:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-isoformswitchanalyzer' .. highlight: bash bioconductor-isoformswitchanalyzer ================================== .. conda:recipe:: bioconductor-isoformswitchanalyzer :replaces_section_title: :noindex: Identify\, Annotate and Visualize Isoform Switches with Functional Consequences from both short\- and long\-read RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/IsoformSwitchAnalyzeR.html :license: GPL (>= 2) :recipe: /`bioconductor-isoformswitchanalyzer `_/`meta.yaml `_ :links: biotools: :biotools:`IsoformSwitchAnalyzeR`, doi: :doi:`10.1158/1541-7786.MCR-16-0459` Analysis of alternative splicing and isoform switches with predicted functional consequences \(e.g. gain\/loss of protein domains etc.\) from quantification of all types of RNASeq by tools such as Kallisto\, Salmon\, StringTie\, Cufflinks\/Cuffdiff etc. .. conda:package:: bioconductor-isoformswitchanalyzer |downloads_bioconductor-isoformswitchanalyzer| |docker_bioconductor-isoformswitchanalyzer| :versions: .. raw:: html
2.2.0-02.0.1-01.20.0-11.20.0-01.16.0-21.16.0-11.16.0-01.14.0-01.12.0-1 ``2.2.0-0``,  ``2.0.1-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.16.0-2``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-bsgenome: ``>=1.70.1,<1.71.0a0`` :depends bioconductor-dexseq: ``>=1.48.0,<1.49.0`` :depends bioconductor-dexseq: ``>=1.48.0,<1.49.0a0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-edger: ``>=4.0.2,<4.1.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :depends bioconductor-pfamanalyzer: ``>=1.2.0,<1.3.0`` :depends bioconductor-pfamanalyzer: ``>=1.2.0,<1.3.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-saturn: ``>=1.10.0,<1.11.0`` :depends bioconductor-saturn: ``>=1.10.0,<1.11.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends bioconductor-sva: ``>=3.50.0,<3.51.0`` :depends bioconductor-sva: ``>=3.50.0,<3.51.0a0`` :depends bioconductor-tximeta: ``>=1.20.0,<1.21.0`` :depends bioconductor-tximeta: ``>=1.20.1,<1.21.0a0`` :depends bioconductor-tximport: ``>=1.30.0,<1.31.0`` :depends bioconductor-tximport: ``>=1.30.0,<1.31.0a0`` :depends bioconductor-xvector: ``>=0.42.0,<0.43.0`` :depends bioconductor-xvector: ``>=0.42.0,<0.43.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dbi: :depends r-dplyr: :depends r-futile.logger: :depends r-ggplot2: ``>=3.3.5`` :depends r-gridextra: :depends r-magrittr: :depends r-plyr: :depends r-rcolorbrewer: :depends r-rcurl: :depends r-readr: :depends r-reshape2: :depends r-stringr: :depends r-tibble: :depends r-tidyr: :depends r-venndiagram: :requirements: .. 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-isoformswitchanalyzer and update with:: mamba update bioconductor-isoformswitchanalyzer To create a new environment, run:: mamba create --name myenvname bioconductor-isoformswitchanalyzer 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-isoformswitchanalyzer: (see `bioconductor-isoformswitchanalyzer/tags`_ for valid values for ````) .. |downloads_bioconductor-isoformswitchanalyzer| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-isoformswitchanalyzer.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-isoformswitchanalyzer :alt: (downloads) .. |docker_bioconductor-isoformswitchanalyzer| image:: https://quay.io/repository/biocontainers/bioconductor-isoformswitchanalyzer/status :target: https://quay.io/repository/biocontainers/bioconductor-isoformswitchanalyzer .. _`bioconductor-isoformswitchanalyzer/tags`: https://quay.io/repository/biocontainers/bioconductor-isoformswitchanalyzer?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-isoformswitchanalyzer/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-isoformswitchanalyzer/README.html