biomaRt

DOI: 10.18129/B9.bioc.biomaRt  

Interface to BioMart databases (i.e. Ensembl)

Bioconductor version: Release (3.17)

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 gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("biomaRt")

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("biomaRt")

 

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

Details

biocViews	Annotation, Software
Version	2.56.1
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
LinkingTo
Suggests	BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr
SystemRequirements
Enhances
URL	https://github.com/grimbough/biomaRt
BugReports	https://github.com/grimbough/biomaRt/issues
Depends On Me	annotation, chromPlot, coMET, customProDB, DrugVsDisease, genefu, GenomicOZone, MineICA, NetSAM, PPInfer, RepViz, VegaMC
Imports Me	ArrayExpressHTS, ASpediaFI, BadRegionFinder, BgeeCall, branchpointer, BUSpaRse, ChIPpeakAnno, CHRONOS, CoGAPS, CoSIA, dagLogo, DEXSeq, DMRcate, DominoEffect, drugTargetInteractions, easyRNASeq, EDASeq, ELMER, EpiMix, epimutacions, ExpHunterSuite, FRASER, GDCRNATools, GeneAccord, GenomicFeatures, GenVisR, gespeR, glmSparseNet, GOexpress, goSTAG, GRaNIE, Gviz, hermes, InterCellar, isobar, LACE, mCSEA, MEDIPS, MetaboSignal, metaseqR2, MGFR, MouseFM, NoRCE, OncoScore, oposSOM, ORFik, pcaExplorer, phenoTest, PrecisionTrialDrawer, 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
Links To Me
Build Report

Package Archives

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

Source Package	biomaRt_2.56.1.tar.gz
Windows Binary	biomaRt_2.56.1.zip
macOS Binary (x86_64)	biomaRt_2.56.1.tgz
macOS Binary (arm64)	biomaRt_2.56.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biomaRt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biomaRt
Bioc Package Browser	https://code.bioconductor.org/browse/biomaRt/
Package Short Url	https://bioconductor.org/packages/biomaRt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive