biomaRt

Interface to BioMart databases (i.e. Ensembl)

Bioconductor version: Release (3.20)

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>

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

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Software
Version	2.62.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License	Artistic-2.0
Depends	methods
Imports	utils, AnnotationDbi, progress, stringr, httr2, digest, BiocFileCache, rappdirs, xml2, curl
System Requirements
URL	https://github.com/grimbough/biomaRt
Bug Reports	https://github.com/grimbough/biomaRt/issues

Suggests	BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2
Linking To
Enhances
Depends On Me	chromPlot, customProDB, DrugVsDisease, GenomicOZone, MineICA, NetSAM, PPInfer, RepViz, VegaMC, annotation
Imports Me	BadRegionFinder, BgeeCall, branchpointer, BUSpaRse, ChIPpeakAnno, CHRONOS, CoSIA, dagLogo, DEXSeq, DMRcate, DominoEffect, dominoSignal, easyRNASeq, EDASeq, ELMER, EpiMix, epimutacions, FRASER, GDCRNATools, GenVisR, gINTomics, glmSparseNet, GOexpress, goSTAG, GRaNIE, Gviz, hermes, InterCellar, isobar, LACE, MEDIPS, MetaboSignal, metaseqR2, MGFR, motifbreakR, MouseFM, OncoScore, oposSOM, ORFik, pcaExplorer, phenoTest, pRoloc, ProteoMM, R453Plus1Toolbox, ramwas, recoup, rgsepd, scPipe, seq2pathway, SeqGSEA, sitadela, SPLINTER, SPONGE, surfaltr, SWATH2stats, TCGAbiolinks, TEKRABber, TFEA.ChIP, transcriptogramer, txdbmaker, yarn, ExpHunterSuite, TCGAWorkflow, biomartr, BioVenn, convertid, DiNAMIC.Duo, GOxploreR, ProFAST, scGOclust, seeker, snplinkage, snplist
Suggests Me	AnnotationForge, bioassayR, celda, ClusterJudge, crisprDesign, cTRAP, Damsel, DELocal, epistack, fedup, FELLA, GeDi, h5vc, MAGeCKFlute, martini, massiR, MineICA, MiRaGE, MIRit, MutationalPatterns, netSmooth, oligo, OrganismDbi, pathlinkR, piano, Pigengene, progeny, R3CPET, RnBeads, rTRM, scater, ShortRead, SIM, sincell, tidysbml, trackViewer, wiggleplotr, zinbwave, BioMartGOGeneSets, BloodCancerMultiOmics2017, leeBamViews, RegParallel, RforProteomics, BED, BioInsight, DGEobj, DGEobj.utils, grandR, kangar00, MoBPS, Patterns, Platypus, scDiffCom, SNPassoc
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	biomaRt_2.62.0.tar.gz
Windows Binary (x86_64)	biomaRt_2.62.0.zip (64-bit only)
macOS Binary (x86_64)	biomaRt_2.62.0.tgz
macOS Binary (arm64)	biomaRt_2.62.0.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