data (e.g. RNA-seq, ATAC-seq), the visualization of cell features (e.g. gene, peak) is frequently affected and unclear, especially when it is overlaid with clustering to annotate cell types. Nebulosa is an R package to visualize data from single cells based on kernel density estimation. It aims to recover the signal from dropped-out features by incorporating the similarity between cells allowing a “convolution” of the cell features.
Network-based cancer gene relationship prediction method reveals perturbations in the cancer gene network. NEtwork-based CAncer gene RElationship prediciton. NECARE is a network-based algrithom which use Relational Graph Convolutional Network (R-GCN) to predict genes inetraction in cancer. The feature NECARE used include:1) knowledge-based feature OPA2Vec; 2)cancer specific feature which means mutation and expression profile of each gene from TCGA.
NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.
N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods. FCIQMC code developed by George Booth and Ali Alavi, 2013.
Combine reference and assembled transcriptomes for RNA-Seq analysis.
A node embedding algorithm for multiplex heterogeneous networks. NECo is a node embedding tool that utilizes multiplex heterogeneous gene phenotype network. NECo allows multi-layer gene and phenotype networks. NECo generates gene embeddings using Gene-Gene, Gene-Phenotype, Phenotype-Gene and Phenotype-Phenotype neibhorhood spaces, using the random walk with restart rankings as node sequences.
Predicting Nash equilibria for microbial metabolic interactions.
A network embedding based method for predicting drug-disease associations. NEDD is an novel computational method, which utilizes heterogeneous information based on the idea of meta path to identify potential novel indications for a given drug.
Identify Lysine Neddylation Sites Using Bi-profile Bayes Feature Extraction via the Chou's 5-steps Rule and General Pseudo Components. Neddylation is a highly dynamic and reversible post-translational modification. The abnormality of neddylation has previously been shown to be closely related to some human diseases. The detection of neddylation sites is essential for elucidating the regulation mechanisms of protein neddylation. As the detection of the lysine neddylation sites by the traditional experimental method is often expensive and time-consuming, it is imperative to design computational methods to identify neddylation sites.
Network medicine for disease module identification and drug repurposing with the NeDRex platform.
Needleman-Wunsch global alignment of two sequences.
Pairwise sequence alignment of DNA or protein sequences using Needleman-Wunsch global alignment.
This program uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length.
Many-to-many pairwise alignments of two sequence sets.
Large-scale genomic prediction with marker-by-environment interaction.
Ultra-sensitive variant caller for multi-sample next generation sequencing data.
Tool for the evaluation of stability changes in proteins caused by amino-acid (AA) mutations.
Main function is to perform EEM parameterization. Can be used to efficiently compute EEM charges, validate them against QM ones and to compute the parameter coverage.
Central European Institute of Technology, Brno
NEFFy is a tool for calculating the Number of Effective Sequences (NEFF) for multiple sequence alignments of proteins, RNA, and DNA. It offers advanced features, scalability, and supports various MSA formats, alongside per-residue NEFF calculation and multimeric protein support.
Collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known 3D structure. It can be used to evaluate protein and domain interactions from new experiments and improve the training of interaction prediction algorithms.
Drug-target interaction prediction based on ensemble learning and logistic regression. This is the repository containing the source code for research, namely NegStacking: drug-target interaction prediction based on ensemble learning and logistic regression.
Incorporating neighbor genotypic identity into genome-wide association studies of field herbivory. R source codes, accession list, and phenotype data used in "Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory on Arabidopsis thaliana" by Yasuhiro Sato, Eiji Yamamoto, Kentaro K. Shimizu and Atsushi J. Nagano
Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq.
A Self-Supervised Framework for Deep Image Denoising.
An interval mapping method for quantitative trait loci underlying plant neighborhood effects. Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects. To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2020) <doi:10.1101/2020.05.20.089474>.
A User-Friendly and Open-Source Implementation of Tree-Based Complex Refractive Index Analysis for Terahertz Spectroscopy.
Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data. NeLS is developed by ELIXIR Norway and funded by the Research Council of Norway. It can be accessed via a web application, web API, and SSH. Online analysis of data is enabled by integrated instances of Galaxy, including a set of pre-defined workflows.
This package allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input a set of pathway components, which were perturbed, and a phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.
An open access data, tools and compute resource operating on neuroelectromagnetic data.
Resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design.
Recognises gene and protein names in biomedical text.
Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation. Neuron Modeling for TMS (NeMo-TMS) toolbox is for multi-scale modeling of the effects of Transcranial Magnetic Stimulation on single neuron activity. The instructions and open-source codes provided here enable users with a different levels of expertese to investigate the neuronal behavior under TMS.
A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain.
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. Source code and data repository associated with the study disclosed in manuscript:. Zahoranszky-Kohalmi et al., A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. Network analysis for therapeutic insights.
Import systems biology markup language data into the graph database Neo4j.
An integrated tool for identification of potential neoantigens. neoANT-HILL is a python toolkit that integrates several pipelines for fully automated identification of potential neoantigens (pNeoAgs) which could be used in personalized immunotherapy due to their ability to elicit and boosting T-cell immune response. It is available as a Docker pre-built image and allows the analysis of single- or multiple samples. As input files is required RNA sequencing reads and/or somatic DNA mutations derived from Next Generating Sequencing.
A multifunctional R package for identification of tumor-specific neoantigens. Abstract It is known that some mutated peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T-cells on the surface of a tumor cell. These peptides are termed neoantigen and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions, and structural variants.
A multifunctional R package for identification of tumor-specific neoantigens. It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
Comprehensive neoantigen database and discovery platform for cancer immunotherapy.
NeoDesign is a computational tool designed to optimize the selection of polyvalent neoantigen combinations for tumor mRNA vaccines. It comprises four modules to minimize linker usage, avoid unexpected neoantigens, and improve mRNA stability.
NeoDisc is a proteogenomic pipeline for identifying immunogenic tumor-specific antigens from multiple sources, integrating genomics, transcriptomics, and immunopeptidomics data. It enables assessment of tumor heterogeneity and the functionality of the antigen processing and presentation machinery, packaged within a Singularity container.
A novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival.
NeoFox (NEOantigen Feature tOolboX) is a toolbox for annotating neoantigen candidates with neoantigen features. NeoFox annotates neoantigen candidate sequences with published neo-epitope descriptors.
Neopeptide discovery in proteomics data.
A Neonatal Resting State fMRI Data Preprocessing Pipeline.
A bioinformatics method for prediction of splice variant neoantigens.
NeoTCR is an immunoinformatics database containing experimentally-supported functional neoantigen-specific TCR sequences. It offers a user-friendly web interface for data retrieval, TCR clonotype analysis, and identification of neoantigen-specific TCRs.
Epitope prediction based on antibody neutralization of viral strains with diverse sequences.
NEPdb is a database of T-cell experimentally-validated neoantigens and pan-cancer predicted neoepitopes for cancer immunotherapy. It contains more than 17,000 validated human immunogenic and non-immunogenic neoepitope entries with human leukocyte antigens (HLAs) and T cell information, curated from published literatures.
NIAID, a cloud based tool for microbiome or metagenomics data analysis. Nephele allows you to process and analyze 16S raw data using pipelines based on QIIME and mothur. It also facilitates WGS functional analyses using bioBakery tools such as MetaPhlAn, HUMMAnN and metagenomic assembly using the a5-miseq/UDBA-UD.
Locate genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies.
An environment for the delivery of genomic medicine. Genomic medicine holds great promise for improving healthcare, but integrating searchable and actionable genetic data into electronic health records remains a challenge. Here, we describe Neptune, a system for managing the interaction between a clinical laboratory and an electronic health record system. Methods< h4> We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis and EHR integration. Results< h4> Neptune enabled the analysis of data for generation of and delivery to EHR systems of over 15,000 clinical genomic reports. These projects demanded customizable clinical reports that contained a variety of genetic data types including SNVs, CNVs, pharmacogenomics and polygenic risk scores
An environment that enables users to identify and report known disease-causing variants in gene sets of interest, to gather curations for potential novel pathogenic variants from an external review system, and to share and update structured genomic knowledge with EHR systems and collaborators.
A web portal providing access to in silico tools for drug discovery. New E-Resource for Drug Discovery. Regioselectivity prediction for phase 1 and phase 2 metabolism.
Biomedical corpus for nested named entity recognition.
A negative data generation framework for machine learning applications of noncoding RNAs.
Nerpa is a tool for linking biosynthetic gene clusters (BGCs) to known nonribosomal peptides (NRPs). BGCs are predicted in genome sequences (FASTA or GBK) with antiSMASH. Known NRPs are accepted in the SMILES format and processed with rBAN.
Corneal confocal microscope images stitching with neural networks.
NerveTracker is a Python-based toolkit for visualizing and tracking nerve fibers in serial block-face microscopy images. It utilizes optic flow and structure tensor algorithms to perform microscopic tractography, offering interactive visualization and manual editing capabilities.
Software Tool to Manage Experimental Data and Its Provenance.
High-throughput sequencing data analysis toolset.
Finding human gene-disease associations using a Network Enhanced Similarity Search (NESS) of multi-species heterogeneous functional genomics data. Network Enhanced Similarity Search (NESS). NESS aggregates and harmonizes heterogeneous graph types including ontologies and their annotations, biological networks, and bipartite representations of experimental study results across species. The tool employs diffusion metrics, specifically a random walk with restart (RWR), to estimate the relations among entities in the graph and to make data-driven comparisons.
A Next-Generation Sequencing Simulator for Metagenomics.
Simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. It is ideal for networks of spiking neurons of any size, for example: 1. Models of information processing e.g. in the visual or auditory cortex of mammals, 2. Models of network activity dynamics, e.g. laminar cortical networks or balanced random networks, 3. Models of learning and plasticity.
Designed to predict the gene essentiality based on protein interaction network and gene expression or CRISPR screen results.
Construct neuronal networks and explore network dynamics
structure-based detection of LTR retrotransposons and their nesting. Software to recursively identify TEs or other inserted sequences and cut them out to enable discovery of similar underlying older sequences.
This software performs feature-level harmonization of radiomic data extracted from medical images. Its primary goal is to reduce variability introduced by differences in acquisition protocols, scanner types, and imaging centers. The tool is based on the ComBat methodology, which uses an empirical Bayes linear model to correct batch effects by estimating location and scale parameters. It offers two harmonization strategies: the ComBat method, which aligns radiomic features to a common scale based on either all centers (ComBat) or a user-defined batch grouping (M-ComBat), and the Nested ComBat method, which enables simultaneous correction for multiple batch effects in hierarchical settings. This tool is intended to improve the robustness and comparability of radiomic features in multi-center studies.
Network-based enrichment analysis of gene sets.
Software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation.
".NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included."
Prediction of substrates of N-acetyltransferase A (NatA).
