BgeeDB

This is the released version of BgeeDB; for the devel version, see BgeeDB.

All versions

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: Release (3.23)

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.

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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software
Version	2.38.1
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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, zellkonverter, anndata, HDF5Array, bread
System Requirements
URL	https://github.com/BgeeDB/BgeeDB_R
Bug Reports	https://github.com/BgeeDB/BgeeDB_R/issues

Suggests	knitr, BiocStyle, testthat, rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me	RITAN
Suggests Me	RITAN
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (big-sur-x86_64)	BgeeDB_2.38.1.tgz
macOS Binary (sonoma-arm64)	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 Short Url	https://bioconductor.org/packages/BgeeDB/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive