biomaRt

DOI: 10.18129/B9.bioc.biomaRt    

Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)

Bioconductor version: Release (3.6)

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 (http://www.biomart.org). 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. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable 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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

Documentation

HTML	R Script	The biomaRt users guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Software
Version	2.34.2
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 13 years)
License	Artistic-2.0
Depends	methods
Imports	utils, XML, RCurl, AnnotationDbi, progress, stringr, httr
LinkingTo
Suggests	annotate, BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me	chromPlot, coMET, customProDB, dagLogo, domainsignatures, DrugVsDisease, genefu, GenomeGraphs, MineICA, PPInfer, PSICQUIC, Roleswitch, Sushi, VegaMC
Imports Me	ArrayExpressHTS, BadRegionFinder, branchpointer, ChIPpeakAnno, CHRONOS, cobindR, customProDB, DEXSeq, diffloop, DOQTL, easyRNASeq, EDASeq, ELMER, GenomicFeatures, GenVisR, gespeR, GOexpress, goSTAG, Gviz, HTSanalyzeR, IdMappingRetrieval, isobar, KEGGprofile, MEDIPS, MetaboSignal, metaseqR, methyAnalysis, MGFR, OncoScore, oposSOM, Pbase, pcaExplorer, PGA, phenoTest, pRoloc, psygenet2r, pwOmics, R453Plus1Toolbox, ramwas, RCAS, recoup, rgsepd, RNAither, RnaSeqSampleSize, scater, scPipe, seq2pathway, SeqGSEA, SPLINTER, TCGAbiolinks, transcriptogramer, trena, yarn
Suggests Me	AnnotationForge, bioassayR, BiocCaseStudies, ccTutorial, cellTree, chromstaR, ClusterJudge, GeneAnswers, Genominator, h5vc, leeBamViews, LINC, massiR, MineICA, MiRaGE, MutationalPatterns, oligo, oligo, oneChannelGUI, OrganismDbi, paxtoolsr, piano, Pigengene, progeny, R3CPET, Rcade, RforProteomics, RIPSeeker, RnaSeqTutorial, RnBeads, rTANDEM, rTRM, ShortRead, SIM, sincell, systemPipeR, trackViewer, wiggleplotr, zinbwave
Build Report

Package Archives

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

Source Package	biomaRt_2.34.2.tar.gz
Windows Binary	biomaRt_2.34.2.zip
Mac OS X 10.11 (El Capitan)	biomaRt_2.34.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biomaRt
Package Short Url	http://bioconductor.org/packages/biomaRt/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive