BgeeDB
This is the released version of BgeeDB; for the devel version, see BgeeDB.
All Bioconductor versions of BgeeDB
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Bioconductor version: 3.23 · Package version: 2.38.1
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.
Author: Andrea Komljenovic [aut, cre], Julien Roux [aut, cre]
Maintainer: Julien Wollbrett <julien.wollbrett at unil.ch>, Julien Roux <julien.roux at unibas.ch>, Andrea Komljenovic <andreakomljenovic at gmail.com>, Frederic Bastian <bgee at sib.swiss>
Citation
From within R, enter citation("BgeeDB"):
Andrea Komljenovic, Julien Roux. BgeeDB: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology. doi:10.18129/B9.bioc.BgeeDB, R package version 2.38.1, https://bioconductor.org/packages/BgeeDB.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BgeeDB")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.38.1 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/BgeeDB/BgeeDB_R |
| Bug Reports | https://github.com/BgeeDB/BgeeDB_R/issues |
| Last updated | 2026-04-29 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10 years) |
| Downloads rank | 1108 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/BgeeDB/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BgeeDB")| BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | BgeeDB_2.38.1.tar.gz |
| Windows binary (x86_64) | BgeeDB_2.38.1.zip |
| macOS binary (arm64) | BgeeDB_2.38.1.tgz |
| macOS binary (x86_64) | BgeeDB_2.38.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BgeeDB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BgeeDB |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |