BgeeDB

This package is for version 3.13 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: 3.13

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GO, GeneExpression, GeneSetEnrichment, Microarray, Sequencing, Software

Version 2.18.1

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

Suggests knitr, BiocStyle, testthat, rmarkdown, markdown

Linking To

Enhances

Depends On Me

Imports Me psygenet2r, RITAN

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package BgeeDB_2.18.1.tar.gz

Windows Binary BgeeDB_2.18.1.zip

macOS 10.13 (High Sierra) BgeeDB_2.18.1.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

Old Source Packages for BioC 3.13 Source Archive