To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

In most cases, you don't need to download the package archive at all.

biomaRt

Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)

Bioconductor version: Release (3.1)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

Author: Steffen Durinck <biomartdev at gmail.com>, Wolfgang Huber

Maintainer: Steffen Durinck <biomartdev at gmail.com>

Citation (from within R, enter citation("biomaRt")):

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("biomaRt")

PDF	R Script	The biomaRt users guide
PDF		Reference Manual

Details

biocViews	Annotation, Software
Version	2.24.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License	Artistic-2.0
Depends	methods
Imports	utils, XML, RCurl, AnnotationDbi
LinkingTo
Suggests	annotate
SystemRequirements
Enhances
URL
Depends On Me	ChIPpeakAnno, coMET, customProDB, dagLogo, domainsignatures, DrugVsDisease, Fletcher2013b, genefu, GenomeGraphs, MineICA, PSICQUIC, Roleswitch, Sushi, VegaMC
Imports Me	ArrayExpressHTS, cobindR, customProDB, DEXSeq, DOQTL, easyRNASeq, EnrichmentBrowser, GenomicFeatures, gespeR, GOexpress, Gviz, HTSanalyzeR, IdMappingRetrieval, KEGGprofile, MEDIPS, metagene, metaseqR, methyAnalysis, oposSOM, Pbase, phenoTest, pRoloc, pwOmics, R453Plus1Toolbox, rgsepd, RNAither, RnaSeqSampleSize, seq2pathway, SeqGSEA
Suggests Me	BiocCaseStudies, ccTutorial, DEGreport, GeneAnswers, Genominator, h5vc, isobar, leeBamViews, massiR, MineICA, MiRaGE, oligo, oligo, oneChannelGUI, paxtoolsr, piano, R3CPET, Rcade, RforProteomics, RIPSeeker, RnaSeqTutorial, RnBeads, rTANDEM, rTRM, ShortRead, SIM, sincell, systemPipeR, trackViewer
Build Report

Package Archives

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

Package Source	biomaRt_2.24.1.tar.gz
Windows Binary	biomaRt_2.24.1.zip
Mac OS X 10.6 (Snow Leopard)	biomaRt_2.24.1.tgz
Mac OS X 10.9 (Mavericks)	biomaRt_2.24.1.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/biomaRt/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/biomaRt/
Package Downloads Report	Download Stats

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