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

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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 <biomartdev@gmail.com>, Wolfgang Huber
Date of publication
None
Maintainer
Steffen Durinck <biomartdev@gmail.com>
License
Artistic-2.0
Version
2.30.0

View on Bioconductor

Man pages

attributePages
Gives a summary of the attribute pages
exportFASTA
Exports getSequence results to FASTA format
filterOptions
Displays the filter options
filterType
Displays the filter type
getBM
Retrieves information from the BioMart database
getBMlist
Retrieves information from the BioMart database
getGene
Retrieves gene annotation information given a vector of...
getLDS
Retrieves information from two linked datasets
getSequence
Retrieves sequences
getXML
Retrieves information from the BioMart database using an XML...
listAttributes
lists the attributes available in the selected dataset
listDatasets
lists the datasets available in the selected BioMart database
listEnsembl
lists the available BioMart databases hosted by Ensembl
listFilters
lists the filters available in the selected dataset
listMarts
lists the avilable BioMart databases
Mart-class
Class Mart
NP2009code
Display the analysis code from the 2009 Nature protocols...
select
Retrieve information from the BioMart databases
useDataset
Select a dataset to use and updates Mart object
useEnsembl
Connects to the selected BioMart database and dataset hosted...
useMart
Connects to the selected BioMart database and dataset

Files in this package

biomaRt/DESCRIPTION
biomaRt/NAMESPACE
biomaRt/NEWS
biomaRt/R
biomaRt/R/biomaRt.R
biomaRt/R/biomaRtClasses.R
biomaRt/R/methods-Mart.R
biomaRt/build
biomaRt/build/vignette.rds
biomaRt/inst
biomaRt/inst/CITATION
biomaRt/inst/doc
biomaRt/inst/doc/biomaRt.R
biomaRt/inst/doc/biomaRt.Rmd
biomaRt/inst/doc/biomaRt.html
biomaRt/inst/scripts
biomaRt/inst/scripts/Integration-NP.R
biomaRt/man
biomaRt/man/Mart-class.Rd
biomaRt/man/NP2009code.Rd
biomaRt/man/attributePages.Rd
biomaRt/man/exportFASTA.Rd
biomaRt/man/filterOptions.Rd
biomaRt/man/filterType.Rd
biomaRt/man/getBM.Rd
biomaRt/man/getBMlist.Rd
biomaRt/man/getGene.Rd
biomaRt/man/getLDS.Rd
biomaRt/man/getSequence.Rd
biomaRt/man/getXML.Rd
biomaRt/man/listAttributes.Rd
biomaRt/man/listDatasets.Rd
biomaRt/man/listEnsembl.Rd
biomaRt/man/listFilters.Rd
biomaRt/man/listMarts.Rd
biomaRt/man/select.Rd
biomaRt/man/useDataset.Rd
biomaRt/man/useEnsembl.Rd
biomaRt/man/useMart.Rd
biomaRt/vignettes
biomaRt/vignettes/biomaRt.Rmd