@@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the
alignments.")
(license license:artistic2.0)))
+(define-public r-genomicfeatures
+ (package
+ (name "r-genomicfeatures")
+ (version "1.42.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicFeatures" version))
+ (sha256
+ (base32
+ "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
+ (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)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://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-genomicranges
(package
(name "r-genomicranges")
@@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.")
(home-page "https://github.com/vcflib/bio-vcf")
(license license:expat)))
-(define-public r-genomicfeatures
- (package
- (name "r-genomicfeatures")
- (version "1.42.3")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "GenomicFeatures" version))
- (sha256
- (base32
- "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
- (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)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://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-go-db
(package
(name "r-go-db")