biomaRt
Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene
and Uniprot)
The package provides and API in R to query BioMart
databases such as Ensembl (http://www.ensembl.org), a software
system which produces and maintains automatic annotation on
metazoan genomes. Two sets of functions are currently
implemented. A first set of functions aims to mimic
functionality of other BioMart APIs such as Martshell,
Martview, etc. (see http://www.biomart.org for more
information). These functions are very general, and can be
used with any BioMart system. They allow retrieval of all
information that other BioMart APIs provide. A Second set of
functions are tailored towards Ensembl and are a set of
commonly used queries in microarray data analysis. With these
two sets of functions, one can for example annotate the
features on your array with the latest annotations starting
from identifiers such as Affymetrix, RefSeq, entrezgene,..
Annotation includes gene names, GO, OMIM annotation, etc. The
package also provides homology mappings between these
identifiers across all species present in Ensembl. Genes can
be pre-selected such that they fulfill a certain requirement
e.g. give all human RefSeq ids of genes known to be involved in
diabetes. On top of this, biomaRt enables you to retrieve any
type of information available from the BioMart databases from
R. Other examples of BioMart databases are Wormbase and
Gramene.
| Author |
Steffen Durinck , Wolfgang Huber
, Sean Davis |
| Maintainer |
Steffen Durinck |
Vignettes (Documentation)
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Package Downloads
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Details
| biocViews |
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| Depends |
methods, XML, RCurl |
| Suggests |
annotate |
| Imports |
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| SystemRequirements |
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| License |
Artistic License 2.0 |
| URL |
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| dependsOnMe |
affycoretools |
| suggestsMe |
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