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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-23 17:35:04 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-07 17:18:17 +0100
commitcb933df6daa08c0fbb0604f32badc7b97281d5e5 (patch)
treeb0d310eb3bb0fc8259949eb02d5ee280ce85fc97
parent03ea5a357ecc8d821078cbbcfb038ee6eeb46898 (diff)
downloadgnu-guix-cb933df6daa08c0fbb0604f32badc7b97281d5e5.tar
gnu-guix-cb933df6daa08c0fbb0604f32badc7b97281d5e5.tar.gz
gnu: Add genomation.
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm43
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f574bde9e7..1d29b7d672 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3912,6 +3912,49 @@ sequence motif occurrences across a large set of sequences centred at a common
reference point and sorted by a user defined feature.")
(license license:gpl3+)))
+(define-public r-genomation
+ (package
+ (name "r-genomation")
+ (version "1.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genomation" version))
+ (sha256
+ (base32
+ "1mzs995snwim13qk9kz4q3nczpnbsy1allwp4whfq0cflg2mndfr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-impute" ,r-impute)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plotrix" ,r-plotrix)
+ ("r-plyr" ,r-plyr)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-seqpattern" ,r-seqpattern)))
+ (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (synopsis "Summary, annotation and visualization of genomic data")
+ (description
+ "This package provides a package for summary and annotation of genomic
+intervals. Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc. The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc. The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals. In addition, it can use BAM or BigWig files as input.")
+ (license license:artistic2.0)))
+
(define-public r-qtl
(package
(name "r-qtl")