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| author | zimoun <zimon.toutoune@gmail.com> | 2021-05-21 22:26:02 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-05-31 15:37:59 +0200 |
| commit | 8d4311bb8e0e7ae68f0182bf232f598ebe2835e5 (patch) | |
| tree | e5d962fc69035572f60798ab903b0c2d05bfe67a /gnu/packages/bioconductor.scm | |
| parent | 96ae9822c4c641587ea151e6a58eddbdb6e66590 (diff) | |
| download | guix-patches-8d4311bb8e0e7ae68f0182bf232f598ebe2835e5.tar guix-patches-8d4311bb8e0e7ae68f0182bf232f598ebe2835e5.tar.gz | |
gnu: r-vsn: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9faf7021da..a631143102 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3746,6 +3746,42 @@ dependencies between GO terms can be implemented and applied.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +their variance is independent of the mean, and they are usually more sensitive +and specific in detecting differential transcription.") + (license license:artistic2.0))) + (define-public r-xvector (package (name "r-xvector") |