recipe bioconductor-enrichviewnet

From functional enrichment results to biological networks






This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

package bioconductor-enrichviewnet

(downloads) docker_bioconductor-enrichviewnet



depends bioconductor-enrichplot:


depends bioconductor-rcy3:


depends r-base:


depends r-gprofiler2:

depends r-jsonlite:

depends r-strex:

depends r-stringr:



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-enrichviewnet

and update with::

   mamba update bioconductor-enrichviewnet

To create a new environment, run:

mamba create --name myenvname bioconductor-enrichviewnet

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

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