BgeeDB

DOI: 10.18129/B9.bioc.BgeeDB    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BgeeDB.

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

Bioconductor version: 3.10

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 "3.6") and enter:

if (!requireNamespace("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	Vignette Title
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software
Version	2.12.1
In Bioconductor since	BioC 3.3 (R-3.3) (4 years)
License	GPL-3
Depends	R (>= 3.3.0), topGO, tidyr
Imports	data.table, RCurl, digest, methods, stats, utils, dplyr, graph, Biobase
LinkingTo
Suggests	knitr, BiocStyle, testthat, rmarkdown
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
Links To Me
Build Report

Package Archives

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

Source Package	BgeeDB_2.12.1.tar.gz
Windows Binary	BgeeDB_2.12.1.zip
Mac OS X 10.11 (El Capitan)	BgeeDB_2.12.1.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