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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 (3.18)

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 2.28.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL https://github.com/BgeeDB/BgeeDB_R
Bug Reports https://github.com/BgeeDB/BgeeDB_R/issues
See More
Suggests knitr, BiocStyle, testthat, rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me psygenet2r, RITAN
Suggests Me RITAN
Links To Me
Build Report Build Report

Package Archives

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

Source Package BgeeDB_2.28.0.tar.gz
Windows Binary BgeeDB_2.28.0.zip
macOS Binary (x86_64) BgeeDB_2.28.0.tgz
macOS Binary (arm64) BgeeDB_2.28.0.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