NetActivity is a Bioconductor package that computes gene set activity scores from previously trained sparsely-connected autoencoders. It enables the combination of bulk RNA-seq and microarray datasets for meta-analyses.
Semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. netAE: network-enhanced autoencoder. Network-enhanced autoencoder (netAE) is a semi-supervised dimensionality reduction method. It was specifically designed to facilitate cell labeling of single cell RNA-sequencing data. This repository was created by Zhengyang (Leo) Dong.
Network alignment tool that allows the identification of conserved protein complexes and pathways across organisms. Predictions to fill missing interaction networks is based on likely conserved interactions based on evolutionary distance. Seven model organisms are included.
NetAllergen-1.0 is a predictive model based on the random forest algorithm. It incorporates novel MHC class II presentation propensity features to improve the allergenicity prediction.
Novel graph clustering technique with significance assessment via hierarchical ANOVA.
Predictions of splice sites in Aspergillus fumigatus and other Aspergillus species DNA sequences.
Matlab software of network-based auto-probit method for protein function prediction.
This package implements a benchmarking of several gene network inference algorithms from gene expression data.
NetBID2 provides comprehensive hidden driver analysis.
A package that provides an effective visualization of large biological networks.
NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Automated Discovery of Biological Process Modules by Network Analysis in R. NetBox is a network-based approach that combines prior knowledge with a network clustering algorithm. The algorithm allows for the identification of functional modules and allows for combining multiple data types, such as mutations and copy number alterations. NetBox performs network analysis on human interaction networks, and comes pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map. GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology.
NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Neural network predictions of C-mannosylation sites in mammalian proteins.
Neural network predictions for cleavage sites of the human proteasome.
An open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II. NetCleave maps reported IEDB peptides to protein sequences in UniProt/UniParc. After the identification of the C-terminal cleavage site, amino acid sequences are coded using QSAR descriptors, including steric, electrostatic and hydrophobic properties. Finally, a neural network architecture is used to generate the predictive model.
Fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data.
Network Construction and Comparison for Microbiome Data in R. NetCoMi (Network Comparison for Microbiome data) provides functions for constructing, analyzing, and comparing networks suitable for the application on microbial compositional data. The package includes existing methods for zero handling, normalization, estimating associations between OTU/taxa as well as dissimilarities between samples. Furthermore, a function for constructing differential association networks including methods for identifying differentially associated taxa is offered.
R package for use in both human protein-protein interaction network analyses as well as analyses of arbitrary networks.
The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.
Determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms’ niches.
A network propagation approach using node coreness. Network propagation using node coreness and a semi-supervised approach for module identification. NetCore is a network propagation approach based on node coreness, for phenotype- genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves better re-ranking of genes after propagation. Furthermore, NetCore implements a semi-supervised approach to identify network modules, which include both well-known genes together with new candidates.
Prediction of Coronavirus 3CL Proteinase cleavage sites on amino acid sequences.
A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.
Prediction of CTL epitopes in protein sequences.
Predict CTL epitopes in protein sequences.
Novel network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks.
The tool predicts whether a single non-synonymous SNP causes a disease or is invariant.
Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. Network-based patient classifier. netDx is a general-purpose algorithm to build a patient classifier from heterogenous patient data.
Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks. The R package NetFrac is used to calculate various distances and indices between species communities in sequence similarity sequence (SSN). Some of these measures are based on the shortest path concept, namely Spp, Spep, Spelp and Spinp distances and the Transfer index, and a few others are adapted from existing concepts in the literature (UniFrac, Motifs). The networks are Igraph objects consisting of nodes and edges.
Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.
A Database of Essential Genes Predicted Using Features From Interaction Networks.
Prediction of glycation of amino groups of lysines in mammalian proteins.
R-Shiny package for network-integrated pathway enrichment analysis. netGO is an R/Shiny package for network-integrated pathway enrichment analysis. netGO provides user-interactive visualization of enrichment analysis results and related networks. and returns a data frame of gene-sets, their p-values, q-values derived from netGO+, Fisher’s exact test and netGO (optional) as well as the scores for the network interaction and overlap.
Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.
Implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. We provide code for formal two-sample testing in Gaussian graphical models (Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (Stadler and Mukherjee, 2013).
The Bayesian Hierarchical Model named Neoantgien-T cell interaction estimation (Netie) is developed to investigate the neoantigens observed in the patient tumors to estimate the history of the impact of the host immune pressure on the evolution of the tumor clones. The estimation results will reveal whether the host immune system has been conferring strong or weaker selection pressure on the tumor clones over the time of tumor development. This may give us a peak into the future of how the mutations and clones will evolve for that patient. The model is based on pyclone/sciclone/phylowgs estimation results.
A Web Server for Prediction of Targets and Therapeutic and Adverse Effects via Network-Based Inference Methods.
Bridging global and local topology in whole-brain networks using the network statistic jackknife. Tools for Working with Samples of Networks. Tools for managing large sets of network data and performing whole network analysis. This package is focused on the network based statistic jackknife method, and implements a framework that can be extended to other network manipulations and analyses.
Linguistic analysis of corpora by means of complex networks.
Agent-based modeling extension linking MATLAB and NetLogo.
A humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS. Given genetic associations from a Phenome-Wide Association Study (PheWAS), a disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between pheno-types. To improve the accessibility of the visualization of shared genetic components across pheno-types, we developed the humaN-disEase phenoType MAp GEnerator (NETMAGE), a web-based tool that produces interactive phenotype network visualizations from summarized PheWAS results.
NetMatch: a Cytoscape plugin for searching biological networks. Searches networks for subcomponents matching a given query. A bioinformatics software platform for the visualization and analysis of biological networks.
Find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models.
On-the-fly knowledge network construction from biomedical literature.
A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Please cite Tal, O.; Selvaraj, G.; Medina, S.; Ofaim, S.; Freilich, S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020, 8, 840. Genome files include species-specific enzymatic reaction content in their EC format. Environment files include lists of metabolites in their KEGG accessions.
Prediction of binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs).
Predict binding of peptides to any known MHC class I molecule.
Predict binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks.
Predict binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules.
Predict binding of peptides to any known MHC molecule using artificial neural networks (ANNs).
Predict the stability of peptide binding to a number of different MHC molecules using artificial neural networks (ANNs).
A network-structured mixture model for reduced-bias estimation of altered subnetworks. NetMix is an algorithm for identifying altered subnetworks with node scores that are distributed differently from other nodes in the network. NetMix improves upon current methods by using a Gaussian Mixture Model to find a less biased estimate of the size of an altered subnetwork. This README is under construction.
Prediction of the leucine-rich nuclear export signals (NES) in eukaryotic proteins.
Predict N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.
Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. .
Produce neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
General framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations: metabolic, reactiomic and genic. It finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.
A non-redundant collection of 125 sequence-based classifiers for linear motifs in phosphorylation-dependent signaling.
Neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
Predict serine and threonine phosphorylation sites in bacterial proteins. This service is closely related to NetPhos, NetPhosK and NetPhosYeast.
A server that produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites.
Predict serine and threonine phosphorylation sites in yeast proteins.
Neural network predictions of cleavage sites of picornaviral proteases.
Neural network predictions of splice sites in Arabidopsis thaliana DNA.
The NET Prediction Utility can be used to compute predicted normalized elution time (NET) values for a list of peptide sequences.
The package is developed to perform network based prediction of unipartite and bipartite networks and use the results to understand the functionality of proteins in an interactome using enrichment analysis.
A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.
Mapping transcription factor networks by exploiting scalable data resources.
Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity. This is the repository for NetQuilt, a multispecies network-based protein function prediction method incorporating homology information with IsoRank.
R package, which provides an implementation for constructing from gene expression data a protein-protein interaction network with StringDB and a weighted gene co-expression network with WGCNA.
Accurate and Fast Maximum Likelihood Phylogenetic Network Inference.
Fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the loss function of the linear model.
Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.
Network-based Rice Expression Analysis Server for abiotic stress conditions.
The Network Seriation and Modularization package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt or other network analysis.
A network analysis pipeline for RNA-Seq time series data.
A JavaScript framework for compositional assessment and comparison of biological networks through Venn integrated Network diagrams. Venn diagrams are frequently used to compare composition of datasets (e.g. datasets containing list of proteins and genes). Network diagram constructed using such datasets are usually generated using 'list of edges', popularly known as edge-lists. An edge-list and the corresponding generated network are however composed of two elements, namely, edges (e.g. protein-protein interactions) and nodes (e.g. proteins). Researchers often use individual lists of edges and nodes to compare composition of biological networks using existing Venn diagram tools.
Network summarization via a hybrid approach leveraging topological properties.
A statistic that integrates protein interaction networks with data from tumor exomes
Gene-network simulator. Simulators are helpful to test and compare the accuracy of different reverse-engineering approaches in a variety of experimental conditions.
It is a package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.
Prediction of solubility and usability of proteins expressed in E. coli
Mathematica software application to split biochemical networks into functional subnetworks.
Neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences.
Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach.
Protein Surface Accessibility and Secondary Structure Predictions.
Re-ranking gene network inference predictions using structural network properties.
Web server for the characterization of directed or rooted reticulate networks, through their assignment to specific categories: “Tree”, “Tree-sibling”, “Tree-child”, “Galled-tree”, “Time-consistent”).
Improving Multitask Transcription Factor Binding Site Prediction with Base-pair Resolution.
Prediction whether an amino acid is located in a Beta-turn or not.
Neural network prediction of splice sites in 5' UTR regions of human genes.
NetVenn is a network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment.
Free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.
networkRF is a tool for disease gene discovery that incorporates network information into a random forest model. It aims to improve identification accuracy when disease genes form modules.
Web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas.
NAP is a network analysis tool and offers: 1) Exploration of a network's topological features 2) Ranking nodes/edge by topological properties 3) Simultaneous comparison of topological features between different networks 4) Basic network visualization
Framework to reconstruct a complete growth history of a present-day network given only a probabilistic model by which the network putatively evolved.
Detect epistasis between SNPs along the edges of a gene-gene interaction network.
A Matlab/Octave toolbox for clustering topological network motifs in large-scale, integrated networks.
The Network of Cancer Genes collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, it provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network.
Designed to perform protein-protein interacton (PPI) network analysis from gene expression data. It integrates differential expression analysis, network construction and network analysis.
Designed to support integrative analysis of gene expression data through statistical, visual and network-based approaches.
An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.
An R package to explore the propagation of extinctions through complex ecological networks. Extinction Simulation in Food Webs. The NetworkExtinction package contains the following man pages: chilean_intertidal CompareExtinctions degree_distribution ExtinctionOrder ExtinctionPlot Less_Connected More_Connected Mostconnected net RandomExtinctions.
A network-based approach for genome-wide association studies in structured populations.
Prediction of in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins.
