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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-18 14:06:52 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-07 17:18:16 +0100
commitc465fa72ed004ebdb18ae67309da85826d426d67 (patch)
tree6757a34fd835dc984a7bd31200dd2866337db925
parent8b7bce740d507d544b6634b0f60be9450b36c5fc (diff)
downloadguix-c465fa72ed004ebdb18ae67309da85826d426d67.tar
guix-c465fa72ed004ebdb18ae67309da85826d426d67.tar.gz
gnu: Add biomaRt.
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm30
1 files changed, 30 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9577f714ff..c8c74ff902 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3515,6 +3515,36 @@ on Bioconductor or which replace R functions.")
annotation data packages using SQLite data storage.")
(license license:artistic2.0)))
+(define-public r-biomart
+ (package
+ (name "r-biomart")
+ (version "2.26.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biomaRt" version))
+ (sha256
+ (base32
+ "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f"))))
+ (properties
+ `((upstream-name . "biomaRt")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-rcurl" ,r-rcurl)
+ ("r-xml" ,r-xml)))
+ (home-page "http://bioconductor.org/packages/biomaRt")
+ (synopsis "Interface to BioMart databases")
+ (description
+ "biomaRt provides an interface to a growing collection of databases
+implementing the @url{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.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")