Package: biomaRt 2.63.0

Mike Smith

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.

Authors:Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre]

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biomaRt.pdf |biomaRt.html✨
biomaRt/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/grimbough/biomart/issues

On BioConductor:biomaRt-2.63.0(bioc 3.21)biomaRt-2.62.0(bioc 3.20)

annotationbioconductorbiomartensembl

15.88 score 36 stars 228 packages 13k scripts 38k downloads 446 mentions 36 exports 61 dependencies

Last updated 1 months agofrom:d5a275caeb. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:attributePagesbiomartCacheClearbiomartCacheInfocolumnsexportFASTAfilterOptionsfilterTypegetBMgetGenegetHomologsgetLDSgetSequencekeyskeytypeslistAttributeslistDatasetslistEnsembllistEnsemblArchiveslistEnsemblGenomeslistFilterOptionslistFilterslistFilterValueslistMartsNP2009codesearchAttributessearchDatasetssearchFilterOptionssearchFilterssearchFilterValuesselectsetEnsemblSSLshowuseDatasetuseEnsembluseEnsemblGenomesuseMart

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc

Accessing Ensembl annotation with biomaRt

Mike L. Smith, Steffen Durinck, Wolfgang Huber

Rendered fromaccessing_ensembl.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-01-24
Started: 2020-01-30

Using a BioMart other than Ensembl

Steffen Durinck, Wolfgang Huber, Mike Smith

Rendered fromaccessing_other_marts.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-06-24
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 getBMlist listFilterValues searchFilterValues
biomaRt result cachingbiomartCacheClear 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 options available for a specified filter.listFilterOptions searchFilterOptions
List or search the filters available in the selected datasetlistFilters searchFilters
lists the available BioMart databaseslistMarts
Class MartMart-class show,Mart-method
Display the analysis code from the 2009 Nature protocols paperNP2009code
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
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