Create randomised networks and randomize existing, real networks.It can process the statistical information gained from the these networks in order to pinpoint their special, non-random characteristics.
netZoo is a software package for higher-order correction of persistent batch effects in correlation networks. It implements the COBRA method to estimate a batch-corrected gene co-expression matrix, allowing control for continuous and categorical covariates.
Predicting genotype-specific gene regulatory networks. netZooR netZooPy netZooM netZooC. netZoo{R,Py,M,C} is a network biology package for the reconstruction and analysis of gene regulatory networks. If you use netZoo, please cite us using the following format:.
NeuCA is is a neural-network based method for scRNA-seq data annotation. It can automatically adjust its classification strategy depending on cell type correlations, to accurately annotate cell. NeuCA can automatically utilize the structure information of the cell types through a hierarchical tree to improve the annotation accuracy. It is especially helpful when the data contain closely correlated cell types.
A scalable computational framework for multiscale exploration of the brain's dynamical organization.
A data-adaptive Bayesian regression approach for polygenic risk prediction.
Analysis Tools for EM Connectomics. Query and View plugins used by the neuPrintExplorer site to generate reusable query forms and visualisations. Implements a connectomics REST interface that leverages the neuprint data model. neuPrintHTTP can be run in a user authenticated mode or without any authentication. Note: that the authenticated mode (which requires more configuration and setup) is needed to use with neuPrintExplorer web application. The un-authenticated mode is the ideal way to access the neuPrint data programmatically. Python client utilties for interacting with the neuPrint connectome analysis service. exploring inter and intra cellular interactions. Query plugins generate a form to take user input and query the neuPrint cypher api to fetch data from the server.
Neural ADMIXTURE is an unsupervised global ancestry inference technique based on ADMIXTURE. By using neural networks, Neural ADMIXTURE offers high quality ancestry assignments with a running time which is much faster than ADMIXTURE's.
NeuralPolish is a Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks. The method is designed as an alignment feature matrix for representing read-to-assembly alignment. Each row of the matrix represents a read, and each column represents the aligned bases at each position of the contig. In the network architecture, a bi-directional GRU network is used to extract the sequence information inside each read by processing the alignment matrix row by row. After that, the feature matrix is processed by another bi-directional GRU network column by column to calculate the probability distribution. Finally, a CTC decoder generates a polished sequence with a greedy algorithm.
Multi-institutional noninvasive in vivo characterization of IDH, 1p/19q, and EGFRvIII in glioma using neuro-Cancer Imaging Phenomics Toolkit (neuro-CaPTk). CaPTk: Cancer Imaging Phenomics Toolkit. CaPTk is a software platform, written in C++, for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer.
A Solution for Collaborative Pattern Analysis of Neuroimaging Data. The code in this repository is no longer under active development since we are focusing on NEURO-LEARN-DOCKER. Please check it out! :-). NEURO-LEARN is a solution for collaborative pattern analysis of neuroimaging data. This documentation contains everything you need to know about NEURO-LEARN, including the core features of the Web platform and how this tool can be utilized to perform collaborative multi-variate pattern analysis on neuroimaging data.
Electronic health record (EHR) trusted research environment (TRE) to support mental healthcare analytics with real-world data.
An ontology-driven deep learning approach in the NeuroBridge Project.
NeuroCirc is an integrative web-based resource of circRNA expression in the human brain, which allows interactive exploration of circRNA expression across multiple datatsets, including circRNA expression in bulk brain tissue, circQTLs, circRNA expression during neuronal differentiation and cellular maturation. NeuroCirc also allows the upload of user-provided circRNA expression data and its exploration in the integrative platform.
Software for microscale brain network dynamics.
NeuroDebian is a popular turnkey platform for Neuroscience, where software is integrated, tested, and delivered conveniently and reliably so you could concentrate on your research and not on "system maintenance". It provides a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives.
An accessible, flexible, and portable data analysis environment for reproducible neuroimaging.
NeuroDevSim is a Neural Development Simulator for Linux of MacOS environments. It is a parallel and phenomenological computational framework to grow large numbers of neuronal morphologies (and resultant microcircuits) simultaneously according to growth-rules expressed in terms of interactions with the environment and internal variables:.
NeuroEditor is a software tool for visualizing and editing neuronal morphologies, offering both manual editing capabilities and automated error correction algorithms. Users can extend the tool’s functionality by programming custom algorithms in Python.
RESTful API which enables the extraction, visualization, and summarization of published data on neurons’ electrophysiological properties.
Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data.
Cell / Neuron Fluorescent Imaging Toolbox for Matlab
A simulation framework for whole-brain neural mass modeling. To browse the source code of neurolib visit out GitHub repository. Read the gentle introduction to neurolib for an overview of the basic functionality and some background information on the science behind whole-brain simulations.
Structural and functional interpretation of brain maps.
An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data.
Neuromechanical model of adult Drosophila melanogaster.
Sharing and characterizing data-driven neuroscience models described in NeuroML.
NeuroMorpho.Org is a curated inventory of digitally reconstructed neurons and glia, continuously updated with new uploads to facilitate quantitative analysis and computational modeling of neuronal morphology. It's the largest collection of publicly accessible 3D neuronal reconstructions and associated metadata.
Stimulates a neuron and monitor what happens. Pause, rewind, and move forward in time in order to observe the ions as they move across the neuron membrane.
tool to automatically extract, count, and localize calcium signals from the whole x,y-t image series. The tool is useful for an unbiased comparison of activity states of neurons, helps to assess local calcium transients, and even visualizes local homeostatic calcium activity.
NeuronCyto II is an interactive and user‐friendly software package for automatic neurite quantification.
Classification and elastic morphing between neuronal arbors using path-wise similarity. "NeuroPath2Path: Classification and elastic morphing between neuronal arbors using path-wise similarity" - Tamal Batabyal, Barry Condron, Scott T. Acton.
NeuroPG is an open source optical pattern generation software for neuroscience that combines digital micro-mirror device control, sample visualization, and data acquisition in one application.
Prediction tool for neuropeptide precursors (NPPs) and neuromodulators.
For scientific enquiries and technical enquiries
NeuroPIpred is an in silico method, which is developed to predict and design insect neuropeptides with better efficacy for controlling pest from infesting various crops.
The Neuroinformatics for Personalized Medicine toolBox (NeuroPM-box) is a free cross-platform user-friendly multitool software for advanced integration of molecular, histopathological, multimodal neuroimaging, and therapeutic data.
A New Model for Predicting Neuropeptides Based on Embeddings of BERT.
NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.
NeuroPred-FRL is an interpretable prediction model for identifying neuropeptide using feature representation learning.
Interpretable and robust model for neuropeptide prediction by protein language model.
A Python Toolbox of Representational Analysis from Multi-modal Neural Data. A Python Toolbox for Multimode Neural Data Representation Analysis. NeuroRA is an easy-to-use toolbox based on Python, which can do some works about RSA among nearly all kinds of neural data, including behavioral, EEG, MEG, fNIRS, sEEG, ECoG, fMRI and some other neuroelectrophysiological data. In addition, users can do Neural Pattern Similarity (NPS), Spatiotemporal Pattern Similarity (STPS) & Inter-Subject Correlation (ISC) on NeuroRA.
A dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Information Framework advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.
NeuroSpeech is a software for modeling pathological speech signals considering different speech dimensions: phonation, articulation, prosody, and intelligibility.
Compilation, curation and exploration of a knowledgebase of environmental neurotoxicants specific to mammals. Neurotoxicants are an important class of hazardous chemicals.
Integrating, validating, and sharing neurodata analysis workflows.
Explainability of deep neural networks for MRI analysis of brain tumors.
Improving locus recovery from the Angiosperms353 probe set. Bioinformatic sequence recovery for universal target-capture bait kits can be substantially improved by appropriate tailoring of target files to the group under study. mega353.fasta A target file for use with target enrichment datasets captured using the Angiosperms353 bait kit.
Integrating literature, sequence, and variation data in a central hub for uORF research.
A web server to predict New use of Old Drugs to facilitate drug repurposing.
The assembly/mapping program developed by 454 Life Sciences for of 454 data
Identify CpG islands in nucleotide sequence(s).
Predicts the DNA-binding proteins when input a protein sequence (Fasta format)
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
Create a sequence file from a typed-in sequence.
Taxonomy database maintained by the UniProt group.
Database of data from the newt Notophthalmus viridescens. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publically available gene sequences.
A comprehensive web-based tool for viewing, constructing, and analyzing biological maps. Welcome to Newt Pathway Viewer & Editor. Newt is a free, web based, open source viewer and editor for pathways in Systems Biological Graphical Notation (SBGN) and Simple Interaction Format (SIF). It was written with a series of libraries and extensions based on Cytoscape.js with utmost customization in mind.
NX is a general-purpose program package for simulating the dynamics of electronically excited molecules and molecular assemblies.
A scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data.
Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes
The Next-Generation (NG) IEDB Tools website provides a redesigned interface for epitope prediction and analysis algorithms, consolidating HLA class I epitope tools and enabling data pipeline building. It provides access to tools for MHC binding, elution, immunogenicity, processing, epitope clustering, and PEPMatch.
The platform enables biologists to examine a gene, protein, compound or disease of interest in a global, biological, or clinical context.
A software suite to analyse and model toxicogenomics data.
Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.
Tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries.
NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.
NextDose is a free, web-based dose calculator employing Bayesian forecasting and target concentration intervention for multiple medications, including voriconazole. The calculator's predictive performance has been evaluated in pediatric patients.
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Designed to perform near real-time tracking of influenza virus evolution.
A collection of links to scripts available for working with data generated by new sequencing technologies.
De novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS. A desktop application for analyzing next generation sequencing data. It does not require scripting.
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.
A comprehensive pipeline for computational neoantigen prediction.
NEXTorch is an open-source software package in Python/PyTorch to faciliate experimental design using Bayesian Optimization (BO).
neXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.
This node module contains methods to access the neXtProt API as well as the SPARQL endpoint.
A meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. It integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose.
NexusLIMS is a laboratory information management system for shared-use electron microscopy facilities.
An interactive and programmable visualization of biological networks in Python.
Workflow optimized for the analysis of rare diseases, designed to detect SNVs and INDELs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow.
nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data.
nf-core/cageseq is a bioinformatics analysis pipeline used for CAGE-seq sequencing data.
nf-core/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
This pipeline is based on the HiC-Pro workflow. It was designed to process Hi-C data from raw FastQ files (paired-end Illumina data) to normalized contact maps. The current version supports most protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C. In practice, this workflow was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data.
nf-core/methylseq is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
nf-core/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.
Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. It's built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline used for small RNA sequencing data.
nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, produces standardised output tables.
nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports short-read Illumina sequencing data from both shotgun (e.g. sequencing directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based).
nf-core/airrflow is a bioinformatics best-practice pipeline to analyze B-cell or T-cell repertoire sequencing data. The input data can be targeted amplicon bulk sequencing data of the V, D, J and C regions of the B/T-cell receptor with multiplex PCR or 5' RACE protocol, single-cell VDJ sequencing using the 10xGenomics libraries, or assembled reads (bulk or single-cell). It can also extract BCR and TCR sequences from bulk or single-cell untargeted RNAseq data. It makes use of the Immcantation toolset as well as other AIRRseq analysis tools. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.
Portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.
Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.
nf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes.
nf-core is a community-led effort providing standardized analysis pipelines built on Nextflow, facilitating FAIR bioinformatics research and enabling collaboration within the scientific community. It provides a library of modules and subworkflows to streamline data analysis workflows.
nf-core/proteinfamilies is a bioinformatics pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits.
nf-encyclopedia is a NextFlow pipeline specifically designed to analyze DIA proteomics experiment that leverage chromatogram libraries; however it is perfectly suited to analyze DIA proteomics experiments without chromatogram libraries as well. The nf-encyclopedia connects three open-source tools---MSconvert, EncyclopeDIA, and MSstats---to go from mass spectra to quantified peptides and proteins.
nf-gwas is a Nextflow pipeline for performing highly parallelized and reproducible genome-wide association studies (GWAS) on biobank-scale data. It automates preprocessing and analysis steps, integrates regression modeling, and provides comprehensive reporting with interactive visualizations.
A Nextflow pipeline for obtaining raw read counts from RNA-seq data using a given reference genome and annotation.
A Nextflow pipeline for the identification and taxonomic classification of foreign/microbial reads reads from high throughput RNA-seq sequencing data
Combine experimental gene expression profiles and data from publicly available databases to identify conditions or experiments that induce similar or opposite gene expression patterns.
NFnetFU (Neuro Fuzzy network Fusion) is a modularised integrative pipeline for microbiome data analysis and diseases specific prioritisation for targeted research which addresses problems surrounding collinearity, sparsity and effect size in data..
Characterizing and Comparing of Annotated Biological Networks.
Next-generation Circos for data visualization and interpretation. NG-Circos - interactive circos for biological data. Circos plots are widely used to display multi-dimensional next-generation genomic data, but existing implementations of Circos are not interactive or can incorporate only limited types of data. Here, we developed Next-Generation Circos (NG-Circos), a flexible JavaScript-based circular genome visualization tool for designing highly interactive Circos plots using 21 functional modules with various data types.
Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions.
nGauge is a Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology. The library structure makes automation of data analysis pipelines easier, leading to faster and more reproducible results.
The National Genomics Data Center (NGDC) provides a data portal and resources for plant genomics, including transcriptomic profiles, variant associations, and the Plant Editosome Database. It also includes the BIG Search engine for biomedical data access.
Plant Genomic Resources at National Genomics Data Center
Tool for publication-ready visualization of syntenic relationships across multiple genomes.
Web application for molecular visualization. It is employed to display molecules like proteins and DNA/RNA with a variety of representations.
An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 85.3% to 91.4% across species.
Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer.
A resource of gene and protein expression in NGLY1 deficient patient-derived cell lines. Currently the dataset comprises bulk gene and protein expression data dervied from 31 donors (14 NGLY1-deficient children, 17 parent controls) representing 4 different cell types.
An automated library building tool to align highly divergent HIV envelope sequences. Verify that version 9.8 (R2020a) of the MATLAB Runtime is installed. NGlyAlignApp_v1.exe -MCRInstaller.exe Note: if end users are unable to download the MATLAB Runtime using the instructions in the previous section, include it when building your component by clicking the "Runtime included in package" link in the Deployment Tool. -This readme file.
An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.
Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa. NGOME-Lite is a fast algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. NGOME-Lite does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Just protein sequences in FASTA or multi-FASTA format is needed to run NGOME-Lite. Prediction of spontaneous asparagine deamidation at a proteomic scale.
Simulation of next-generation proteomics (NGP) based on single-molecule sequencing.
Classification of adaptor proteins using recurrent neural networks and PSSM profiles. Adaptor proteins are carrier proteins that play a crucial role in signal transduction. We collected all the proteins from UniProt with GO molecular function annotations related to adaptor proteins.
An efficient tool for combining multiple NGS data tracks using minimum Bayes' factors. NGS Integrator Tool (NGS-Integrator) is a Java-based tool that integrates multiple genome-wide NGS data via the minimum Bayes' Factor from density of sequence reads mapped on the genome. To integrate multiple NGS data, homogeneous replicates or heterogeneous NGS data can be integrated into the single data track based on the complements of the minimum Bayes factor (cMBF) (range: 0-1) calculated from signal-to-background noise ratios as a function of genomic position. NGS-Integrator is a Java-based commandline tool that integrates multiple genome-wide NGS data via the minimum Bayes' Factor from density of sequence reads mapped on the genome.
Complete solution for human re-sequencing projects.
High-throughput primer design for multiplex polymerase chain reactions. NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design. It includes four Python-scripts:. NGS-PrimerPlex can be run as a Docker image. In this way you only need to install Docker (for windows 7 users this install steps should be performed). If you have "VD-x, VD-t error", you need to turn on virtualization in BIOS CPU section.
Comparative analysis between ChIP-seq and other enrichment-related NGS datasets requires prior characterization of their degree of technical similarity. The Galaxy tool NGS-QC Generator is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.
Collection of command-line scripts for providing annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl.
Next Generation Sequencing Transcriptome profile explorer.
Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.
A Bioconductor package for managing FastQC reports and other NGS related log files. The shiny app that accompanies the ngsReports R package
ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descriptions.
This tool simulates an Illumina run and provides plots of false positives and false negatives. It allows for a range of simulation parameters to be set.
Tool to assess the efficiency of targeted enrichment sequencing.
RNA-seq analysis of non-model species using cloud computing.
ngsComposer is an automated pipeline for empirically based NGS data quality filtering.
Provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer.
Multicomponent pipeline for NGS using a set of versioned, modular and reusable container building blocks.
Population genetic analysis of next-generation DNA sequencing data with Julia language. Templates and functions in Julia language to process next-generation sequencing (NGS) data for population genetic analysis. ngsJulias receives NGS data files as input and provides routines and functions to parse files, perform data filtering and implement custom population genetic analyses.
Database that contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. The database is currently populated with human, mouse and Arabidopsis data.
A medium for the representation and exchange of NGS data.
R package to estimate the optimal window size in the analysis of very low coverage next-generation sequence data.
Used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.
A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data. Estimating relatedness coefficients from admixed populations. It can take called genotypes in PLINK format and genotype likelihoods in a beagle format. The method is implemented in an R package and as a commandline based C++ program embeded in the R package.
Tool for researchers concerned with target enrichment issues in next-generation sequencing. It evaluates the target enrichment performance of target regions given in BED format and outputs summary statistics, visualizations, and some additional files giving details on the analysis.
Collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data.
NGSUtils is a suite of software tools for working with next-generation sequencing datasets
High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.
An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis.
Protocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available).
nhKcr is a bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identification of Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and expensive when compared with computational approaches. To date, several predictors for Kcr site prediction have been developed, most of which are capable of predicting crotonylation sites on either histones alone or mixed histone and nonhistone proteins together. These methods exhibit high diversity in their algorithms, encoding schemes, feature selection techniques and performance assessment strategies. However, none of them were designed for predicting Kcr sites on nonhistone proteins.
Allows to predict binding peptide for 67 MHC Class I alleles. This also allow to predict the proteasome cleavage site and binding peptide that have cleavage site at C terminus (potential T cell epitopes).
U-Net Model for Brain Extraction on Non-human Primates. U-Net model and PRIME-DE skull-stripped brain masks (pre-release). This is a pre-release of skull-stripped brian masks of T1w images for 136 macaque monkeys (20 sites) from PRIME-DE. The masks are created from a convolutional network - UNet model, initially trained on a human sample and upgraded with macaque data.
Program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).
Implements a method for deffining causal networks corrected for the problem of interference between dynamically similar regulators within the context of a sparse linear auto-regression model.
Network-informed adaptive positive-unlabeled learning for disease gene identification.
Server to help the analysis of the conformational preferences of amino acid residues in proteins.
Genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database has plant and microorganism search systems to provide information on research materials, including passport and evaluation data for genetic resources with the desired properties. A database of plant diseases in Japan has been developed based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan.
NIBNA is a network-based node importance approach for identifying breast cancer drivers. Specifically, the well-known Louvain algorithm is used for detecting communities, and a centrality-based metric is used to compute node importance by measuring the distortion in the community structure upon the node's removal from the network.
World-wide gel-based proteomics database.
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.
NiCo is a computational framework that integrates single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing data to infer the influence of the spatial niche on the cell state. It identifies extrinsic drivers of cell state modulation by niche covariation analysis.
NIDM is a tool for network impulsive dynamics on multiplex biological network for disease-gene prediction.
Predictor that can be used to predict if your binding peptides are Naturally Presented Peptides (NPP) or parts of any protein are NPP.
This service will retrieve registry data records from NIF.
Non-negative Independent Factor Analysis for single cell RNA-seq. The main function is NIFA() and there is a simulated example under the directory inst/doc/vignette.R.
An informatics program for identification of NifH proteins using deep neural networks.
A software package for multi-contrast Magnetic Resonance Imaging that provides a unified model-fitting framework.
Python package for quantitative analysis of dynamic PET data.
Software platform, offering high-throughput PET image reconstruction as well as image processing and analysis.
NiftyTorch is a Python framework for deploying deep neural networks for Neuroimaging research.
Adapting Surface Normal Knowledge for Intrinsic Image Decomposition in Indoor Scenes.
An R/CRAN package to accomplish NomInal data Mining Analysis.
A Negative Binomial Regression based Integrative Method for Mutation Burden Analysis. Identifying highly mutated regions is a key way that scientists can use on population scale sequencing to discover key genomic regions associated with complex diseases such as cancer.
a gene regulatory network inference approach based on multi time delays causal entropy. NIMCE is a network inference method based on information-theoretic to reconstruct GRNs.
Gene regulatory network inference using multiple ensemble feature importance algorithms.
NinimHMDA: Neural Integration of Neighborhood Information on a Multiplex Heterogeneous Network for Multiple Human Microbe-Disease Association Types Prediction.
Nearly Infinite Neighbor Joining Application
Software to identify the NIP (normalized interface packing) and NSc (normalized surface complementarity) at the protein-protein contacts. The software has shows demonstrated performance in discriminating biological interfaces from non-biological one. The time efficient performance of the software allows the integration in the large scale screening of protein-protein contacts.
nipalsMCIA is an R package implementing Multiple Co-Inertia Analysis (MCIA) for dimensionality reduction in multi-block datasets. It utilizes a modification to the Nonlinear Iterative Partial Least Squares (NIPALS) method and provides options for preprocessing and variance explained calculation, supporting single-cell and bulk-omics studies.
Method to predict nuclear import activity based on characterization of NLS-import receptor interaction using molecular interaction energy components (MIECs).
