@@ 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")