From unknown Tue Jun 17 22:07:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61931] [PATCH] gnu: Add r-oscope. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 10:57:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61931 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61931@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167784101029391 (code B ref -1); Fri, 03 Mar 2023 10:57:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Mar 2023 10:56:50 +0000 Received: from localhost ([127.0.0.1]:59753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY35l-0007dy-Qb for submit@debbugs.gnu.org; Fri, 03 Mar 2023 05:56:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:59448) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY35k-0007dm-Gb for submit@debbugs.gnu.org; Fri, 03 Mar 2023 05:56:49 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pY35i-0006Cd-OK for guix-patches@gnu.org; Fri, 03 Mar 2023 05:56:46 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pY35g-0003xn-EV for guix-patches@gnu.org; Fri, 03 Mar 2023 05:56:46 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1677840996; x=1679655397; bh=zYTno3xh2roUaXu YhJM6+XVJJuU/IY5Nu8fYZLKbftQ=; b=RzEcjlGVS63YsGU5zeY4U/QLiiKksnN SF980XOC3+60CxE5n9N9ST2rlJz4Q2jGV4A9KmHRL/UHR23g+p+lQW+ddU3YvACr ljpn0FJkZ5uez/lrVlMCI3rp6xt+nqbHQp56p1pIzEI4Zod7jgCwgkvFPHOXNTBh +pK90PzY0KJM= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id DB1FA160207 for ; Fri, 3 Mar 2023 11:56:36 +0100 (CET) Received: from localhost.localdomain (10.84.128.46) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 11:56:36 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 11:56:25 +0100 Message-ID: <20230303105625.36854-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.46] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--4.640700-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEF+2 MpmaGp/lRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRrgM3jtyHSSQjFK /NcS7G4k/jpOn/YFJRafK+3ppGuGg6Cz2uwhBKVMM6z3iDvziBwseQVcTRnF2lwV2iaAfSWcURS Scn+QSXhhJCIHRlO51+gtHj7OwNO22utO5qEfOUcZhXUVPqUm5fYvwXY3V+feCgOM7Ig97+OaKa lMd8nwZq4muunxBQZDQ8VeoGqqFVKL3bsAu3zXgxpvdSXvfqX3woIRdstW4/XQJ88ZHP8DjvmJf 6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.640700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: F1BAF1886D2232BD74CC9CAC88A6350EEC89BA27512A78C1E60897CDD2F9D1182002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-oscope): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22be8d3772..78eb24625f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7425,6 +7425,32 @@ (define-public r-organismdbi the fact that each of these packages implements a select methods.") (license license:artistic2.0))) +(define-public r-oscope + (package + (name "r-oscope") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Oscope" version)) + (sha256 + (base32 + "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://bioconductor.org/packages/Oscope") + (synopsis + "Scillatory genes identifier in unsynchronized single cell RNA-seq") + (description + "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. +This statistical pipeline has been developed to identify and recover the +base cycle profiles of oscillating genes in an unsynchronized single cell +RNA-seq experiment. The Oscope pipeline includes three modules: a sine model +module to search for candidate oscillator pairs; a K-medoids clustering module +to cluster candidate oscillators into groups; and an extended nearest insertion +module to recover the base cycle order for each oscillator group.") + (license license:asl2.0))) + (define-public r-pcaexplorer (package (name "r-pcaexplorer") -- 2.34.1 From unknown Tue Jun 17 22:07:51 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#61931: closed ([PATCH] gnu: Add r-oscope.) Message-ID: References: <87pm9qdrh8.fsf@elephly.net> <20230303105625.36854-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61931 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61931@debbugs.gnu.org Date: Fri, 03 Mar 2023 11:07:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1677841622-7295-1" This is a multi-part message in MIME format... ------------=_1677841622-7295-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61931: [PATCH] gnu: Add r-oscope. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 61931@debbugs.gnu.org. --=20 61931: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61931 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1677841622-7295-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61931-done) by debbugs.gnu.org; 3 Mar 2023 11:06:21 +0000 Received: from localhost ([127.0.0.1]:59779 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY3Ez-0001sT-Ak for submit@debbugs.gnu.org; Fri, 03 Mar 2023 06:06:21 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21082) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY3Ew-0001sK-VK for 61931-done@debbugs.gnu.org; Fri, 03 Mar 2023 06:06:20 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677841575; cv=none; d=zohomail.com; s=zohoarc; b=Kq+6iiKO8Sc0c+sXAEPN0aLSoJRwVZ9HefTHr7yosN/cQMVUvgPI+Cis24LMNwVfzr5yWTpdEkHZyV31D0uNxPdugOJlVr7xUU3AAJqo0Nn3S4z0turJY1HcV5Jqu8VQ9g/S1cARW/9u/SL22lzVqb0IEwOWhdCRBaTHzzNDtNs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677841575; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=TSQ3+uQ8G+iR3cR1VioAVuiz2Tj0Tj7HpJFnGyG1WY4=; b=WV8/Uxpf23d+DB7xz/6QAzQ/kH1JYkQMGdNmKRj6dTfYqPiqMkzHjXKCNowaGRdH+Ad7GhaO+VjzBhHoeQIYJXt4ivLQwXBJcHCEJOZMycjN90VJ90cQNI4BN+6zzlNh1WIcI2oH/nGvWi6vcGksU4ARZASLDAw34InMxjBbhdU= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677841575; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=TSQ3+uQ8G+iR3cR1VioAVuiz2Tj0Tj7HpJFnGyG1WY4=; b=S1niKRyfwg+995oxnzBv7Val/SyN/ZZ7/+NZ7MHHmkuX3wHV9zVKr+s0HbL53TwB MTD32GyZgKCvLYsaa+36WmlwsgJOIiEvGhNEmeRbaEoATLp0RFA8SnESK9FDqRtZKiU UUy62aNS6ci6AaYygWRsN/izG2UGq/nDm3OpAztw= Received: from localhost (133-110-142-46.pool.kielnet.net [46.142.110.133]) by mx.zohomail.com with SMTPS id 1677841574742576.6789542602256; Fri, 3 Mar 2023 03:06:14 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61931-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-oscope. Date: Fri, 03 Mar 2023 12:05:25 +0100 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 Message-ID: <87pm9qdrh8.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 61931-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: -1.0 (-) Thanks for the patch. I have applied it with commit 4f681cdbc27e6a922f24d4297efe3c0b823195f0. -- Ricardo ------------=_1677841622-7295-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Mar 2023 10:56:50 +0000 Received: from localhost ([127.0.0.1]:59753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY35l-0007dy-Qb for submit@debbugs.gnu.org; Fri, 03 Mar 2023 05:56:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:59448) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY35k-0007dm-Gb for submit@debbugs.gnu.org; Fri, 03 Mar 2023 05:56:49 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pY35i-0006Cd-OK for guix-patches@gnu.org; Fri, 03 Mar 2023 05:56:46 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pY35g-0003xn-EV for guix-patches@gnu.org; Fri, 03 Mar 2023 05:56:46 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1677840996; x=1679655397; bh=zYTno3xh2roUaXu YhJM6+XVJJuU/IY5Nu8fYZLKbftQ=; b=RzEcjlGVS63YsGU5zeY4U/QLiiKksnN SF980XOC3+60CxE5n9N9ST2rlJz4Q2jGV4A9KmHRL/UHR23g+p+lQW+ddU3YvACr ljpn0FJkZ5uez/lrVlMCI3rp6xt+nqbHQp56p1pIzEI4Zod7jgCwgkvFPHOXNTBh +pK90PzY0KJM= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id DB1FA160207 for ; Fri, 3 Mar 2023 11:56:36 +0100 (CET) Received: from localhost.localdomain (10.84.128.46) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 11:56:36 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-oscope. Date: Fri, 3 Mar 2023 11:56:25 +0100 Message-ID: <20230303105625.36854-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.46] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--4.640700-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEF+2 MpmaGp/lRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRrgM3jtyHSSQjFK /NcS7G4k/jpOn/YFJRafK+3ppGuGg6Cz2uwhBKVMM6z3iDvziBwseQVcTRnF2lwV2iaAfSWcURS Scn+QSXhhJCIHRlO51+gtHj7OwNO22utO5qEfOUcZhXUVPqUm5fYvwXY3V+feCgOM7Ig97+OaKa lMd8nwZq4muunxBQZDQ8VeoGqqFVKL3bsAu3zXgxpvdSXvfqX3woIRdstW4/XQJ88ZHP8DjvmJf 6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.640700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: F1BAF1886D2232BD74CC9CAC88A6350EEC89BA27512A78C1E60897CDD2F9D1182002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-oscope): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22be8d3772..78eb24625f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7425,6 +7425,32 @@ (define-public r-organismdbi the fact that each of these packages implements a select methods.") (license license:artistic2.0))) +(define-public r-oscope + (package + (name "r-oscope") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Oscope" version)) + (sha256 + (base32 + "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://bioconductor.org/packages/Oscope") + (synopsis + "Scillatory genes identifier in unsynchronized single cell RNA-seq") + (description + "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. +This statistical pipeline has been developed to identify and recover the +base cycle profiles of oscillating genes in an unsynchronized single cell +RNA-seq experiment. The Oscope pipeline includes three modules: a sine model +module to search for candidate oscillator pairs; a K-medoids clustering module +to cluster candidate oscillators into groups; and an extended nearest insertion +module to recover the base cycle order for each oscillator group.") + (license license:asl2.0))) + (define-public r-pcaexplorer (package (name "r-pcaexplorer") -- 2.34.1 ------------=_1677841622-7295-1--