biomaRt

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

Bioconductor version: Release (2.7)

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, Wolfgang Huber

Maintainer: Steffen Durinck

To install this package, start R and enter:

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

Documentation

PDF

R Script

The biomaRt users guide

Reference Manual

Details

biocViews	Annotation
Depends	methods
Imports	XML, RCurl
Suggests	annotate
System Requirements
License	Artistic-2.0
URL
Depends On Me	ChIPpeakAnno, GenomeGraphs, domainsignatures, gene2pathway
Imports Me	ChIPpeakAnno, GenomicFeatures, HTSanalyzeR, R453Plus1Toolbox, RNAither, affycoretools
Suggests Me	BiocCaseStudies, GeneAnswers, GenomicFeatures, Genominator, SIM, ShortRead, maDB, oneChannelGUI
Version	2.6.0

Package Downloads

Package Source	biomaRt_2.6.0.tar.gz
Windows Binary	biomaRt_2.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	biomaRt_2.6.0.tgz
Package Downloads Report	Download Stats