recipe bioconductor-cogaps

Coordinated Gene Activity in Pattern Sets



BSD_3_clause + file LICENSE



Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

package bioconductor-cogaps

(downloads) docker_bioconductor-cogaps



depends bioconductor-biocparallel:


depends bioconductor-biocparallel:


depends bioconductor-biomart:


depends bioconductor-biomart:


depends bioconductor-fgsea:


depends bioconductor-fgsea:


depends bioconductor-rhdf5:


depends bioconductor-rhdf5:


depends bioconductor-s4vectors:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends bioconductor-summarizedexperiment:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-bh:

depends r-cluster:

depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-gplots:

depends r-msigdbr:

depends r-rcolorbrewer:

depends r-rcpp:



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-cogaps

and update with::

   mamba update bioconductor-cogaps

To create a new environment, run:

mamba create --name myenvname bioconductor-cogaps

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<tag>

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

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