From patchwork Tue Oct 8 17:35:16 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15674 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id CD8781754D; Tue, 8 Oct 2019 18:57:47 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 809671754B for ; Tue, 8 Oct 2019 18:57:47 +0100 (BST) Received: from localhost ([::1]:59610 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iHtk2-0007YE-Or for patchwork@mira.cbaines.net; Tue, 08 Oct 2019 13:57:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51478) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iHtP2-0006xB-3J for guix-patches@gnu.org; Tue, 08 Oct 2019 13:36:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iHtP0-0005rB-KT for guix-patches@gnu.org; Tue, 08 Oct 2019 13:36:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42627) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iHtP0-0005r1-Gt for guix-patches@gnu.org; Tue, 08 Oct 2019 13:36:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iHtP0-0006Hd-BI for guix-patches@gnu.org; Tue, 08 Oct 2019 13:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37666] [PATCH 1/2] gnu: Add r-htqpcr. References: <20191008165307.903-1-zimon.toutoune@gmail.com> In-Reply-To: <20191008165307.903-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 08 Oct 2019 17:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37666 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37666@debbugs.gnu.org Cc: zimoun Received: via spool by 37666-submit@debbugs.gnu.org id=B37666.157055614324110 (code B ref 37666); Tue, 08 Oct 2019 17:36:02 +0000 Received: (at 37666) by debbugs.gnu.org; 8 Oct 2019 17:35:43 +0000 Received: from localhost ([127.0.0.1]:51445 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iHtOh-0006Go-D7 for submit@debbugs.gnu.org; Tue, 08 Oct 2019 13:35:43 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:50617) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iHtOc-0006GT-3c for 37666@debbugs.gnu.org; Tue, 08 Oct 2019 13:35:41 -0400 Received: by mail-wm1-f52.google.com with SMTP id 5so4089113wmg.0 for <37666@debbugs.gnu.org>; Tue, 08 Oct 2019 10:35:38 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=4FkCApbLNMj9G+G/j9f4QjRPwF/OMXpghAjr35XZQik=; b=f8QQo9VjAvVBdl2aJ+TxBNAErEnZ3e/6VfWBc8Pe6zc3rzucPhWFGdSqT4RlpFVpZT TXyMxO7TKr038VAoKcjNmeqwnKeYob+yFFK0xKcOWQqKjBuQmzEeoYxwMn5VdWPW2f44 u/bodlS22da34lL/xcB6uQt1RFNPsF+yUpLn1YUJ8ur2fRb19SaOMUU2pzGm5kglxdX9 HjoLc8lARRlQMzbF/5qD4bbm0mhySOZZ70cb5JznS/bi3R87QhLMFCqoSTeBwA0X3ZZd Ir9EFBvhYE++saqC91W/MHRWk/+hghVZhLlg7fkJN+rdWS3+eW77YsLt6+Jdj91X5q9z TqOg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=4FkCApbLNMj9G+G/j9f4QjRPwF/OMXpghAjr35XZQik=; b=tchi4konkGfFqSfTXE2cyPodmmJfyXCKeJ6BsaB1QuKLQeblkXp2jn+B7iiktyTCIL oiC05TugNDVisosIYfNf1qz7y1XO3jlnxOuhN03ynCRiahAf4aMR2R02PZ0WcGirTZXO M1NnG1f58FTCfYaB9/zDjXMCUcG1ODzvzHv+4ilI95ROk18ro1sBkODs2qpbspUxvLLU t6Zgb8bfhQKtvQpg+618e4jZh83YPMFKVtjsJUuS80yjYtyFrCrYfBIouxh5x0c0KDuE 16HIfJWuUw+B2qiLyQ9fPf22FO7XXsodC/wLeGWEjRRhFRZKMr2iQxYU/T7t/vL1joSn qaZQ== X-Gm-Message-State: APjAAAXx6e7ba1m0DiV5n4QwRXrsrILrTFOaG9Besq01fXdGylrrpVSs icpbihb27xKkVEYGwoqKJpSWrCS6 X-Google-Smtp-Source: APXvYqxaUsw1CZx2SOhkeTOVZzGusQhVUk5q204aS8jWx+ZfMZNCBprirDO76IoFMB2iGD/qpyPNjA== X-Received: by 2002:a1c:1acd:: with SMTP id a196mr4691839wma.19.1570556132010; Tue, 08 Oct 2019 10:35:32 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s10sm5311960wmf.48.2019.10.08.10.35.31 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Tue, 08 Oct 2019 10:35:31 -0700 (PDT) From: zimoun Date: Tue, 8 Oct 2019 19:35:16 +0200 Message-Id: <20191008173518.1074-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-htqpcr): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b0405427c..4fc4ffbce2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2019 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -6048,3 +6049,36 @@ attributable to individual, tissue, time point, or technical variables. The package includes dream differential expression analysis for repeated measures.") (license license:gpl2+))) + +(define-public r-htqpcr + (package + (name "r-htqpcr") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HTqPCR" version)) + (sha256 + (base32 + "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) + (properties `((upstream-name . "HTqPCR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-gplots" ,r-gplots) + ("r-limma" ,r-limma) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "http://www.ebi.ac.uk/bertone/software") + (synopsis "Automated analysis of high-throughput qPCR data") + (description + "Analysis of Ct values from high throughput quantitative real-time +PCR (qPCR) assays across multiple conditions or replicates. The input data +can be from spatially-defined formats such ABI TaqMan Low Density Arrays or +OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad +Laboratories; conventional 96- or 384-well plates; or microfluidic devices +such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data +loading, quality assessment, normalization, visualization and parametric or +non-parametric testing for statistical significance in Ct values between +features (e.g. genes, microRNAs).") + (license license:artistic2.0)))