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Fri, 21 May 2021 13:26:48 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:02 +0200 Message-Id: <20210521202622.26591-30-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1621629207; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; 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spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=FJXahakv; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 53FDC1AF1A X-Spam-Score: 2.66 X-Migadu-Scanner: scn1.migadu.com X-TUID: cHiAwMvp0ZV5 * gnu/packages/bioinformatics.scm (r-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 --------------------------------- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0ebcf8481..05c4896276 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3480,6 +3480,42 @@ 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") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7256df3f83..600c2ca81e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (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-ensembldb (package (name "r-ensembldb") -- 2.30.1