recipe bioconductor-isoformswitchanalyzer

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Homepage

https://bioconductor.org/packages/3.11/bioc/html/IsoformSwitchAnalyzeR.html

License

GPL (>= 2)

Recipe

/bioconductor-isoformswitchanalyzer/meta.yaml

Links

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

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 of all types of RNASeq by tools such as Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.

package bioconductor-isoformswitchanalyzer

Versions

1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-dexseq >=1.34.0,<1.35.0

• bioconductor-drimseq >=1.16.0,<1.17.0

• bioconductor-edger >=3.30.0,<3.31.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-tximport >=1.16.0,<1.17.0

• bioconductor-xvector >=0.28.0,<0.29.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• r-base >=4.0,<4.1.0a0

• 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)