recipe bioconductor-msigdb

An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/msigdb.html

License:

CC BY 4.0

Recipe:

/bioconductor-msigdb/meta.yaml

This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object.

package bioconductor-msigdb

versions:

1.8.0-0,  1.6.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-experimenthub:

>=2.8.0,<2.9.0

depends bioconductor-gseabase:

>=1.62.0,<1.63.0

depends bioconductor-org.hs.eg.db:

>=3.17.0,<3.18.0

depends bioconductor-org.mm.eg.db:

>=3.17.0,<3.18.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-msigdb

and update with::

   mamba update bioconductor-msigdb

To create a new environment, run:

mamba create --name myenvname bioconductor-msigdb

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-msigdb:<tag>

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

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Link to this page

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