From b4569f95fc2610382206c8dc592df7c45f1ff6fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 18 Dec 2015 14:06:52 +0100 Subject: [PATCH 10/17] gnu: Add biomaRt. * gnu/packages/bioinformatics.scm (r-biomart): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea78798..4e4bc54 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3546,6 +3546,37 @@ 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") + (r-repository . bioconductor))) + (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") -- 2.1.0