recipe bioconductor-rgsepd

Gene Set Enrichment / Projection Displays

Homepage:

https://bioconductor.org/packages/3.18/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:

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0, 

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  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:

>=1.64.0,<1.65.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-goseq:

>=1.54.0,<1.55.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-gplots:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-rgsepd

and update with::

   mamba update bioconductor-rgsepd

To create a new environment, run:

mamba create --name myenvname bioconductor-rgsepd

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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Link to this page

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