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 (3.12)

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")):

Installation

To install this package, start R (version "4.0") 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 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 2.16.0
In Bioconductor since BioC 3.3 (R-3.3) (4.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6.0), topGO, tidyr
Imports data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, 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_2.16.0.tar.gz
Windows Binary BgeeDB_2.16.0.zip
macOS 10.13 (High Sierra) BgeeDB_2.16.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: