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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-18 14:08:36 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-07 17:18:16 +0100
commitd8a828af78ce92c583bedb23e379b5b4dd332ab1 (patch)
treee10e8fbabac0303b01857ce2defdeeab8a685e8d /gnu
parent6e76dda2d08581d554b1605c819ec53958a4188f (diff)
downloadpatches-d8a828af78ce92c583bedb23e379b5b4dd332ab1.tar
patches-d8a828af78ce92c583bedb23e379b5b4dd332ab1.tar.gz
gnu: Add GenomicAlignments.
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm33
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4da9954c5b..1969b72a04 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3668,6 +3668,39 @@ typically represent genomic ranges of interest and the columns represent
samples.")
(license license:artistic2.0)))
+(define-public r-genomicalignments
+ (package
+ (name "r-genomicalignments")
+ (version "1.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicAlignments" version))
+ (sha256
+ (base32
+ "03pxzkmwcpl0d7a09ahan0nllfv7qw2i7w361w6af2s4n3xwrniz"))))
+ (properties
+ `((upstream-name . "GenomicAlignments")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/GenomicAlignments")
+ (synopsis "Representation and manipulation of short genomic alignments")
+ (description
+ "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome). This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")