recipe bioconductor-rgsepd

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/rgsepd.html

License

GPL-3

Recipe

/bioconductor-rgsepd/meta.yaml

Links

biotools: rgsepd, doi: 10.1038/nmeth.3252

package bioconductor-rgsepd

(downloads) docker_bioconductor-rgsepd

Versions

1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-go.db

>=3.7.0,<3.8.0

Depends bioconductor-goseq

>=1.34.0,<1.35.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-gplots

Depends r-hash

Requirements

Installation

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

conda install bioconductor-rgsepd

and update with:

conda update bioconductor-rgsepd

or use the docker container:

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

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

Link to this page

Render an install-with-bioconda 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-rgsepd/README.html)