recipe bioconductor-bgeedb

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology



GPL-3 + file LICENSE




biotools: bgeedb, doi: 10.12688/f1000research.9973.1

A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

package bioconductor-bgeedb

(downloads) docker_bioconductor-bgeedb



depends bioconductor-biobase:


depends bioconductor-graph:


depends bioconductor-topgo:


depends r-base:


depends r-curl:

depends r-data.table:

depends r-digest:

depends r-dplyr:

depends r-r.utils:

depends r-rcurl:

depends r-rsqlite:

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-bgeedb

and update with::

   mamba update bioconductor-bgeedb

To create a new environment, run:

mamba create --name myenvname bioconductor-bgeedb

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

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