DOI: 10.18129/B9.bioc.biomaRt  

This is the development version of biomaRt; for the stable release version, see biomaRt.

Interface to BioMart databases (i.e. Ensembl)

Bioconductor version: Development (3.18)

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. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Author: Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre]

Maintainer: Mike Smith <grimbough at>

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


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HTML R Script Accessing Ensembl annotation with biomaRt
HTML R Script Using a BioMart other than Ensembl
PDF   Reference Manual
Text   NEWS


biocViews Annotation, Software
Version 2.57.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License Artistic-2.0
Depends methods
Imports utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr, httr, digest, BiocFileCache, rappdirs, xml2
Suggests BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr
Depends On Me annotation, chromPlot, coMET, customProDB, DrugVsDisease, genefu, GenomicOZone, MineICA, NetSAM, PPInfer, RepViz, VegaMC
Imports Me BadRegionFinder, BgeeCall, branchpointer, BUSpaRse, ChIPpeakAnno, CHRONOS, CoGAPS, CoSIA, dagLogo, DEXSeq, DMRcate, DominoEffect, drugTargetInteractions, easyRNASeq, EDASeq, ELMER, EpiMix, epimutacions, ExpHunterSuite, FRASER, GDCRNATools, GenomicFeatures, GenVisR, gespeR, glmSparseNet, GOexpress, goSTAG, GRaNIE, Gviz, hermes, InterCellar, isobar, LACE, mCSEA, MEDIPS, MetaboSignal, metaseqR2, MGFR, MouseFM, NoRCE, OncoScore, oposSOM, ORFik, pcaExplorer, phenoTest, pRoloc, ProteoMM, psygenet2r, pwOmics, R453Plus1Toolbox, ramwas, recoup, rgsepd, RIPAT, RnaSeqSampleSize, scPipe, seq2pathway, SeqGSEA, sitadela, SPLINTER, SPONGE, surfaltr, SWATH2stats, TCGAbiolinks, TCGAWorkflow, TEKRABber, TFEA.ChIP, TimiRGeN, transcriptogramer, trena, ViSEAGO, yarn
Suggests Me AnnotationForge, bioassayR, BioMartGOGeneSets, BloodCancerMultiOmics2017, ccTutorial, celda, chromstaR, ClusterJudge, CNVgears, crisprDesign, cTRAP, DELocal, epistack, fedup, FELLA, h5vc, leeBamViews, MAGeCKFlute, martini, massiR, MethReg, MineICA, MiRaGE, MutationalPatterns, netSmooth, oligo, OmnipathR, OrganismDbi, piano, Pigengene, progeny, R3CPET, RegParallel, RforProteomics, RnBeads, rTRM, scater, ShortRead, SIM, sincell, SummarizedBenchmark, trackViewer, wiggleplotr, zinbwave
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