recipe bioconductor-reactomegsa

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis






The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

package bioconductor-reactomegsa

(downloads) docker_bioconductor-reactomegsa



depends r-base:


depends r-dplyr:

depends r-ggplot2:

depends r-gplots:

depends r-httr:

depends r-jsonlite:

depends r-progress:

depends r-rcolorbrewer:

depends r-tidyr:



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-reactomegsa

and update with::

   mamba update bioconductor-reactomegsa

To create a new environment, run:

mamba create --name myenvname bioconductor-reactomegsa

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

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