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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2017-08-09 19:40:22 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-08-14 12:00:51 +0200 |
| commit | 86763fdd70b48df5e4be5f2df6ac4335d9f7abe5 (patch) | |
| tree | cebe96695862c24fde26fd29fb083a5b171abb33 | |
| parent | 233f4f43bfe851d9b7a3dee7e881dcd017a2c1a3 (diff) | |
| download | guix-86763fdd70b48df5e4be5f2df6ac4335d9f7abe5.tar guix-86763fdd70b48df5e4be5f2df6ac4335d9f7abe5.tar.gz | |
gnu: Add r-dexseq.
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
| -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 92c64cffa0..c5a4dcad93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5791,6 +5791,49 @@ differential expression based on a model using the negative binomial distribution.") (license license:lgpl3+))) +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg")))) + (properties `((upstream-name . "DEXSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biomart" ,r-biomart) + ("r-deseq2" ,r-deseq2) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-statmod" ,r-statmod) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "http://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + (define-public r-annotationforge (package (name "r-annotationforge") |