From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: [PATCH] gnu: Add r-edger. Date: Tue, 03 May 2016 09:36:28 +0200 Message-ID: <87lh3r61ab.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34215) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axUt2-0005dL-Ij for guix-devel@gnu.org; Tue, 03 May 2016 03:36:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1axUsq-00061v-Mr for guix-devel@gnu.org; Tue, 03 May 2016 03:36:47 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:46112) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axUsq-0005zY-If for guix-devel@gnu.org; Tue, 03 May 2016 03:36:40 -0400 Received: from [143.121.239.252] (port=37958 helo=roel-tp) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1axUsl-0006kk-JR for guix-devel@gnu.org; Tue, 03 May 2016 03:36:36 -0400 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel Dear Guix, Here is a package for 'r-edger'. I sent another e-mail with the dependency 'r-limma'. Kind regards, Roel Janssen >From 5f31983e32f381dd5e98c93f8402770196fce4f2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 3 May 2016 09:26:37 +0200 Subject: [PATCH] gnu: Add r-edger. * gnu/packages/bioinformatics.scm (r-edger): New variable. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 079fd46..dc43fc0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4015,6 +4015,31 @@ use multiple corrections. Visualization of data can be done either by barplots or heatmaps.") (license license:gpl2+))) +(define-public r-edger + (package + (name "r-edger") + (version "3.12.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "edgeR" version)) + (sha256 + (base32 + "1s5xliiswij1v3nqgkf4999njwdr9jirg6ypza4002xz8mwmyki6")))) + (properties `((upstream-name . "edgeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma))) + (home-page "http://bioinf.wehi.edu.au/edgeR") + (synopsis "EdgeR does empirical analysis of digital gene expression data") + (description "This package can do differential expression analysis of +RNA-seq expression profiles with biological replication. It implements a range +of statistical methodology based on the negative binomial distributions, +including empirical Bayes estimation, exact tests, generalized linear models +and quasi-likelihood tests. It be applied to differential signal analysis of +other types of genomic data that produce counts, including ChIP-seq, SAGE and +CAGE.") + (license license:gpl2+))) + (define-public r-biocgenerics (package (name "r-biocgenerics") -- 2.7.4