Rapid k-mer-based software package for detection of fetal aneuploidies.
Toward optimal fingerprint indexing for large scale genomics.
In order to estimate the coefficient of the gene interactions NIR solves a linear regression problem for each gene considering a fixed number of k regressors. The regressor set is chosen according the residual sum of square error (RSS) minimization criterion. In this version, this tool exhaustively searches the best regressors in the space of all the possible k-tuples of genes.
NIRSpredict is a Shiny application that predicts plant traits from near-infrared spectroscopy data. It provides predictions of 81 Arabidopsis thaliana traits and allows users to submit their own datasets to extend the database.
NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Available for several platforms including Windows, MacOS, Linux and Solaris.
Scalable Species Tree Inference with External Constraints.
A Toolkit for Generating Analytic Specifications for Data Visualization from Natural Language Queries. NL4DV is a Python toolkit that takes a natural language (NL) query about a given dataset as input and outputs a structured JSON object containing Data attributes, Analytic tasks, and Visualizations (Vega-Lite specifications).
Bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.
Manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.
The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.
MATLAB script for estimating parameters in NLME growth models
NLoed (suggested pronounciation: "en-load") is an open source Python package for building and optimizing experimental designs for fitting nonlinear models, with a specific emphasis on applications in systems biology. The package is primarily focused on generating optimal designs for improved parameter estimation using a relaxed formulation of the design optimization problem. Objectives in NLoed are primarily based on the expected Fisher information matrix.
Predicting Discharge Disposition Following Meningioma Resection Using a Multi-Institutional Natural Language Processing Model. This application predicts likelihood of home discharge following craniotomy for meningioma resection.
Natural Language Processing Algorithm for Detection of Incidental Durotomy in Operative Notes.
Exploring the Universe of NLP Papers. Understanding the current research trends, problems, and their innovative solutions remains a bottleneck due to the ever-increasing volume of scientific articles. In this paper, we propose NLPExplorer, a completely automatic portal for indexing, searching, and visualizing Natural Language Processing (NLP) research volume. NLPExplorer presents interesting insights from papers, authors, venues, and topics.
NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.
Tool to rapidly annotate the NLR (nucleotide-binding leucine-rich repeat) complement from sequenced plant genomes.
Bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity.
NLRscape is an interactive atlas of plant NLRs equipped with a collection of easy, ready to use bioinformatic tools aimed for the exploration of the complex sequence landscape of this class of receptors in plants.
Simple Hidden Markov Model for nuclear localization signal prediction.
Modeling the Domain Shift for Crowd Counting. PyTorch implementations of the paper: "Neuron Linear Transformation: Modeling the Domain Shift for Crowd Counting (T-NNLS, 2021).".
Predicting 2’-O-Methylation (Nm) Sites in Nanopore RNA Sequencing Data.
Tool for systematic classification of nonsense mediated decay (NMD) events.
A Network-Based Drug Repurposing Method Via Non-Negative Matrix Factorization.
Implements the Non-negative Matrix Factorization (NMF) algorithm by making use of Graphics Processing Units (GPUs).
The theory and methods behind NMFF are based on searching along a few lowest frequency normal mode vectors, constructed from a multi-resolution elastic network representation of the atomic structure of interest, to maximize the correlation between the computed electron density for the flexible model and the experimental density.
NMFNA: a non-negative matrix factorization network analysis method for identifying communities and characteristic genes from pancreatic cancer data. we have provided demo data and Pancreatic Cancer data for NMFNA, if you want to run NMFNA method, please run the script "Demo.m" directly.
High-throughput morphological screening of neuromuscular junctions identifies subtle changes in mouse neuromuscular disease models. NMJ-Analyser requires NMJs to be separated by at least 20um. Images which contain superimposed NMJs are not ideal for analysis. The NMJ Analyser takes as input directories where jpg or png files have been stored.
Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
Database of novel protein families from microbial metagenomes and metatranscriptomes.
De Novo Molecule Identification from NMR Spectra. Molecule identification from NMR spectrum using de novo molecule generator. This code is for reference only as it requires MPI and Gaussian environment which is hard to ensure among different clusters. Also, for the NMR spectrum prediction part, we have used a Gaussain encapsulation package which we can not make public for now. Replacing this part by a traditional Gaussian code or other NMR spectrum prediction method would solve the problem.
NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.
Cloud-based virtual machine loaded with NMR software.
Provides a simple and fast NMR protein structure refinement.
Identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences.
Enhanced software for biomolecular NMR spectroscopy.
NMRium is a web-based software for processing and interpreting 1D and 2D NMR data, designed for both teaching and analytical chemistry. It allows students to analyze spectra directly from a web browser and provides a user-friendly interface for data processing and structure elucidation.
NMRlipids Databank is a community-driven database providing programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. The data can be used for data-driven analyses and machine learning applications to understand cellular membranes.
This tool is used to support the nmrML data standard for nuclear magnetic resonance raw data in metabolomics. It converts native Bruker, Jeol and Agilent vendor formats into the open access nmrML data standard that is used by an ever-so growing number of small molecule NMR repositories.
Deep learning approach to automated peak picking of protein NMR spectra (part of a Dumpling software).
An interactive 1D NMR spectra processing tool dedicated to metabolomics. This open source software provides a complete set of tools for processing and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.
ibrary for reading, writing, and accessing BMRB entries in NMR-STAR and JSONized NMR-STAR formats.
An online platform for automated biomolecular NMR spectra analysis.
Webserver for modeling biologically relevant protein conformational changes. The approach has been shown to reproduce experimentally observed conformational variabilities in the case of domain and loop motions and is able to generate meaningful pathways of conformational transitions.
Prediction of breast cancer proteins using molecular descriptors and artificial neural networks. neural-networks-for-breast-cancer-proteins. Machine Learning for breast cancer protein screening. This project is a collaboration from different institutions:.
Neural network-based model for prediction of mRNA sub-cellular localization using distance-based sub-sequence profiles.
Discovering sequence motifs in quantitative peptide data. It allows generating artificial neural network models of receptor-ligand interactions. It takes as input a set of ligand sequences with target values; it returns a sequence alignment, a binding motif of the interaction, and a model that can be used to scan for occurrences of the motif in other sequences.
Using 2D-recursive neural networks, it is a web server for predicting protein contact maps.
The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes.
Mean-Field Based Analysis Tools for Neuronal Network Models.
Nearest Neighbor Networks is a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated.
This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
Neural network program for analysing case-control multi-locus genotype data using a permutation test.
A neural network-based method for polypharmacy side effects prediction.
nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. In 3D biomedical image segmentation, dataset properties like imaging modality, image sizes, voxel spacings, class ratios etc vary drastically. In current research practice, segmentation pipelines are designed manually and with one specific dataset in mind.
nnU-Net is a self-configuring method for deep learning-based biomedical image segmentation, developed by the Applied Computer Vision Lab (ACVL) of Helmholtz Imaging and the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). It is designed to automatically adapt to a given dataset, analyzing the provided training cases to configure a matching U-Net-based segmentation pipeline without requiring expertise from the user. The tool provides pretrained models for Pancreas and Pancreas tumor segmentation, Colon cancer primaries segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation, Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus (MR data) segmentation
The Neural Network Verification Tool for Deep Neural Networks and Learning-Enabled Cyber-Physical Systems. This paper presents the Neural Network Verification (NNV) software tool, a set-based verification framework for deep neural networks (DNNs) and learning-enabled cyber-physical systems (CPS). The crux of NNV is a collection of reachability algorithms that make use of a variety of set representations, such as polyhedra, star sets, zonotopes, and abstract-domain representations. NNV supports both exact (sound and complete) and over-approximate (sound) reachability algorithms for verifying safety and robustness properties of feed-forward neural networks (FFNNs) with various activation functions. F
The NOA (Network Ontology Analysis) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges.
Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases.
Facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.
NoD is a predictor of nucleolar localization sequences (NoLSs) in proteins. NoLSs are short basic motifs that localize proteins to the nucleolus, a sub-compartment of the nucleus. You can search the set of NoLSs predicted in 9531 human proteins out of the 43534 human proteins considered (from IPI version 3.40).
Predicting protein subcellular location using learned distributed representations from a protein-protein network | Predicting protein subcellular location using node embedding | we present a deep learning based method, node2loc, to predict protein subcellular location. node2loc first learns distributed representations of proteins in a protein-protein network, which acquires representations from unlabeled data for downstream tasks. Then the learned representations are further fed into a recurrent neural network (RNN) to predict subcellular locations | To identify the functions of a protein, we first need know where this protein is located. Interacting proteins tend to locate in the same subcellular location. Thus, it is imperative to take the protein-protein interactions into account for computational identification of protein subcellular locations
Accurately modeling biased random walks on weighted networks using node2vec+.
Network-Oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. Rapid development of high-throughput technologies has permitted the identification of an increasing number of disease-associated genes (DAGs), which are important for understanding disease initiation and developing precision therapeutics. However, DAGs often contain large amounts of redundant or false positive information, leading to difficulties in quantifying and prioritizing potential relationships between these DAGs and human diseases. Here, a network-oriented gene entropy approach (NOGEA) is proposed for accurately inferring master genes that contribute to specific diseases by quantitatively calculating their perturbation abilities on directed disease-specific gene networks.
Remove mark-up (e.g. HTML tags) from an ASCII text file.
Effects of technical noise on bulk RNA-seq differential gene expression inference. Abstract Motivation Inconsistent, analytical noise introduced either by the sequencing technology or by the choice of read-processing tools can bias bulk RNA-seq analyses by shifting the focus to the variation in expression of low-abundance transcripts; as a consequence these highly-variable genes are often included the differential expression (DE) call and impact the interpretation of results. Results To illustrate the effects of “noise”, we present simulated datasets following closely the characteristics of a H.sapiens and a M.musculus dataset, respectively, highlighting the extent of technical-noise in both a high inter-individual variability ( H. sapiens ) and reduced variability ( M. Musculus ) setup.
Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.
Learning Self-supervised Denoising from Corrupted Image. PyTorch Code for "Noisy-As-Clean: Learning Self-supervised Denoising from Corrupted Image", TIP 2020. To reproduce the results in the NAC paper:. Training and test for Set12 at the same time.
Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output.
A decoy-free approach to the identification of peptides.
NoLiTiA is a free, open-source Matlab toolbox for nonlinear time series analysis. It incorporates methods from dynamical systems theory, recurrence quantification analysis and information theory.
Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.
Analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major Mycobacterium tuberculosis lineages.
Homolgy-driven assembly tool to create a NOn-redundant protEin Sequence Set for mass spectrometry.
Quantifying morphometric deviation from normality over the lifetime in the adult human brain. NOrmative Morphometry Image Statistics. NOMIS is a free tool to compute normative morphometric values for FreeSurfer 6 developed by the MEDICS laboratory at the CERVO Brain Research Centre / Universite Laval, Quebec, Canada.
