recipe bioconductor-fedup

Fisher's Test for Enrichment and Depletion of User-Defined Pathways






An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

package bioconductor-fedup

(downloads) docker_bioconductor-fedup



depends bioconductor-rcy3:


depends r-base:


depends r-data.table:

depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-ggthemes:

depends r-openxlsx:

depends r-rcolorbrewer:

depends r-tibble:



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-fedup

and update with::

   mamba update bioconductor-fedup

To create a new environment, run:

mamba create --name myenvname bioconductor-fedup

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

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