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biomaRt

Interface to BioMart databases (i.e. Ensembl)

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. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Functions (23)

Mart-class

Class Mart

NP2009code

Display the analysis code from the 2009 Nature protocols paper

attributePages

Gives a summary of the attribute pages

biomartCache

biomaRt result caching

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

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

listFilterValues

List or search the options available for a specified filter.

listFilters

List or search the filters available in the selected dataset

listMarts

lists the available BioMart databases

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 by Ensembl

useMart

Connects to the selected BioMart database and dataset

biomaRt

Interface to BioMart databases (i.e. Ensembl)

v2.46.3

Artistic-2.0

Authors

Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre] (<https://orcid.org/0000-0002-7800-3848>)

Initial release

biomaRt

Functions (23)

biomaRt

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