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

Bioconductor version: 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 ( 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>, Wolfgang Huber

Maintainer: Steffen Durinck <durincks at>

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PDF R Script The biomaRt users guide
PDF   Reference Manual


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
Depends On Me ChIPpeakAnno, customProDB, dagLogo, domainsignatures, DrugVsDisease, 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
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Package Source biomaRt_2.22.0.tar.gz
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