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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-05-17 16:38:17 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-05-22 18:54:59 +0200 |
| commit | 296b3c631c2e8cf42f5a0920cd11c424daec9ea4 (patch) | |
| tree | 198e2d036be3b6d7d03f5dcf49145f9c3cfe37bb /gnu/packages | |
| parent | 7b46532779ddc6b01f99989be0eda91149809ce4 (diff) | |
| download | patches-296b3c631c2e8cf42f5a0920cd11c424daec9ea4.tar patches-296b3c631c2e8cf42f5a0920cd11c424daec9ea4.tar.gz | |
gnu: Add r-edaseq.
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 55c076ca1b..21bf2d409a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9052,6 +9052,44 @@ differential expression based on a model using the negative binomial distribution.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-deseq" ,r-deseq) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package |