diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-18 14:09:18 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-07 17:18:16 +0100 |
| commit | 2fd7c04984cf204dc90d5def68cad02002cd5937 (patch) | |
| tree | 1744d0e6d8926113f18e0a7f976fa7d06c884fda /gnu/packages/bioinformatics.scm | |
| parent | 317755ff0fbd443466b162b358f650edeff10b69 (diff) | |
gnu: Add GenomicFeatures.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c7728160e6..34a0e76f75 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3746,6 +3746,47 @@ built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.22.7") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "1jb4s49ar5j9qslpd3kfdg2wrl4q7ciysd55h9a7zvspymxcngq8")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") |