recipe bioconductor-categorycompare

Meta-analysis of high-throughput experiments using feature annotations






Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

package bioconductor-categorycompare

(downloads) docker_bioconductor-categorycompare



depends bioconductor-annotate:


depends bioconductor-annotationdbi:


depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-category:


depends bioconductor-gostats:


depends bioconductor-graph:


depends bioconductor-gseabase:


depends bioconductor-rcy3:


depends cytoscape:


depends r-base:


depends r-colorspace:

depends r-hwriter:



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-categorycompare

and update with::

   mamba update bioconductor-categorycompare

To create a new environment, run:

mamba create --name myenvname bioconductor-categorycompare

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

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