biomaRt

This is the development version of biomaRt; for the stable release version, see biomaRt.

Interface to BioMart databases (i.e. Ensembl)

Bioconductor version: Development (3.23)

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 (). 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.

Author: Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb] ORCID: 0000-0002-7800-3848 , Hugo Gruson [ctb, cre] ORCID: 0000-0002-4094-1476 , German Network for Bioinformatics Infrastructure - de.NBI [fnd]

Maintainer: Hugo Gruson <hugo.gruson at embl.de>

Citation (from within R, enter citation("biomaRt")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("biomaRt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Software
Version	2.67.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 20.5 years)
License	Artistic-2.0
Depends	methods, R (>= 4.5.0)
Imports	AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr, utils, xml2
System Requirements
URL	https://github.com/Huber-group-EMBL/biomaRt https://huber-group-embl.github.io/biomaRt/
Bug Reports	https://github.com/Huber-group-EMBL/biomaRt/issues

Suggests	BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/biomaRt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biomaRt
Package Short Url	https://bioconductor.org/packages/biomaRt/
Package Downloads Report	Download Stats