recipe bioconductor-gep2pep

Creation and Analysis of Pathway Expression Profiles (PEPs)






Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

package bioconductor-gep2pep

(downloads) docker_bioconductor-gep2pep



depends bioconductor-biobase:


depends bioconductor-gseabase:


depends bioconductor-rhdf5:


depends r-base:


depends r-digest:

depends r-foreach:

depends r-iterators:

depends r-repo:


depends r-xml:



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-gep2pep

and update with::

   mamba update bioconductor-gep2pep

To create a new environment, run:

mamba create --name myenvname bioconductor-gep2pep

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-gep2pep/tags`_ for valid values for ``<tag>``)

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