Dynamic prediction of long-term survival in patients with primary gastric diffuse large B-cell lymphoma | BACKGROUND:This study investigated a large number of patients to develop a predictive nomogram for survival and a web-based survival rate calculator that can dynamically predict the long-term survival of patients with primary gastric diffuse large B-cell lymphoma. METHODS:A total of 2647 patients diagnosed with primary gastric diffuse large B-cell lymphoma from 1998 to 2014 were extracted from the SEER database. We used the Lasso Cox regression model to identify independent risk factors for long-term survival and to develop a predictive nomogram for survival and a web-based survival rate calculator. RESULTS:The median (mean) follow-up time was 30 months (52.8 months). Cancer-specific survival rates decreased with time, while the 5-year conditional survival increased with time
An open-source python package for processing high resolution mass spectrometry data on natural organic matter.
This tool identifies antiviral peptides (AVPs) and predicts their functional types using a two-stage computational framework integrating contrastive learning and multi-feature fusion. A user-friendly web interface is available for accessing the tool’s functionality.
It is a non-canonical (non-B) structure database database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively.
The code simulates magnocellular cells in Retina and lateral geniculate nucleus.
A statistical non-parametric multivariable test based on the Fisher's method for combination of partial tests.
Non-parametric Multivariate Permutation Test
Prediction of Thiopurine Metabolite Levels Based on Haematological and Biochemical Parameters. Absolute number of lymphocytes [x10^9/l]. Imuputed absolute number of lymphocytes data:.
Robust and efficient prediction of non-classically secreted proteins by integrating subset-specific optimal models of imbalanced data. Nonclassically secreted proteins (NCSPs) are proteins that are located in the extracellular environment although the lack of known signal peptides or secretion motifs. In this work, a new computational predictor was developed for NCSP prediction of gram-positive bacteria. The subset-specific optimal feature combination process was adopted to characterize the original data from different aspects, and all subdataset based models were integrated into a unified model NonClasGP-Pred, which achieved an excellent performance and outperformed state-of-the-art available toolkits. Prediction of non-classically secreted proteins of Gram-positive bacteria.
Database of all kinds of noncoding RNAs (except tRNAs and rRNAs). It also provides an efficient search option, allowing recovery of sequence, related publications and other information.
Exon array-based detection of long non-coding RNAs.
A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that aim to potentially provide a high-quality data resource for exploring drug sensitivity resistance-related ncRNAs in various human cancers. ncRNA are RNA molecular that do not encode proteins, but are involved in gene regulation and cellular functions in variety of human diseases, including neurodegenerative diseases and cancers. Here, we developed NoncoRNA which contained 8233 entries between 5568 ncRNAs and 154 drugs in 134 cancers. Each entry in the NoncoRNA contains detailed information on the ncRNAs, drugs, and cancers, the ncRNA expression pattern and experimental detection techniques, drug response and other targets, literature references, and other information
Methods to model and impute non-detects in the results of qPCR experiments.
Correct nonlinear drift distortions in scanning probe images.
Nonlinear Drift Correction from Scanning Probe Microscopy (SPM) Orthogonal Image Pairs
Computes Michaelis-Menten model parameters
Estimate metagenomic coverage and sequence diversity
Software for design of hard-to-synthesize structures.
R function for compound, adducts and ion series detection using isotopic distributions.
k-mer based motif discovery in ChIP-Seq data without peak calling. NoPeak: Binding Motif Discovery from ChIP-Seq Data without Peak calling. Binding motif discovery through Chromatin immunoprecipitation with high-throughput DNA sequencing (ChIP-Seq) data is an important tool for understanding regulatory processes. The NoPeak Software uses the integration profile of k-mers based on mapped reads.
Non-coding RNA Sets Cis Enrichment Tool (NoRCE) performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out by using the functional annotations of the coding genes located proximally to the input ncRNAs. NoRCE allows incorporating other biological information such as the topologically associating domain (TAD) regions, co-expression patterns, and miRNA target information.
NOREC4DNA is an all-in-one Suite for analyzing, testing and converting Data into DNA-Chunks to use for a DNA-Storage-System using integrated DNA-Rules as well as the MOSLA DNA-Simulation-API.
Remove carriage return from ASCII files.
NORmalization and EVAluation of MS-based metabolomics data. Enables performance evaluation of various normalization methods from multiple perspectives. In particular, it integrates 5 well-established criteria, each with a distinct underlying theory, to ensure a more comprehensive evaluation than any single criterion. Moreover, it provides various available and popular normalization methods, with a unique feature of allowing quality control based correction sequentially followed by data normalization.
A platform for curated products from novel open reading frames prompts reinterpretation of disease variants.
NORMA is a handy tool for interactive network annotation, visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Annotations and/or node groups can be precomputed or automatically calculated and users can combine several networks and groupings they are interested in. Annotated networks can be visualized using both pie-chart nodes and shaded convex hulls and can be shown using several layouts while users can isolate the groups of interest interactively. In addition, NORMA is suitable for direct comparison of topological features between one or more networks.
NOrMAL (NucleOsome Mapping ALgorithm) is a command line tool for accurate placing of the nucleosomes. It was designed to resolve overlapping nucleosomes and extract extra information (“fuzziness”, probability, etc.) of nucleosome placement.
To calculate NTCP models for rectal and bladder toxicity based on DVHs
This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
A tool for overviewing the effects of different normalisation methods on omics data.
A tool for analysis of normalisation effects on quantitative omics data and for subsequent differential expression analysis. The tool provides multiple normalisation methods and access to different statistical tests and generates reports and data matrices
Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry.
An R package to remove systematic biases in genome architecture mapping data. normGAM is an R package for normalizing genome architecture mapping (GAM) data. It implements five normalization methods, including normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), iterative correction and eigenvector decomposition (ICE), and Knight-Ruiz 2-norm (KR2). The normalization procedure can remove known and unknown systematic biases, the known biases including window detection frequency, fragment length, mappability, and GC content.
Tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies. GitLab is a single application for the entire software development lifecycle. From project planning and source code management to CI/CD, monitoring, and security.
Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.
Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.
Tool for evaluation, selection and visualization of RNA-Seq normalization methods.
Grant 2R01-LM07329-01 from the National Library of Medicine
Identification unstructured loops from sequence.
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
A stochastic agent-based transmission chain simulation framework in R. A Forward Agent-Based Transmission Chain Simulator. The aim of nosoi (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. bioRxiv 2020.03.03.973107). It is named after the daimones of plague, sickness and disease that escaped Pandora’s jar in the Greek mythology. nosoi is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
Remove whitespace from an ASCII text file.
Replace tabs with spaces in an ASCII text file.
Write to file a subset of an input stream of sequences.
Software tool that offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks.
Program designed to analysis complexome profiling data.
The algorithm presented here segments retinal blood vessels with a high degree of accuracy.
Novel Retinal Vessel Segmentation Algorithm: Fundus Images
A computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data
NOVIFAST is a fast algorithm for accurate and precise VFA MRI. A fast non-linear least squares method for accurate and precise estimation of T1 from SPGR signals.
Tool designed for mapping short reads from Illumina, IonTorrent or 454 platforms onto a reference genome. This is a commercial product.
Tool designed for mapping short reads in color space from the SOLID platform onto a reference genome. This is a commercial product.
A Bayesian network approach for de novo variant calling from pedigree and population sequence data. novoCaller is a Bayesian de novo variant calling algorithm that uses information from read-level data both in the pedigree and in unrelated samples. The method was extensively tested using large trio sequencing studies, and it consistently achieved over 98% sensitivity while giving significantly more specificity than other well known methods for the same sensitivity values.
Program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.
Software for hidden Markov model for de novo peptide sequencing.
NovoLign is a metaproteomics pipeline that performs sequence alignment of *de novo* sequences to enable rapid taxonomic profiling and evaluation of database searching outcomes. It supports the creation of reference sequence databases and is publicly available via GitHub.
Fast, real-time peptide ''de novo'' sequencing engine.
novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data. An existing reference database of marker genes is not required, but significantly enhances performance if available.
NOVOWrap is an automated solution for plastid genome assembly and structure standardization.
A Large, Systematic, and Extendable Repository of 3D Reconstructed Images of a Living Human Brain Cum Head and Neck.
The NP-MRD is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD accepts NMR data and associated metadata from newly undertaken NP studies.
NP Analyst is a platform-independent tool for integrating bio-activity data with metabolomics data.
NP_Fingerprints is a Python package for computing molecular fingerprints, designed for evaluating their performance on natural product chemical space. The tool addresses the challenges of encoding natural products and provides an open-source solution for computing various fingerprints and analyzing their suitability for bioactivity prediction.
Computational and graphical representation tool for gene identification and sequence annotation. Identifies sequence segments of any length with statistically-significant 3-base compositional periodicities and associated with ORF structures .
NPACT is a curated database of Plant derived natural compounds that exhibit anti-cancerous activity.
npact : Naturally occuring Plant based Anticancerous Compound-Activity-Target DataBase
nparACT computes the interdaily stability (IS), intradaily variability (IV) and relative amplitude (RA) of activity and gives the start times and average activity values of M10 (i.e. the ten hours with maximal activity) and L5 (i.e. the five hours with least activity) from actigraphy data.
Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science.
Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning. The Natural Product Atlas MAP4 TMAP colored by fungal (in magenta) or bacterial (in green) origin. a first jupyter lab notebook containing the code to reproduce this work NPAtlas.ipynb;. The Natural Products Atlas Network views of chemical space.
A chemical data resource with relational data between natural products and biological sources. NPBS Database of Shanghai Institute of Organic Chemistry.
A new PacBio sequencing simulator is developed for producing CLR reads. It simulator firstly samples the read sequences according to the read length logarithmic normal distribution, and choses different base quality values with different proportions. Then, it computes the overall error probability of each base in the read sequence with an empirical model, and calculates the deletion, substitution and insertion probabilities with the overall error probability to generate the PacBio CLR reads.
The Database of Natural Products for CAncer gene REgulation in Cancer Types.
Natural product-based drug combination and its disease-specific molecular regulation.
A Deep Neural Network-Based Structural Classification Tool for Natural Products. We typitcally will deploy this locally. To bring everything up. CC1C(O)CC2C1C(OC1OC(COC(C)=O)C(O)C(O)C1O)OC=C2C(O)=O. We pass through tensorflow serving at this url:. You can also provide cached flag to the params to get the cached version so make it faster.
This service provides various ways to retrieve information from The Nuclear Protein Database.
Web server for modeling of RNA-protein and DNA-protein complex structures.
Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding. Nearest-neighbor Projected-Distance Regression (NPDR) detects network interactions and controls for confounding and multiple testing. Nearest-neighbor Projected-Distance Regression (NPDR).
Assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads.
Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We can reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package.
