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

Bioconductor version: Release (3.19)

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.

Author: Andrea Komljenovic [aut, cre], Julien Roux [aut, cre]

Maintainer: Julien Wollbrett <julien.wollbrett at>, Julien Roux <julien.roux at>, Andrea Komljenovic <andreakomljenovic at>, Frederic Bastian <bgee at>

Citation (from within R, enter citation("BgeeDB")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests HTML R Script
Reference Manual PDF


biocViews DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software
Version 2.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6.0), topGO, tidyr
Imports R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase
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Suggests knitr, BiocStyle, testthat, rmarkdown, markdown
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Depends On Me
Imports Me psygenet2r, RITAN
Suggests Me RITAN
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Follow Installation instructions to use this package in your R session.

Source Package BgeeDB_2.30.0.tar.gz
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macOS Binary (x86_64) BgeeDB_2.30.0.tgz
macOS Binary (arm64) BgeeDB_2.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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