Interface to BioMart databases (i.e. Ensembl)

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Documentation for package ‘biomaRt’ version 2.65.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

attributePages	Gives a summary of the attribute pages
biomaRt-deprecated	Deprecated and defunct functions in package 'biomaRt'
biomartCacheClear	biomaRt result caching
biomartCacheInfo	biomaRt result caching
columns	Retrieve information from the BioMart databases
columns-method	Retrieve information from the BioMart databases
exportFASTA	Exports getSequence results to FASTA format
filterOptions	Deprecated and defunct functions in package 'biomaRt'
filterType	Displays the filter type
getBM	Retrieves information from the BioMart database
getBMlist	Deprecated and defunct functions in package 'biomaRt'
getGene	Retrieves gene annotation information given a vector of identifiers
getHomologs	List homologous genes between two species.
getLDS	Retrieves information from two linked datasets
getSequence	Retrieves sequences
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	List or search the datasets available in the selected BioMart database
listEnsembl	lists the available BioMart databases hosted by Ensembl
listEnsemblArchives	Lists the available archived versions of Ensembl
listEnsemblGenomes	lists the available BioMart databases hosted by Ensembl
listFilterOptions	List or search the options available for a specified filter.
listFilters	List or search the filters available in the selected dataset
listFilterValues	Deprecated and defunct functions in package 'biomaRt'
listMarts	lists the available BioMart databases
Mart-class	Class Mart
NP2009code	Display the analysis code from the 2009 Nature protocols paper
searchAttributes	lists the attributes available in the selected dataset
searchDatasets	List or search the datasets available in the selected BioMart database
searchFilterOptions	List or search the options available for a specified filter.
searchFilters	List or search the filters available in the selected dataset
searchFilterValues	Deprecated and defunct functions in package 'biomaRt'
select	Retrieve information from the BioMart databases
select-method	Retrieve information from the BioMart databases
select-methods	Retrieve information from the BioMart databases
setEnsemblSSL	Save system specific SSL settings for contacting Ensembl
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
useEnsemblGenomes	Connects to the selected BioMart database and dataset hosted by Ensembl
useMart	Connects to the selected BioMart database and dataset