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BgeeDB

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software
Version 2.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 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
Linking To
Suggests knitr, BiocStyle, testthat, rmarkdown, markdown
System Requirements
Enhances
URL https://github.com/BgeeDB/BgeeDB_R
Bug Reports https://github.com/BgeeDB/BgeeDB_R/issues
See More
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_2.26.0.tar.gz
Windows Binary BgeeDB_2.26.0.zip
macOS Binary (x86_64) BgeeDB_2.26.0.tgz
macOS Binary (arm64) BgeeDB_2.26.0.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