biomaRt

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

Bioconductor version: 2.8

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 <sdurinck at gmail.com>, Wolfgang Huber <huber at ebi.ac.uk>

Maintainer: Steffen Durinck <sdurinck at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("biomaRt")

To cite this package in a publication, start R and enter:

    citation("biomaRt")

Documentation

PDF R Script The biomaRt users guide
PDF   Reference Manual

Details

biocViews Annotation
Depends methods
Imports XML, RCurl
Suggests annotate
System Requirements
License Artistic-2.0
URL
Depends On Me ChIPpeakAnno, domainsignatures, gene2pathway, GenomeGraphs
Imports Me affycoretools, ArrayExpressHTS, ChIPpeakAnno, GenomicFeatures, HTSanalyzeR, phenoTest, R453Plus1Toolbox, RNAither
Suggests Me BiocCaseStudies, ccTutorial, GeneAnswers, GenomicFeatures, Genominator, leeBamViews, maDB, oneChannelGUI, ShortRead, SIM
Version 2.8.1
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source biomaRt_2.8.1.tar.gz
Windows Binary biomaRt_2.8.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary biomaRt_2.8.1.tgz
Package Downloads Report Download Stats

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