recipe bioconductor-isoformswitchanalyzer

IsoformSwitchAnalyzeR enables identification and analysis of alternative splicing and isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/IsoformSwitchAnalyzeR.html

License

GPL (>= 2)

Recipe

/bioconductor-isoformswitchanalyzer/meta.yaml

Links

biotools: IsoformSwitchAnalyzeR, doi: 10.1158/1541-7786.MCR-16-0459

package bioconductor-isoformswitchanalyzer

Versions

1.4.0-0, 1.2.0-0, 1.0.0-0

Depends

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-dexseq >=1.28.0,<1.29.0

• bioconductor-drimseq >=1.10.0,<1.11.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-tximport >=1.10.0,<1.11.0

• libgcc-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-dbi

• r-dplyr

• r-futile.logger

• r-ggplot2

• r-gridextra

• r-magrittr

• r-plyr

• r-rcolorbrewer

• r-readr

• r-reshape2

• r-stringr

• r-venndiagram

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-isoformswitchanalyzer

and update with:

conda update bioconductor-isoformswitchanalyzer

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-isoformswitchanalyzer:<tag>

(see bioconductor-isoformswitchanalyzer/tags for valid values for <tag>)

Link to this page

Render an 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)