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/3.16/bioc/html/IsoformSwitchAnalyzeR.html

License:

GPL (>= 2)

Recipe:

/bioconductor-isoformswitchanalyzer/meta.yaml

Links:

biotools: IsoformSwitchAnalyzeR, 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.

package bioconductor-isoformswitchanalyzer

Versions:

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, 

1.20.0-0,  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

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-dexseq >=1.44.0,<1.45.0

• bioconductor-drimseq >=1.26.0,<1.27.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-tximeta >=1.16.0,<1.17.0

• bioconductor-tximport >=1.26.0,<1.27.0

• bioconductor-xvector >=0.38.0,<0.39.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.2,<4.3.0a0

• r-dbi

• r-dplyr

• r-futile.logger

• r-ggplot2

• r-gridextra

• r-magrittr

• r-plyr

• r-rcolorbrewer

• r-rcurl

• r-readr

• r-reshape2

• r-stringr

• r-tibble

• r-venndiagram

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-isoformswitchanalyzer/README.html)