: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: ``1.12.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.2-0``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bioconductor-annotationhub: ``>=4.0.0,<4.1.0`` :depends bioconductor-annotationhub: ``>=4.0.0,<4.1.0a0`` :depends bioconductor-biocfilecache: ``>=3.0.0,<3.1.0`` :depends bioconductor-biocfilecache: ``>=3.0.0,<3.1.0a0`` :depends bioconductor-biocgenerics: ``>=0.56.0,<0.57.0`` :depends bioconductor-biocgenerics: ``>=0.56.0,<0.57.0a0`` :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0`` :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0a0`` :depends bioconductor-biostrings: ``>=2.78.0,<2.79.0`` :depends bioconductor-biostrings: ``>=2.78.0,<2.79.0a0`` :depends bioconductor-bsgenome: ``>=1.78.0,<1.79.0`` :depends bioconductor-bsgenome: ``>=1.78.0,<1.79.0a0`` :depends bioconductor-delayedarray: ``>=0.36.0,<0.37.0`` :depends bioconductor-delayedarray: ``>=0.36.0,<0.37.0a0`` :depends bioconductor-delayedmatrixstats: ``>=1.32.0,<1.33.0`` :depends bioconductor-delayedmatrixstats: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-genefilter: ``>=1.92.0,<1.93.0`` :depends bioconductor-genefilter: ``>=1.92.0,<1.93.0a0`` :depends bioconductor-genomeinfodb: ``>=1.46.0,<1.47.0`` :depends bioconductor-genomeinfodb: ``>=1.46.2,<1.47.0a0`` :depends bioconductor-genomicranges: ``>=1.62.0,<1.63.0`` :depends bioconductor-genomicranges: ``>=1.62.1,<1.63.0a0`` :depends bioconductor-h5mread: ``>=1.2.0,<1.3.0`` :depends bioconductor-h5mread: ``>=1.2.1,<1.3.0a0`` :depends bioconductor-hdf5array: ``>=1.38.0,<1.39.0`` :depends bioconductor-hdf5array: ``>=1.38.0,<1.39.0a0`` :depends bioconductor-iranges: ``>=2.44.0,<2.45.0`` :depends bioconductor-iranges: ``>=2.44.0,<2.45.0a0`` :depends bioconductor-nxtirfdata: ``>=1.16.0,<1.17.0`` :depends bioconductor-nxtirfdata: ``>=1.16.0,<1.17.0a0`` :depends bioconductor-ompbam: ``>=1.14.0,<1.15.0`` :depends bioconductor-ompbam: ``>=1.14.0,<1.15.0a0`` :depends bioconductor-rhdf5: ``>=2.54.0,<2.55.0`` :depends bioconductor-rhdf5: ``>=2.54.1,<2.55.0a0`` :depends bioconductor-rtracklayer: ``>=1.70.0,<1.71.0`` :depends bioconductor-rtracklayer: ``>=1.70.1,<1.71.0a0`` :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0`` :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc: ``>=14`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends liblzma: ``>=5.8.2,<6.0a0`` :depends libstdcxx: ``>=14`` :depends libzlib: ``>=1.3.1,<2.0a0`` :depends r-base: ``>=4.5,<4.6.0a0`` :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