An accurate and contiguous phasing method for polyploids. Ploidy agnostic phasing pipeline and algorithm. nPhase is a ploidy agnostic tool developed in python which predicts the haplotypes of a sample that was sequenced by both long and short reads by aligning them to a reference. It should work with any ploidy.
NPI-GNN is a tool for predicting ncRNA–protein interactions with deep graph neural networks.
Fast predicting ncRNA-protein interactions using the Relational Graph Convolutional Network Auto-Encoder.
Identification of Neuronal Polarity by Node-Based Machine Learning. FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. For more details, please read the associated manuscript -- "Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution" (Current Biology 2011, 21(1), pp.1-11). Registration is only necessary for users who want to up/download data or activate 3D viewer to view more than 5 images.
Efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.
Omics Playground is a user-friendly, centralized bioinformatics software designed for RNA-Seq and proteomics data analysis, offering interactive visualization and data sharing capabilities. It addresses batch effect correction using the NPmatch method, freely available on GitHub and within the software.
A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters.
NpPred is a method developed for predicting nuclear proteins. This method has been developed on a non-redundant dataset consists of 2710 nuclear and 7662 non-nuclear proteins.
Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
Interactive Web server dedicated to protein sequence analysis and available for the biologist community.
Deep learning-enabled MS/MS spectrum prediction facilitates automated identification of novel psychoactive substances.
Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning.
A hybrid sequence assembler that can scaffold and complete fragmented short read assemblies with sequence data streaming from the nanopore sequencing while sequencing is still in progress. Furthermore, it continuously reports assembly quality during the experiment so that users can terminate the sequencing when an assembly of sufficient quality and completeness is obtained.
R package for the significance analysis of sequencing data. The statistic used is exactly the same as that in SAM 4.0. The only difference is that our tool uses symmetric cutoffs, while SAM uses asymmetric cutoffs. Therefore, for some datasets, all significant genes obtained by SAM are either all up-regulated or all down-regulated, but npSeq almost always gives significant genes that include both up-regulated genes and down-regulated genes.
NP3 MS Workflow is an open-source software system designed for LC-MS/MS untargeted metabolomic data processing and analysis, aimed at ranking bioactive natural products directly from complex mixtures. It allows for customization and diagnostic statistics to optimize data processing and integrates tools for ion deconvolution, structural annotation, and quantification.
NPSV is Python-based tool for stand-alone genotyping of deletion and insertion structural variants (SVs) in short-read whole genome sequencing (WGS) data. NPSV implements a machine learning-based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline.
An Interactive Visualizer of Peptidic Natural Product-MS/MS Matches.
Suite of tools for analysis and quality control of Olink NGS data.
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
An open-source platform for digital control-loops in quantum-optical experiments. In this paper, we present NQontrol, a digital feedback-control solution based on the ADwin platform that delivers eight simultaneous feedback loops running with 200 kHz sampling frequency and offers five second-order filtering sections per channel for flexible shaping of the feedback loop. With this system, we demonstrate a Pound-Drever-Hall lock of an optical resonator and compare its performance to an analog reference implementation. A comprehensive support package written in Python, together with a web-based graphical user interface, makes the system quick to setup and easy to use, while maintaining the full flexibility of open-source platforms
nQuack is an R package that estimates ploidal level from sequence data using site-based heterozygosity, addressing shortcomings in existing methods and leveraging Gaussian Mixture Models.
Predicting the binding of small molecules to nuclear receptors using machine learning.
The ArcGIS National Responsibility Assessment Tool (NRA-Tool) can be used to create hierarchical lists of national responsibilities and priorities for global species conservation. Our tool will allow conservationists to prioritize conservation efforts and to focus limited resources on relevant species and regions. We showcase our tool with data on 258 bird species and various biophysical regions, including Environmental Zones in 58 Asian countries and regions. Our tool provides a decision support system for conservation policy with attractive and easily interpretable visual outputs illustrating national responsibilities and priorities for species conservation. The graphical output allows for smooth integration into assessment reports, such as the European Article 17 report, the Living Planet Index report, or similar regional and global reports.
A new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets.
NRG-CING: database of macromolecular NMR ensembles from the Protein Data Bank. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING).
NRGTEN (Najmanovich Research Group Toolkit for Elastic Networks) is an extensible Python toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes.
An application to streamline biophysical modeling of synaptic integration using NEURON.
SVM based tool for the classification of nuclear receptors on the basis of amino acid composition or dipeptide composition. The overall prediction accuracy of amino acid composition and dipeptide composition based methods is 82.6% and 97.2%
It is a novel automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. The main idea of this algorithm is to define a distance metric that corresponds to the similarity of the subsequences and reflects how the human brain can distinguish between different sequences.
NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.
NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity.
Multi-purpose collection of tools for the analyses of nuclear hormone receptors.
Predict the potential target proteins of the given drug. It is proposed based on the assumption that similar drugs often target similar target proteins and the framework of Random Walk with Restart (RWR).
A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing. Necessary and Sufficient Forest (NS-Forest) for Cell Type Marker Determination from cell type clusters.
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis | Non-specific lipid transfer protein structure modeling | Theoretical structures have been calculated for the 787 other proteins using the @tome2 suite of programs to perform homology modeling. The quality of each final structure model has been evaluated by a set of several tools including Qmean (Benkert, Tosatto et al. 2008). Structures with low quality (i.e. for which the cysteine scaffold could not be fully modeled) were discarded from further analysis
A manually curated database of experimentally supported ncRNAs associated with nervous system diseases.
NSF4SL is a negative-sample-free model for prediction of synthetic lethality (SL) based on a self-supervised contrastive learning framework.
Programs that perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.
Designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously.
Characterizing the disease association of multiple genetic interactions at single-subject resolution.
Multivariate regression model capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures.
nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.
A chemical-based sequencing method for genomic methylome profiling.
Scalable genomics application for polishing genome assembly drafts. It simplifies polishing and "haploidization" of gene and genome sequences with its re-usable Bloom filter design.
Streaming algorithm for cardinality estimation in genomics data.
An electronic medical record system for neglected tropical diseases.
Efficient Targeted Error Resolution and Automated Finishing of Long-Read Genome Assemblies.
Recursive spaced seed hashing for nucleotide sequences.
De novo repeat identification of genomics data using a streaming approach. ntHits is a method for identifying repeats in high-throughput DNA sequencing data. ntHits uses OpenMP for parallelization, which requires a modern compiler such as GCC 4.2 or greater. If you have an older compiler, it is best to upgrade your compiler if possible. If you have multiple versions of GCC installed, you can specify a different compiler:.
Write to file a single sequence from an input stream of sequences.
Read and write (return) one set of sequences from many.
Toolkit for de novo genome assembly scaffolding and mapping using long reads.
Tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
Robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences.
ntsm: an alignment-free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection
Benefits of a bilingual web-based anatomy atlas for nursing students in learning anatomy.
Nutrient Use Efficiency. Repository of NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare)), two alien species related to wheat (Triticum urartu and Aegilops tauschii), and two model species (Brachypodium distachyon and Arabidopsis thaliana).
This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.
The aim of NTXpred server is to predict Neurotoxins and its source and probable function from primary amino acid sequence using SVM based on composition and PSI-Blast.
A fast and RAM-efficient tool to de-duplicate sequencing reads without mapping. nubeam-dedup is a fast and easy-to-use bioinformatics tool removing exact PCR duplicates for sequencing reads, single-end or paired-end. We appreciate your interest in nubeam-dedup. If you use nubeam-dedup, please kindly cite:.
Location of structural errors in a genome assembly by using paired-end Illumina reads. NucBreak detects structural errors in assemblies and structural variants between pairs of genomes when only a genome of one organism and Illumina paired-end reads from another organism are available. It is able to detect insertions, deletions, different inter- and intra-chromosomal translocations, and inversions. However, the types of detected breakpoints are not specified. It was written in Python and uses Bowtie2 for reads alignment. The tool is described in the manuscript mentioned in Section 5.
Database of nuclear envelope proteins and their interactions.
Reads wedge (or local doublet) and basepair parameters calculates local helical parameters from local doublet parameters, then applies the base-pair and helical parameters to succesive basepairs after transforming the already generated ones to bring the topmost one in the (x-y) plane.
It is a simple decay calculator with most of the nuclear medicine isotopes.
A molecular-class information system that collects, combines, validates and stores large amounts of data on Nuclear Hormone Receptors (NHRs). Contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.
Nuclei Counter automatically count the number of nucleus in a microscope image.
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. This package is no longer being actively maintained; feel free to post issues that others in the community may respond to, but this package will likely not be updated further. Additionally, if anyone wants to maintain a fork of the package or has developed an alternative package for similar purposes, would be happy to link to that repo here. 2025 Python Packaging Survey is now live!. Please cite our paper at Genome Research if you use this tool in your research. New Authentication Rolling Out - We're upgrading our sign-in process to give you one account across all Anaconda products! Browser users will see a refreshed sign-in flow, while CLI users will experience no changes. Home: http://nucleoatac.readthedocs.io/en/latest/. Documentation can be found at http://nucleoatac.readthedocs.org/en/latest/. Python package for calling nucleosomes using ATAC-Seq data.
Addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample.
A computational tool for identifying nucleosomes in ultra-high resolution contact maps.
A web server for the identification of nucleotide-binding sites in protein structures.
This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform.
Prediction of Nucleosomes Positions on the Genome
Nucleosome positioning for Tiling Arrays and NGS experiments.
Simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D.
Integrated nuclei tracking application .
NucliTrack is a MATLAB tool for nuclei tracking with GUI for visualising and ammending tracks.
Set of computational tools designed to analyze gene positioning in yeast nuclei by automated processing of fluorescence microscopy images.
Repository containing the codebase corresponding to the following two papers: - Amgad M, Atteya LA, Hussein H, Mohammed KH, Hafiz E, Elsebaie MA, Alhusseiny AM, AlMoslemany MA, Elmatboly AM, Pappalardo PA, Sakr RA. NuCLS: A scalable crowdsourcing approach & dataset for nucleus classification and segmentation in breast cancer. (Under review). - Amgad M, Atteya LA, Hussein H, Mohammed KH, Hafiz E, Elsebaie MA, Mobadersany P, Manthey D, Gutman DA, Elfandy H, Cooper LA. Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings. Bioinformatics. 2021 Sep 29.
NucMap is a database providing genome-wide nucleosome positioning maps across various species, offering services for querying, visualization, enrichment, and comparative analysis. It integrates omics data, including RNA-seq and ChIP-seq, to facilitate the interpretation of nucleosome positioning.
A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.
A database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.
A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences.
Program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers.
Bioinformatic tool that generates nucleosome occupation maps.
Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample).
Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.
NulceiHomo is a hybrid morphological reconstruction for pre-processing of nuclei image.
Pipeline to generate complete public health microbiology reports from isolates sequenced with Illumina paired-end sequencing.
Creates Random Coding Sequences with specified GC content and Amino Acid usage.
