:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-splicewiz' .. highlight: bash bioconductor-splicewiz ====================== .. conda:recipe:: bioconductor-splicewiz :replaces_section_title: :noindex: interactive analysis and visualization of alternative splicing in R :homepage: https://bioconductor.org/packages/3.20/bioc/html/SpliceWiz.html :license: MIT + file LICENSE :recipe: /`bioconductor-splicewiz `_/`meta.yaml `_ The analysis and visualization of alternative splicing \(AS\) events from RNA sequencing data remains challenging. SpliceWiz is a user\-friendly and performance\-optimized R package for AS analysis\, by processing alignment BAM files to quantify read counts across splice junctions\, IRFinder\-based intron retention quantitation\, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage\, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny\-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi\-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall\, SpliceWiz streamlines AS analysis\, enabling reliable identification of functionally relevant AS events for further characterization. .. conda:package:: bioconductor-splicewiz |downloads_bioconductor-splicewiz| |docker_bioconductor-splicewiz| :versions: ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.2-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-annotationhub: ``>=3.14.0,<3.15.0`` :depends bioconductor-annotationhub: ``>=3.14.0,<3.15.0a0`` :depends bioconductor-biocfilecache: ``>=2.14.0,<2.15.0`` :depends bioconductor-biocfilecache: ``>=2.14.0,<2.15.0a0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0`` :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0`` :depends bioconductor-biocparallel: ``>=1.40.0,<1.41.0a0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0`` :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0a0`` :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0`` :depends bioconductor-bsgenome: ``>=1.74.0,<1.75.0a0`` :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0`` :depends bioconductor-delayedarray: ``>=0.32.0,<0.33.0a0`` :depends bioconductor-delayedmatrixstats: ``>=1.28.0,<1.29.0`` :depends bioconductor-delayedmatrixstats: ``>=1.28.0,<1.29.0a0`` :depends bioconductor-genefilter: ``>=1.88.0,<1.89.0`` :depends bioconductor-genefilter: ``>=1.88.0,<1.89.0a0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0`` :depends bioconductor-genomeinfodb: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0`` :depends bioconductor-genomicranges: ``>=1.58.0,<1.59.0a0`` :depends bioconductor-hdf5array: ``>=1.34.0,<1.35.0`` :depends bioconductor-hdf5array: ``>=1.34.0,<1.35.0a0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0`` :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0`` :depends bioconductor-nxtirfdata: ``>=1.12.0,<1.13.0`` :depends bioconductor-nxtirfdata: ``>=1.12.0,<1.13.0a0`` :depends bioconductor-ompbam: ``>=1.10.0,<1.11.0`` :depends bioconductor-ompbam: ``>=1.10.0,<1.11.0a0`` :depends bioconductor-rhdf5: ``>=2.50.0,<2.51.0`` :depends bioconductor-rhdf5: ``>=2.50.0,<2.51.0a0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0`` :depends bioconductor-rtracklayer: ``>=1.66.0,<1.67.0a0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0`` :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0`` :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=13`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends liblzma: ``>=5.6.3,<6.0a0`` :depends libstdcxx: ``>=13`` :depends libzlib: ``>=1.3.1,<2.0a0`` :depends r-base: ``>=4.4,<4.5.0a0`` :depends r-data.table: :depends r-dt: :depends r-fst: :depends r-ggplot2: :depends r-heatmaply: :depends r-htmltools: :depends r-httr: :depends r-magrittr: :depends r-matrixstats: :depends r-patchwork: :depends r-pheatmap: :depends r-plotly: :depends r-progress: :depends r-r.utils: :depends r-rcolorbrewer: :depends r-rcpp: ``>=1.0.5`` :depends r-rcppprogress: :depends r-rhandsontable: :depends r-rsqlite: :depends r-rvest: :depends r-scales: :depends r-shiny: :depends r-shinydashboard: :depends r-shinyfiles: :depends r-shinywidgets: :depends r-stringi: :requirements: :additional platforms: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-splicewiz and update with:: mamba update bioconductor-splicewiz To create a new environment, run:: mamba create --name myenvname bioconductor-splicewiz with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-splicewiz: (see `bioconductor-splicewiz/tags`_ for valid values for ````) .. |downloads_bioconductor-splicewiz| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-splicewiz.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-splicewiz :alt: (downloads) .. |docker_bioconductor-splicewiz| image:: https://quay.io/repository/biocontainers/bioconductor-splicewiz/status :target: https://quay.io/repository/biocontainers/bioconductor-splicewiz .. _`bioconductor-splicewiz/tags`: https://quay.io/repository/biocontainers/bioconductor-splicewiz?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-splicewiz/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-splicewiz/README.html