biomaRt v2.28.0

by Steffen Durinck

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.

Functions in biomaRt

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

Contributors Sean Davis , Francois Pepin, Vince S. Buffalo
biocViews Annotation
License Artistic-2.0
LazyLoad yes

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