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

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Documentation for package ‘biomaRt’ version 2.28.0

Help Pages

attributePages Gives a summary of the attribute pages
columns Retrieve information from the BioMart databases
columns-method Retrieve information from the BioMart databases
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 identifiers
getLDS Retrieves information from two linked datasets
getSequence Retrieves sequences
getXML Retrieves information from the BioMart database using an XML query
keys Retrieve information from the BioMart databases
keys-method Retrieve information from the BioMart databases
keytypes Retrieve information from the BioMart databases
keytypes-method Retrieve information from the BioMart databases
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 paper
select Retrieve information from the BioMart databases
select-method Retrieve information from the BioMart databases
select-methods Retrieve information from the BioMart databases
show-method Class Mart
useDataset Select a dataset to use and updates Mart object
useEnsembl Connects to the selected BioMart database and dataset hosted by Ensembl
useMart Connects to the selected BioMart database and dataset