recipe bioconductor-rgsepd

Gene Set Enrichment / Projection Displays

Homepage

https://bioconductor.org/packages/3.10/bioc/html/rgsepd.html

License

GPL-3

Recipe

/bioconductor-rgsepd/meta.yaml

Links

biotools: rgsepd, doi: 10.1038/nmeth.3252

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.

package bioconductor-rgsepd

Versions

1.18.0-0, 1.16.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0

Depends

• bioconductor-annotationdbi >=1.48.0,<1.49.0

• bioconductor-biomart >=2.42.0,<2.43.0

• bioconductor-deseq2 >=1.26.0,<1.27.0

• bioconductor-go.db >=3.10.0,<3.11.0

• bioconductor-goseq >=1.38.0,<1.39.0

• bioconductor-org.hs.eg.db >=3.10.0,<3.11.0

• bioconductor-summarizedexperiment >=1.16.0,<1.17.0

• r-base >=3.6,<3.7.0a0

• r-gplots

• r-hash

Required By

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 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)