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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")
AuthorSteffen Durinck <biomartdev@gmail.com>, Wolfgang Huber
Bioconductor views Annotation
Date of publicationNone
MaintainerSteffen Durinck <biomartdev@gmail.com>
LicenseArtistic-2.0
Version2.32.0

View on Bioconductor

Functions

attributePages Man page
columns Man page
columns,Mart-method Man page
exportFASTA Man page
filterOptions Man page
filterType Man page
getBM Man page
getBMlist Man page
getGene Man page
getLDS Man page
getSequence Man page
getXML Man page
keys Man page
keys,Mart-method Man page
keytypes Man page
keytypes,Mart-method Man page
listAttributes Man page
listDatasets Man page
listEnsembl Man page
listFilters Man page
listMarts Man page
Mart-class Man page
NP2009code Man page
select Man page
select,Mart-method Man page
select-methods Man page
show,Mart-method Man page
useDataset Man page
useEnsembl Man page
useMart Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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