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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>

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

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

Details

biocViews Annotation, Software
Version 2.56.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License Artistic-2.0
Depends methods
Imports utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr, httr, digest, BiocFileCache, rappdirs, xml2
Linking To
Suggests BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr
System Requirements
Enhances
URL https://github.com/grimbough/biomaRt
Bug Reports https://github.com/grimbough/biomaRt/issues
See More
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, 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