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Bioconductor - BgeeDB

BgeeDB

This is the released version of BgeeDB; for the devel version, see BgeeDB.

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

Bioconductor version: Release (3.21)

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 "4.5") 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 2.34.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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, zellkonverter, anndata, HDF5Array, bread System Requirements URL https://github.com/BgeeDB/BgeeDB_R Bug Reports https://github.com/BgeeDB/BgeeDB_R/issues See More Package Archives

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

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