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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-23 17:35:04 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-07 17:18:17 +0100 |
| commit | cb933df6daa08c0fbb0604f32badc7b97281d5e5 (patch) | |
| tree | b0d310eb3bb0fc8259949eb02d5ee280ce85fc97 /gnu/packages | |
| parent | 03ea5a357ecc8d821078cbbcfb038ee6eeb46898 (diff) | |
| download | patches-cb933df6daa08c0fbb0604f32badc7b97281d5e5.tar patches-cb933df6daa08c0fbb0604f32badc7b97281d5e5.tar.gz | |
gnu: Add genomation.
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 43 |
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") |