biomaRt

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Interface to BioMart databases (i.e. Ensembl)

Bioconductor version: Development (3.24)

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 (<https://www.ensembl.org/info/data/biomart/index.html>). 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 maintained 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] ORCID: 0000-0002-7800-3848 , Hugo Gruson [ctb, cre] ORCID: 0000-0002-4094-1476 , German Network for Bioinformatics Infrastructure - de.NBI [fnd]

Maintainer: Hugo Gruson <hugo.gruson at embl.de>

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

Steffen Durinck, Wolfgang Huber. biomaRt: Interface to BioMart databases (i.e. Ensembl). doi:10.18129/B9.bioc.biomaRt, R package version 2.69.3, https://bioconductor.org/packages/biomaRt.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	2.69.3
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 years)
License	Artistic-2.0
Depends	methods, R (>= 4.5.0)
Imports	AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr, utils, xml2
System Requirements
URL	https://github.com/Huber-group-EMBL/biomaRt https://huber-group-embl.github.io/biomaRt/
Bug Reports	https://github.com/Huber-group-EMBL/biomaRt/issues

Suggests	BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>= 3.0.0), withr
Linking To
Enhances
Depends On Me	chromPlot, customProDB, DrugVsDisease, genefu, GenomicOZone, MantaID, NetSAM, PPInfer, RepViz, VegaMC
Imports Me	BadRegionFinder, biomartr, BioVenn, branchpointer, BUSpaRse, ChIPpeakAnno, CHRONOS, convertid, CoSIA, dagLogo, DEXSeq, DiNAMIC.Duo, DMRcate, DominoEffect, dominoSignal, drugTargetInteractions, easyRNASeq, EDASeq, ELMER, EpiMix, epimutacions, FRASER, GDCRNATools, geneClusterPattern, GenVisR, GExPipe, gINTomics, glmSparseNet, GOexpress, goSTAG, GPlinksR, GRaNIE, Gviz, hermes, InterCellar, isobar, LACE, mCSEA, MEDIPS, MetaboSignal, metaseqR2, MGFR, motifbreakR, MouseFM, netZooR, NoRCE, OncoScore, oposSOM, ORFik, pcaExplorer, phenoTest, pRoloc, ProteoMM, R453Plus1Toolbox, ramwas, recoup, ReducedExperiment, rgsepd, RnaSeqSampleSize, scafari, scGOclust, scPipe, scQTLtools, seq2pathway, SeqGSEA, singIST, sitadela, snplinkage, snplist, SpliceImpactR, SPLINTER, SPONGE, surfaltr, SurfR, SWATH2stats, TCGAbiolinks, TEKRABber, terapadog, TFEA.ChIP, transcriptogramer, txdbmaker, ViSEAGO, yarn
Suggests Me	AnnotationForge, BED, bioassayR, BioInsight, BioMartGOGeneSets, BloodCancerMultiOmics2017, celda, CimpleG, ClusterJudge, CNVScope, crisprDesign, cTRAP, Damsel, DELocal, DGEobj, DGEobj.utils, diffwrap, DOTSeq, epistack, ExpHunterSuite, fedup, FELLA, gaawr2, GeDi, geneviewer, grandR, GRIN2, IDConverter, IOBR, kangar00, leeBamViews, martini, massiR, MiRaGE, MIRit, MoBPS, MosaiClusteR, MutationalPatterns, netSmooth, oligo, OrganismDbi, pathlinkR, Patterns, piano, Pigengene, ProFAST, progeny, R3CPET, RegParallel, RforProteomics, RnBeads, rtemis.a3, rTRM, scater, scDiffCom, SCORPION, ShortRead, SIM, sincell, SNPassoc, tidysbml, trackViewer, wiggleplotr, zinbwave
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	biomaRt_2.69.3.tar.gz
Windows Binary (x86_64)	biomaRt_2.69.0.zip
macOS Binary (big-sur-x86_64)	biomaRt_2.69.3.tgz
macOS Binary (sonoma-arm64)	biomaRt_2.69.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biomaRt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biomaRt
Package Short Url	https://bioconductor.org/packages/biomaRt/
Package Downloads Report	Download Stats