Package: biomaRt 2.69.0

Hugo Gruson

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 (<https://www.ensembl.org/info/data/biomart/index.html>). 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 maintained 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.

Authors:Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb], Hugo Gruson [ctb, cre], German Network for Bioinformatics Infrastructure - de.NBI [fnd]

biomaRt_2.69.0.tar.gz
biomaRt_2.69.0.zip(r-4.7)biomaRt_2.69.0.zip(r-4.6)biomaRt_2.69.0.zip(r-4.5)
biomaRt_2.69.0.tgz(r-4.6-any)biomaRt_2.69.0.tgz(r-4.5-any)
biomaRt_2.69.0.tar.gz(r-4.7-any)biomaRt_2.69.0.tar.gz(r-4.6-any)
biomaRt_2.69.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
biomaRt/json (API)
NEWS

# Install 'biomaRt' in R:
install.packages('biomaRt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huber-group-embl/biomart/issues

Pkgdown/docs site:https://huber-group-embl.github.io

On BioConductor:biomaRt-2.69.0(bioc 3.24)biomaRt-2.68.0(bioc 3.23)

annotationbioconductorbiomartensembl

16.50 score 49 stars 214 packages 17k scripts 41k downloads 446 mentions 36 exports 55 dependencies

Last updated from:0b83a479a1. Checks:1 WARNING, 4 ERROR, 2 OK, 3 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING167
linux-devel-x86_64ERROR233
source / vignettesOK386
linux-release-x86_64ERROR233
macos-release-arm64ERROR354
macos-oldrel-arm64ERROR179
windows-develNOTE159
windows-releaseNOTE151
windows-oldrelNOTE151
wasm-releaseOK123

Exports:attributePagesbiomartCacheClearbiomartCacheInfocolumnsexportFASTAfilterOptionsfilterTypegetBMgetGenegetHomologsgetLDSgetSequencekeyskeytypeslistAttributeslistDatasetslistEnsembllistEnsemblArchiveslistEnsemblGenomeslistFilterOptionslistFilterslistFilterValueslistMartsNP2009codesearchAttributessearchDatasetssearchFilterOptionssearchFilterssearchFilterValuesselectsetEnsemblSSLshowuseDatasetuseEnsembluseEnsemblGenomesuseMart

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrxml2XVector

Accessing Ensembl annotation with biomaRt

Rendered fromaccessing_ensembl.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-09-29
Started: 2020-01-30

Using a BioMart other than Ensembl

Rendered fromaccessing_other_marts.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-09-29
Started: 2020-11-10

Readme and manuals

Help Manual

Help pageTopics
Gives a summary of the attribute pagesattributePages
Deprecated and defunct functions in package 'biomaRt'biomaRt-deprecated filterOptions listFilterValues searchFilterValues
'biomaRt' result cachingbiomartCache biomartCacheClear biomartCacheInfo
Exports getSequence results to FASTA formatexportFASTA
Displays the filter typefilterType
Retrieves information from the BioMart databasegetBM
Retrieves gene annotation information given a vector of identifiersgetGene
List homologous genes between two species.getHomologs
Retrieves information from two linked datasetsgetLDS
Retrieves sequencesgetSequence
lists the attributes available in the selected datasetlistAttributes searchAttributes
List or search the datasets available in the selected BioMart databaselistDatasets searchDatasets
lists the available BioMart databases hosted by EnsembllistEnsembl listEnsemblGenomes
Lists the available archived versions of EnsembllistEnsemblArchives
List or search the filters available in the selected datasetlistFilters searchFilters
lists the available BioMart databaseslistMarts
Display the analysis code from the 2009 Nature protocols paperNP2009code
List or search the options available for a specified filter.listFilterOptions searchFilterOptions
Retrieve information from the BioMart databasescolumns columns,Mart-method keys keys,Mart-method keytypes keytypes,Mart-method select select,Mart-method select-methods
Save system specific SSL settings for contacting EnsemblsetEnsemblSSL
Class MartMart-class show,Mart-method
Select a dataset to use and updates Mart objectuseDataset
Connects to the selected BioMart database and dataset hosted by EnsembluseEnsembl useEnsemblGenomes
Connects to the selected BioMart database and datasetuseMart