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/3.14/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

1.16.0-0,  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, 

1.16.0-0,  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 >=2.54.0,<2.55.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-dexseq >=1.40.0,<1.41.0

• bioconductor-drimseq >=1.22.0,<1.23.0

• bioconductor-edger >=3.36.0,<3.37.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-limma >=3.50.0,<3.51.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-tximeta >=1.12.0,<1.13.0

• bioconductor-tximport >=1.22.0,<1.23.0

• bioconductor-xvector >=0.34.0,<0.35.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.4.0

• liblapack >=3.8.0,<4.0a0

• r-base >=4.1,<4.2.0a0

• 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 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>)

Download stats

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