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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-09-05 11:45:57 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-09-05 11:46:29 +0200 |
| commit | 38babeaaa46c2293f0d59f6fc6e2de52d9f7b6aa (patch) | |
| tree | 13471d0186157bbdad1c607b0ee4c01a8e733dd4 | |
| parent | 46721deaf80ec8150ad22e853766e69fff31c670 (diff) | |
| download | patches-38babeaaa46c2293f0d59f6fc6e2de52d9f7b6aa.tar patches-38babeaaa46c2293f0d59f6fc6e2de52d9f7b6aa.tar.gz | |
gnu: Add r-watermelon.
* gnu/packages/bioconductor.scm (r-watermelon): New variable.
| -rw-r--r-- | gnu/packages/bioconductor.scm | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f80f975be7..8f1a4ef39f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5319,3 +5319,40 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") "This package provides manifests and annotation for Illumina's 450k array data.") (license license:artistic2.0))) + +(define-public r-watermelon + (package + (name "r-watermelon") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wateRmelon" version)) + (sha256 + (base32 + "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) + (properties `((upstream-name . "wateRmelon"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-illuminahumanmethylation450kanno-ilmn12-hg19" + ,r-illuminahumanmethylation450kanno-ilmn12-hg19) + ("r-illuminaio" ,r-illuminaio) + ("r-limma" ,r-limma) + ("r-lumi" ,r-lumi) + ("r-matrixstats" ,r-matrixstats) + ("r-methylumi" ,r-methylumi) + ("r-roc" ,r-roc))) + (home-page "https://bioconductor.org/packages/wateRmelon/") + (synopsis "Illumina 450 methylation array normalization and metrics") + (description + "The standard index of DNA methylation (beta) is computed from methylated +and unmethylated signal intensities. Betas calculated from raw signal +intensities perform well, but using 11 methylomic datasets we demonstrate that +quantile normalization methods produce marked improvement. The commonly used +procedure of normalizing betas is inferior to the separate normalization of M +and U, and it is also advantageous to normalize Type I and Type II assays +separately. This package provides 15 flavours of betas and three performance +metrics, with methods for objects produced by the @code{methylumi} and +@code{minfi} packages.") + (license license:gpl3))) |