From unknown Mon Aug 18 08:55:15 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#26963 <26963@debbugs.gnu.org> To: bug#26963 <26963@debbugs.gnu.org> Subject: Status: Add r-edaseq. Reply-To: bug#26963 <26963@debbugs.gnu.org> Date: Mon, 18 Aug 2025 15:55:15 +0000 retitle 26963 Add r-edaseq. reassign 26963 guix-patches submitter 26963 Ricardo Wurmus severity 26963 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Wed May 17 10:39:33 2017 Received: (at submit) by debbugs.gnu.org; 17 May 2017 14:39:33 +0000 Received: from localhost ([127.0.0.1]:51001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB06u-00072c-Ri for submit@debbugs.gnu.org; Wed, 17 May 2017 10:39:33 -0400 Received: from eggs.gnu.org ([208.118.235.92]:55956) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB06t-00072P-7a for submit@debbugs.gnu.org; Wed, 17 May 2017 10:39:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dB06n-0000MD-Fp for submit@debbugs.gnu.org; Wed, 17 May 2017 10:39:26 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:44412) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dB06n-0000M3-CA for submit@debbugs.gnu.org; Wed, 17 May 2017 10:39:25 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:46917) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dB06m-0006lc-Cw for guix-patches@gnu.org; Wed, 17 May 2017 10:39:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dB06j-0000LQ-C4 for guix-patches@gnu.org; Wed, 17 May 2017 10:39:24 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21016) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dB06j-0000KU-2s for guix-patches@gnu.org; Wed, 17 May 2017 10:39:21 -0400 Received: from localhost (port-92-200-235-5.dynamic.qsc.de [92.200.235.5]) by mx.zohomail.com with SMTPS id 1495031955546570.2083195297439; Wed, 17 May 2017 07:39:15 -0700 (PDT) User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: guix-patches@gnu.org Subject: Add r-edaseq. X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 17 May 2017 16:39:12 +0200 Message-ID: <8737c3sg33.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) The following three patches add bioinfo tools for R. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed May 17 10:53:05 2017 Received: (at 26963) by debbugs.gnu.org; 17 May 2017 14:53:05 +0000 Received: from localhost ([127.0.0.1]:51010 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0K1-0007Lh-3h for submit@debbugs.gnu.org; Wed, 17 May 2017 10:53:05 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21102) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0Jy-0007LH-LW for 26963@debbugs.gnu.org; Wed, 17 May 2017 10:53:03 -0400 Received: from localhost (port-92-200-235-5.dynamic.qsc.de [92.200.235.5]) by mx.zohomail.com with SMTPS id 149503277861738.790141878178815; Wed, 17 May 2017 07:52:58 -0700 (PDT) From: Ricardo Wurmus To: 26963@debbugs.gnu.org Subject: [PATCH 1/3] gnu: Add r-aroma-light. Date: Wed, 17 May 2017 16:52:51 +0200 Message-Id: <20170517145253.28057-1-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26963 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * gnu/packages/bioinformatics.scm (r-aroma-light): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f5d8141d..cf3da3dac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8956,6 +8956,33 @@ algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3)))) +(define-public r-aroma-light + (package + (name "r-aroma-light") + (version "3.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "aroma.light" version)) + (sha256 + (base32 + "10snykmmx36qaymyf5s1n1km8hsscyzpykcpf0mzsrcv8ml9rp8a")))) + (properties `((upstream-name . "aroma.light"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrixstats" ,r-matrixstats) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/aroma.light") + (synopsis "Methods for normalization and visualization of microarray data") + (description + "This package provides methods for microarray analysis that take basic +data types such as matrices and lists of vectors. These methods can be used +standalone, be utilized in other packages, or be wrapped up in higher-level +classes.") + (license license:gpl2+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.12.2 From debbugs-submit-bounces@debbugs.gnu.org Wed May 17 10:53:07 2017 Received: (at 26963) by debbugs.gnu.org; 17 May 2017 14:53:07 +0000 Received: from localhost ([127.0.0.1]:51013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0K3-0007Lx-BL for submit@debbugs.gnu.org; Wed, 17 May 2017 10:53:07 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21106) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0K2-0007Lp-4W for 26963@debbugs.gnu.org; Wed, 17 May 2017 10:53:06 -0400 Received: from localhost (port-92-200-235-5.dynamic.qsc.de [92.200.235.5]) by mx.zohomail.com with SMTPS id 1495032781686404.68784883896456; Wed, 17 May 2017 07:53:01 -0700 (PDT) From: Ricardo Wurmus To: 26963@debbugs.gnu.org Subject: [PATCH 2/3] gnu: Add r-deseq. Date: Wed, 17 May 2017 16:52:52 +0200 Message-Id: <20170517145253.28057-2-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170517145253.28057-1-rekado@elephly.net> References: <20170517145253.28057-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26963 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * 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 From debbugs-submit-bounces@debbugs.gnu.org Wed May 17 10:53:14 2017 Received: (at 26963) by debbugs.gnu.org; 17 May 2017 14:53:14 +0000 Received: from localhost ([127.0.0.1]:51016 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0KA-0007MH-KE for submit@debbugs.gnu.org; Wed, 17 May 2017 10:53:14 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21087) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dB0K8-0007M8-JR for 26963@debbugs.gnu.org; Wed, 17 May 2017 10:53:13 -0400 Received: from localhost (port-92-200-235-5.dynamic.qsc.de [92.200.235.5]) by mx.zohomail.com with SMTPS id 1495032784991977.7099486581124; Wed, 17 May 2017 07:53:04 -0700 (PDT) From: Ricardo Wurmus To: 26963@debbugs.gnu.org Subject: [PATCH 3/3] gnu: Add r-edaseq. Date: Wed, 17 May 2017 16:52:53 +0200 Message-Id: <20170517145253.28057-3-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 In-Reply-To: <20170517145253.28057-1-rekado@elephly.net> References: <20170517145253.28057-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26963 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) * gnu/packages/bioinformatics.scm (r-edaseq): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c37435ad..35f1e77f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9014,6 +9014,44 @@ differential expression based on a model using the negative binomial distribution.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-deseq" ,r-deseq) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.12.2 From debbugs-submit-bounces@debbugs.gnu.org Tue May 30 17:06:13 2017 Received: (at 26963-done) by debbugs.gnu.org; 30 May 2017 21:06:13 +0000 Received: from localhost ([127.0.0.1]:45764 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dFoLF-0005ZN-3s for submit@debbugs.gnu.org; Tue, 30 May 2017 17:06:13 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21104) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dFoLC-0005ZE-VS for 26963-done@debbugs.gnu.org; Tue, 30 May 2017 17:06:11 -0400 Received: from localhost (port-92-200-122-160.dynamic.qsc.de [92.200.122.160]) by mx.zohomail.com with SMTPS id 1496178367504148.45285293017798; Tue, 30 May 2017 14:06:07 -0700 (PDT) References: <8737c3sg33.fsf@elephly.net> <20170517145253.28057-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: 26963-done@debbugs.gnu.org Subject: Re: bug#26963: [PATCH 1/3] gnu: Add r-aroma-light. In-reply-to: <20170517145253.28057-1-rekado@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 30 May 2017 23:06:05 +0200 Message-ID: <87tw422gxu.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26963-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Pushed with commit 296b3c631c2e8cf42f5a0920cd11c424daec9ea4. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Mon Aug 18 08:55:15 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 28 Jun 2017 11:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator