@@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
CAGE.")
(license license:gpl2+)))
+(define-public r-ensembldb
+ (package
+ (name "r-ensembldb")
+ (version "2.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ensembldb" version))
+ (sha256
+ (base32
+ "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationfilter" ,r-annotationfilter)
+ ("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)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (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-fastseg
(package
(name "r-fastseg")
@@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has
previously been used in XCMS.")
(license license:artistic2.0)))
-(define-public r-ensembldb
- (package
- (name "r-ensembldb")
- (version "2.14.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "ensembldb" version))
- (sha256
- (base32
- "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("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)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (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-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))