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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-11-07 15:32:35 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-11-07 23:32:42 +0100 |
| commit | aa30ab5aeebc14376ccc29a68d8b4e4fb8184fca (patch) | |
| tree | de36bf1ff4d4d34f8ad2331fecf8c74321b3679e | |
| parent | 763e98103a0cd39715e619eca2cc3c7806498b1e (diff) | |
| download | patches-aa30ab5aeebc14376ccc29a68d8b4e4fb8184fca.tar patches-aa30ab5aeebc14376ccc29a68d8b4e4fb8184fca.tar.gz | |
gnu: Add r-ensembldb.
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 227bc34296..b6a3aa9722 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9599,6 +9599,50 @@ filters for manipulating Bioconductor annotation resources. The filters are used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (license license:artistic2.0))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-qvalue (package (name "r-qvalue") |