The fundamental package for scientific computing with Python
Optimally partitioning data into piece-wise linear segments.
Program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices.
R package for Nucleosome Positioning Prediction. This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available.
A curated dataset of nuclear receptor modulators. Nuclear receptors (NRs) are key regulators of human health and constitute a relevant target for medicinal chemistry applications as well as for toxicological risk assessment. Several open databases dedicated to small molecules that modulate NRs exist; however, depending on their final aim (i.e., adverse effect assessment or drug design), these databases contain a different amount and type of annotated molecules, along with a different distribution of experimental bioactivity values. Stemming from these considerations, in this work we aim to provide a unified dataset, NURA (NUclear Receptor Activity) dataset, collecting curated information on small molecules that modulate NRs, to be intended for both pharmacological and toxicological applications
Efficient and reliable tool for estimating the isoform expression level. Given the reads mapping result and gene annotation file, it will output the expression estimation result.
NuST is a set of tools and data sets that can be used to analyze the aggregation of a set of genes along the genome coordinate, at different scales of observation.
A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. Nutil simplifies and streamlines the pre-and-post processing of 2D brain image data from mouse and rat.
Open Source Software for M/EEG Source Reconstruction. NUTMEG (Neurodynamic Utility Toolbox for Magnetoencephalography) is an open-source MATLAB toolbox for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. .
Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models. Structure Learning with Copula Graphical Model. Statistical tool for learning the structure of direct associations among variables for continuous data, discrete data and mixed discrete-continuous data. The package is based on the copula graphical model in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>
Database generated by text mining of 21 million MEDLINE abstracts, with information that links plant-based foods with their small molecule components and human disease phenotypes.
NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA.
An R package for the assessment of RNA-Seq normalization methods.
Finds potential nucleosome-free regions of DNA sequences. It can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.
Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.
Phase guided method for Nyquist ghost correction in 3D EPSI data
Nyquist artifact correction in 3D Echo Planar Spectroscopic Imaging (EPSI) data
An R package to import, clean and update data from the New Zealand Freshwater Fish Database.
A Database of Experimentally Identified O-GlcNAc Sites and Proteins.
Integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique.
A Formal-Language-Based Generator of O-Glycosylation Networks.
Webserver that automates the analysis and annotation of complex -omics data. Specifically deals with genomics and transcriptomics data.
A Novel Framework With Deep Fusion of CNN and Transformer for Simultaneous Segmentation and Classification.
Reconstructing who-infected-whom from routinely collected surveillance data. o2geosocial: Integrating geographical and social contact data to reconstruct transmission chains. o2geosocial was developed to infer probabilistic transmission trees from routinely-collected epidemiological data. It combines the age group, location, onset date and genotype of cases to infer their import status, and their likely infector. o2geosocial is based upon the R package "outbreaker2" (https://github.com/reconhub/outbreaker2), it is designed to study datasets that do not include genetic sequences but genotype of the cases. o2geosocial clusters cases from different genotypes in different trees, without computing the genetic distance between cases.
A database of putative RNA binding protein target sites in the transcriptomes of model species. Dashboard - Overview of the database. Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes. Here, we developed a computational tool to enable the global mapping of putative RBP target motifs across full transcriptomes, including messenger RNAs (mRNAs) and non-coding RNAs, in multiple species. The oRNAment database provides a user-friendly interface to parse the motif scan data. See tutorial for further detail
Prediction of human O-linked threonine glycosites using multi-feature fusion.
The Pedunculate oak (Quercus robur) root database (OakRootRNADB) consolidates information currently available on RNA-seq research conducted on both coding and non-coding RNA. The database contains the sequences of genes, transcripts, proteins, and microRNA obtained from the meristematic and elongation zones of both taproot and lateral roots of Q. robur.
OakVar is a Python-based genomic variant analysis platform. It is a fork of OpenCRAVAT and further developed with newer visions.
Multi-omics molecular biomarkers and database of osteoarthritis.
Oarfish is a new method and software tool for long-read transcript quantification that incorporates a novel coverage score to improve accuracy. It is implemented in Rust and available as free and open-source software under the BSD 3-clause license.
A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences.
De novo transcriptome assembler designed to produce transcripts from short read sequencing technologies. It uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.
It is a web application that allows for the fast and flexible online analysis of small-RNA-seq data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system.
OASIS (Omics Analysis, Search & Information System) is an information system for analyzing, searching, and visualizing associations between phenotypes, genotypes, and other types of omics data (such as transcriptomics, metabolomics, etc.). It is designed to enable discovery by connecting to the thought processes of biological researchers in a way that allows them to search results from an initial GWAS (or other association study), ask follow-up questions, and get answers in real-time. OASIS accomplishes this with a web-based search system and a variety of real-time analysis tools including conditional & multi-covariate analysis, and real-time linkage disequilibrium (LD) calculations. On-demand visualizations are provided in the form of boxplots, histograms, LocusZoom & Haploview plots. The OASIS search reports contain a broad spectrum of annotation from Annovar and WGSA plus a variety of links to external resources such as gnomAD, GTEx, HaploReg, Roadmap, UCSC and NCBI.
OASIS 2 is a user-friendly, offline suite for secure survival analysis, providing a portable version of the online tool to facilitate data security and accessibility without an internet connection. It provides functionalities for Cox proportional hazards regression, Wilcoxon-Breslow-Gehan test, and other survival analysis methods.
A verified and validated moving domain computational fluid dynamics solver with applications to cardiovascular flows.
Uses OrthoANI to measure overall similarity between two genome sequences.
Method to assess the likelihood that a protein will succeed in a high-throughput crystallography experiment.
One-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data. obaDIA takes a FASTA fromat protein sequence file and a fragment-level, peptide-level or protein-level abundance matrix file from data-independent acquisition (DIA) mass spectrometry experiment, and performs differential protein expression analysis, functional annotation and enrichment analysis in a completely automated way.
OBAMA for Bayesian amino-acid model averaging. A BEAST2 package for amino acid/protein site model averaging.
Software we designed to perform organelle-based colocalisation analysis from multi-fluorophore microscopy 2D, 3D and 4D cell imaging.
An identical-by-descent mapping tool based on SNP streak. obelisc (Observational linkage scan) is an identical-by-descent (IBD) mapping tool based on the SNP streak approach. obelisc is a command line tool to perform two effective nonparametric linkage analyses (i.e., SNP streak-based IBD mapping and runs of homozygosity (ROH) mapping). obelisc also supports an intuitive visualization of the analytical results.
A computational tool for the analysis and systematization of the positive selection in proteins.
Aligns multiple LC-MS(/MS) datasets in retention time by dynamic time warping.
Omics-Based Interaction Framework – a systems model to reveal molecular drivers of synergy. OBIF Package in R includes the analytical components of the Omics-Based Interaction Framework. This framework and package are used to discover molecular drivers of non-additive phenotypes (synergistic or angatonistic responses) from single- or multi-Omics data.
R package for generating indicators from OBIS Compute biodiversity indicators for marine data from obis
Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.
OMERO-based integrated workflow for annotating microbes in the cloud.
ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a syntax for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables is ideal for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.
Community development of interoperable ontologies for the biological sciences
A unified framework to integrate and analyze single-cell RNA-seq data.
An NGS-based bulk segregant analysis tool for outcross populations.
occAssess is an R package for assessing potential biases in species occurrence data.
Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.
ChIP-Seq Peak Calling Based on Internal Background Modelling.
OCD is a command-line tool for the calculation of immunoglobulin inter-domain orientations. The OCD tool automatically creates a reasonable coordinate system for the characterization of inter-domain orientations based on a user-provided reference structure.
A web service to explore the biodiversity and biogeography of marine organisms. - "Community ecological analysis" allows one to search for a taxon in a metabarcoding database in order to obtain. ecological analyses (alpha and beta diversity) using graphical representations (NMDS, boxplot..). - "Sequence based query" allows one to interrogate a metabarcoding database in order to obtain the abundance,.
Mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks.
Exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools | resistome on TARA ocean samples
The « Ocean Read Atlas » web service allows to search one or several sequences across all of Tara Oceans metagenomic raw sequencing data using kmindex, a new tool that performs indexing and queries using orders of magnitudes with less resources. It enables the visualization of the results on a geographic map and their correlation with each of the 56 environmental variables collected during the circumnavigation campaign. This server enables to perform instant searches on a large and complex dataset, providing new perspectives on the deep exploitation of Tara Oceans resources.
An infrastructure for data-driven research to discover and design crystalline organic semiconductors.
oCEM is a tool for automatic detection and analysis of overlapping co-expressed gene modules.
Creates an overlapping class system from an unweighted simple graph G = (V,E).OCG is essentially a hierarchical ascending algorithm. By default, it will fuse the initial classes until further fusions do not increase the modularity but other options are available.
"The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records."
An ontology for ocular immune-mediated inflammatory diseases
Generation and application of river network analogues for use in ecology and evolution. Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology.
This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).
Performs OCR on regions of interest specified in an openDS object, and updates the openDS regions with transcriptions
OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes
Developed to provide users a comprehansive seed expression sequence tags database of oil crops for comparative analysis. In ocsEASTdb, it provided ESTs and unigenes detail information of four oil crop species, A.hypogaea, B.napus (high or low oil), G.max, S.indicum.
A command line tool for converting optical coherence tomography angiography (OCTA) data.
A tool for calculating distortion parameters in spin crossover and coordination complexes.
Draw a White-Wimley protein hydropathy plot.
Scientific Programming Language Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools Free software, runs on GNU/Linux, macOS, BSD, and Microsoft Windows Drop-in compatible with many Matlab scripts
OCTID is a one-class learning-based Python package for tile-level tumor detection. OCTID can capture patterns from the available normal whole slide images (WSIs) to identify and remove normal tiles from the training dataset.
Prediction of membrane protein topology and signal peptides.
Retrieve and process large sets of next-generation sequencing (NGS) data with a single step. Automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, bwtool, Samtools FastQC, Trimmomatic, HISAT2, STAR, and HOMER applications.
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.
OCTSEG (Optical Coherence Tomography Segmentation and Evaluation GUI) is a GUI and function collection to segment and visualize retinal layers on OCT data.
OctSurf is a efficient hierarchical voxel-based molecular surface representation tool for protein-ligand affinity prediction.
A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments. An interface to convert odML structues to and from table-like representations, such as spreadsheets. Table-based editing of odML metadata collections — odMLtables 1.0.0 documentation. data model for storing arbitrary metadata. Open metadata markup language - odML -. odMLtables provides a set of functions to simplify the setup, maintenance and usage of a metadata management structure using odML. In addition to the Python API, odMLtables provides its main functionality also via a graphical user interface. odMLtables - Table-based editing of odML metadata collections¶. An interface to convert odML structures to and from table-like representations, such as spreadsheets
A Python package to study molecular relationship between environmental factors and rare diseases.
Contains all known and conserved operons in completely sequenced genomes.