To install this package, start R and enter:

source("http://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 (3.0)

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 <durincks at gene.com>, Wolfgang Huber

Maintainer: Steffen Durinck <durincks at gene.com>

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

Installation

To install this package, start R and enter:

source("http://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 2.22.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License Artistic-2.0
Depends methods
Imports utils, XML, RCurl, AnnotationDbi
Suggests annotate
System Requirements
URL
Depends On Me ChIPpeakAnno, customProDB, dagLogo, domainsignatures, DrugVsDisease, ESNSTCC, Fletcher2013b, genefu, GenomeGraphs, MineICA, PSICQUIC, Roleswitch, Sushi, VegaMC
Imports Me affycoretools, ArrayExpressHTS, cobindR, customProDB, DEXSeq, DOQTL, easyRNASeq, GenomicFeatures, GOexpress, Gviz, HTSanalyzeR, IdMappingRetrieval, KEGGprofile, MEDIPS, metaseqR, methyAnalysis, oposSOM, phenoTest, R453Plus1Toolbox, RNAither, SeqGSEA
Suggests Me BiocCaseStudies, ccTutorial, DEGreport, GeneAnswers, Genominator, h5vc, isobar, leeBamViews, massiR, MineICA, MiRaGE, oneChannelGUI, paxtoolsr, Pbase, piano, Rcade, RforProteomics, RIPSeeker, RnaSeqTutorial, rTANDEM, rTRM, ShortRead, SIM, systemPipeR, trackViewer

Package Archives

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

Package Source biomaRt_2.22.0.tar.gz
Windows Binary biomaRt_2.22.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) biomaRt_2.22.0.tgz
Mac OS X 10.9 (Mavericks) biomaRt_2.22.0.tgz
Browse/checkout source (username/password: readonly)
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