recipe bioconductor-isoformswitchanalyzer

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

Homepage

https://bioconductor.org/packages/3.9/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

(downloads) docker_bioconductor-isoformswitchanalyzer

Versions

1.4.0-0, 1.2.0-0, 1.0.0-0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-bsgenome

>=1.50.0,<1.51.0

Depends bioconductor-dexseq

>=1.28.0,<1.29.0

Depends bioconductor-drimseq

>=1.10.0,<1.11.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-tximport

>=1.10.0,<1.11.0

Depends libgcc-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dbi

Depends r-dplyr

Depends r-futile.logger

Depends r-ggplot2

Depends r-gridextra

Depends r-magrittr

Depends r-plyr

Depends r-rcolorbrewer

Depends r-readr

Depends r-reshape2

Depends r-stringr

Depends r-venndiagram

Requirements

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>)