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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
In most cases, you don't need to download the package archive at all.
biomaRt
Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)
Bioconductor version: 3.0
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. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.
Author: Steffen Durinck <durincks at gene.com>, Wolfgang Huber
Maintainer: Steffen Durinck <durincks at gene.com>
Citation (from within R,
enter citation("biomaRt")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("biomaRt")
| R Script | The biomaRt users guide | |
| Reference Manual |
Details
| biocViews | Annotation, Software |
| Version | 2.22.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | Artistic-2.0 |
| Depends | methods |
| Imports | utils, XML, RCurl, AnnotationDbi |
| LinkingTo | |
| Suggests | annotate |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ChIPpeakAnno, customProDB, dagLogo, domainsignatures, DrugVsDisease, Fletcher2013b, genefu, GenomeGraphs, MineICA, PSICQUIC, Roleswitch, Sushi, VegaMC |
| Imports Me | affycoretools, ArrayExpressHTS, cobindR, customProDB, DEXSeq, DOQTL, easyRNASeq, GenomicFeatures, GOexpress, Gviz, HTSanalyzeR, IdMappingRetrieval, KEGGprofile, MEDIPS, metaseqR, methyAnalysis, oposSOM, phenoTest, R453Plus1Toolbox, RNAither, SeqGSEA |
| Suggests Me | BiocCaseStudies, ccTutorial, DEGreport, GeneAnswers, Genominator, h5vc, isobar, leeBamViews, massiR, MineICA, MiRaGE, oneChannelGUI, paxtoolsr, Pbase, piano, Rcade, RforProteomics, RIPSeeker, RnaSeqTutorial, rTANDEM, rTRM, ShortRead, SIM, systemPipeR, trackViewer |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | biomaRt_2.22.0.tar.gz |
| Windows Binary | biomaRt_2.22.0.zip |
| Mac OS X 10.6 (Snow Leopard) | biomaRt_2.22.0.tgz |
| Mac OS X 10.9 (Mavericks) | biomaRt_2.22.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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