BgeeDB

DOI: 10.18129/B9.bioc.BgeeDB  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software
Version	2.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 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
LinkingTo
Suggests	knitr, BiocStyle, testthat, rmarkdown, markdown
SystemRequirements
Enhances
URL	https://github.com/BgeeDB/BgeeDB_R
BugReports	https://github.com/BgeeDB/BgeeDB_R/issues
Depends On Me
Imports Me	psygenet2r, RITAN
Suggests Me	RITAN
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BgeeDB_2.24.0.tar.gz
Windows Binary	BgeeDB_2.24.0.zip
macOS Binary (x86_64)	BgeeDB_2.24.0.tgz
macOS Binary (arm64)	BgeeDB_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BgeeDB
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BgeeDB
Bioc Package Browser	https://code.bioconductor.org/browse/BgeeDB/
Package Short Url	https://bioconductor.org/packages/BgeeDB/
Package Downloads Report	Download Stats