From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:51359) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dB0L1-0003H0-Of for guix-patches@gnu.org; Wed, 17 May 2017 10:54:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dB0Kx-0005Fl-6Z for guix-patches@gnu.org; Wed, 17 May 2017 10:54:07 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:48347) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dB0Kx-0005Fc-3U for guix-patches@gnu.org; Wed, 17 May 2017 10:54:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dB0Kw-0007Ni-TU for guix-patches@gnu.org; Wed, 17 May 2017 10:54:02 -0400 Subject: bug#26963: [PATCH 2/3] gnu: Add r-deseq. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 17 May 2017 16:52:52 +0200 Message-Id: <20170517145253.28057-2-rekado@elephly.net> In-Reply-To: <20170517145253.28057-1-rekado@elephly.net> References: <20170517145253.28057-1-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: 26963@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (r-deseq): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cf3da3dac..4c37435ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8983,6 +8983,37 @@ standalone, be utilized in other packages, or be wrapped up in higher-level classes.") (license license:gpl2+))) +(define-public r-deseq + (package + (name "r-deseq") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "0j3dgcxd64m9qknmlcbdzvg4xhp981xd6nbwsvnqjfn6yypslgyw")))) + (properties `((upstream-name . "DESeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-lattice" ,r-lattice) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "http://www-huber.embl.de/users/anders/DESeq") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.12.2