From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:47897) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dhy5J-0004jJ-Vr for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:11 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhy5D-0003kU-Vp for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:09 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:59930) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dhy5D-0003kP-SA for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dhy5D-0004tC-Lz for guix-patches@gnu.org; Wed, 16 Aug 2017 09:10:03 -0400 Subject: [bug#28109] [PATCH 04/10] gnu: Add r-qvalue. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 16 Aug 2017 15:08:53 +0200 Message-Id: <20170816130859.15069-4-rekado@elephly.net> In-Reply-To: <20170816130859.15069-1-rekado@elephly.net> References: <20170816130859.15069-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 28109@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (r-qvalue): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4207b2a9d..7cc48b3df 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9317,6 +9317,35 @@ formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-qvalue + (package + (name "r-qvalue") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "qvalue" version)) + (sha256 + (base32 + "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2))) + (home-page "http://github.com/jdstorey/qvalue") + (synopsis "Q-value estimation for false discovery rate control") + (description + "This package takes a list of p-values resulting from the simultaneous +testing of many hypotheses and estimates their q-values and local @dfn{false +discovery rate} (FDR) values. The q-value of a test measures the proportion +of false positives incurred when that particular test is called significant. +The local FDR measures the posterior probability the null hypothesis is true +given the test's p-value. Various plots are automatically generated, allowing +one to make sensible significance cut-offs. The software can be applied to +problems in genomics, brain imaging, astrophysics, and data mining.") + ;; Any version of the LGPL. + (license license:lgpl3+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3