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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-11-03 14:40:59 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-11-04 16:30:11 +0100 |
| commit | cb0e60cccfa88ed642a947d146bdc3c0da8d31ec (patch) | |
| tree | 687e9495b543be6d12d51215218d47e67a063471 /gnu/packages | |
| parent | 9dcd8802f5bc472579f23a38dcf437f8a9ac976c (diff) | |
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.
* gnu/packages/bioconductor.scm
(r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.
Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ccc5f49b2..38f9ce64ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name "r-bsgenome-hsapiens-ucsc-hg38-masked") + (version "1.4.5") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version + 'annotation)) + (sha256 + (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m")))) + (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38 + r-genomeinfodb)) + (home-page + "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked") + (synopsis + "Full masked genomic sequences for Homo sapiens (UCSC version hg38)") + (description + "This package provides the complete genome sequences for Homo sapiens as +provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). +The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each +of them has the 4 following masks on top: + +@enumerate +@item the mask of assembly gaps (AGAPS mask); +@item the mask of intra-contig ambiguities (AMB mask); +@item the mask of repeats from @code{RepeatMasker} (RM mask); +@item the mask of repeats from Tandem Repeats Finder (TRF mask). +@end enumerate + +Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored +in @code{MaskedDNAString} objects.") + (license license:artistic2.0))) + (define-public r-hpo-db (package (name "r-hpo-db") |