From unknown Mon Aug 18 07:43:54 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61921] [PATCH] gnu: Add r-oscope. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 02 Mar 2023 16:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61921 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61921@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167777573125696 (code B ref -1); Thu, 02 Mar 2023 16:49:01 +0000 Received: (at submit) by debbugs.gnu.org; 2 Mar 2023 16:48:51 +0000 Received: from localhost ([127.0.0.1]:58260 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6s-0006gO-L9 for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:40340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6p-0006gE-SG for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:48 -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 1pXm6p-0004Ms-7y for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:47 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pXm6m-0007i4-OH for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:46 -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=1677775711; x=1679590112; bh=oii7NA4gPGIAQcf Ip4urfDRritU6hfyWTIAMRrsMw9Q=; b=at5OFq2Y44aDsh5ERlakzrNDHaATXxc n6bCI/QkLOTeHOdDjh+fmkGjNJjapEdYuFdXpngDbO5vhFiFs4nRJduz5szBRDwD cHvehTRfDpjrO87oVbTE3/zjqpPTBtjwFvpZMEe2JiwayDS+fNMgC2xIv6apUuOq peY4c+ONSEUU= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1DE6BA0268 for ; Thu, 2 Mar 2023 17:48:30 +0100 (CET) Received: from localhost (141.80.218.27) 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; Thu, 2 Mar 2023 17:48:30 +0100 From: Navid Afkhami Date: Thu, 2 Mar 2023 16:48:03 +0000 Message-ID: <20230302164803.71966-1-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: [141.80.218.27] 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-14.0.0.3092-9.0.1002-27480.001 X-TM-AS-Result: No-10--7.627800-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIyd mby1eQX7K1OIo1kOJjPuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/F0kjYVlocoaY5ZGw7wyeHm1L VbqyavHICBvE1eIcYKmIE2wu8D/s4xGoL6ZNDLbNT3j6uyvUYPA47FdvA20VAD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58I/9UW5M5dRMpg5yOcdoVgvcUt5lc1lLgoGRyAacnhab3j9qEHCD2WKGUz 541wQvAVEps1bJtZAbBdtWJkhAMBH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.627800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.001 X-TM-SNTS-SMTP: 7E733F6A764EAE22DC12745819A03181531DBDA77CF03C29DD2AD6A3BE59ACA22002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bfca85bbc..c4fb44f7b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1702,6 +1702,37 @@ (define-public r-curatedtcgadata across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-oscope + (let ((commit "32e0ea72236128731f35a60fb5abcde5b5d35433") + (revision "1")) + (package + (name "r-oscope") + (version (git-version "1.29.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.bioconductor.org/packages/Oscope") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02929i7zd4fwdhxi0h2i7y3sn6v1k3srahn5a6v9wvihp5nmgcig")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://git.bioconductor.org/packages/Oscope") + (synopsis + "Oscillatory 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-parathyroidse (package (name "r-parathyroidse") -- 2.34.1 From unknown Mon Aug 18 07:43:54 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#61921: closed ([PATCH] gnu: Add r-oscope.) Message-ID: References: <87lekedp2v.fsf@elephly.net> <20230302164803.71966-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61921 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61921@debbugs.gnu.org Date: Fri, 03 Mar 2023 11:59:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1677844742-13014-1" This is a multi-part message in MIME format... ------------=_1677844742-13014-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61921: [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 61921@debbugs.gnu.org. --=20 61921: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61921 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1677844742-13014-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61921-done) by debbugs.gnu.org; 3 Mar 2023 11:58:11 +0000 Received: from localhost ([127.0.0.1]:59830 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY438-0003Mm-QY for submit@debbugs.gnu.org; Fri, 03 Mar 2023 06:58:10 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY436-0003Mb-6O for 61921-done@debbugs.gnu.org; Fri, 03 Mar 2023 06:58:09 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677844685; cv=none; d=zohomail.com; s=zohoarc; b=D8ugZDIQzXgfXY8g6CxeGk8yTdrgA+QnnVVYkI8f50vSTSfUh0li6YD+rFLlanR5KP7OgM40rsJjBut0tkM/QBiSmc/X2ybGPjbtcPSx60PlYxXja5Q64ZjKxZUnckiS5HtyZOB2FIMf6TEa2gLuhYWR2XSUtUB2dVBOWenRto4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677844685; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=70qHoYto23oe2qNM9v8pxxNDMc49G/ms4pnAATO57SA=; b=UCA9AM7Sm0AyupLXq5gHzC+OCwrVeqpEPKTDT6yVeiWdnXXUPcFpcSPWc3ZpWV2+m4S3s9E41UY5DNV9NG7nzIrSR1IYNdsIGxnt/30QkFkIu2oCLEq4uy/iPCLWDsWeEOvQm2dkPkg/cgB33STrgh5kB/Ewb4wY/vu4x4/jgZU= 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=1677844685; 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=70qHoYto23oe2qNM9v8pxxNDMc49G/ms4pnAATO57SA=; b=Uu0pH4fLennDdDOpLtkNJNuhq6XD3gW38k38gKDgKSirv1e23pdVm1UIdPR/d5Bw Rwyt0agrAUevKNTAOA6gqX5SGwpxPJz0cSBXSGY42VQLaDSvIZ1v4kgXgHaWAotRDix tnyGmB6KmBT7/StQRnlxIQHr+5M1a5vVFFp9PZO0= Received: from localhost (133-110-142-46.pool.kielnet.net [46.142.110.133]) by mx.zohomail.com with SMTPS id 1677844683284163.60570687272502; Fri, 3 Mar 2023 03:58:03 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61921-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-oscope. Date: Fri, 03 Mar 2023 12:57:14 +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: <87lekedp2v.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 61921-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 (-) Superseded by issue 61931. -- Ricardo ------------=_1677844742-13014-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 2 Mar 2023 16:48:51 +0000 Received: from localhost ([127.0.0.1]:58260 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6s-0006gO-L9 for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:50 -0500 Received: from lists.gnu.org ([209.51.188.17]:40340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXm6p-0006gE-SG for submit@debbugs.gnu.org; Thu, 02 Mar 2023 11:48:48 -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 1pXm6p-0004Ms-7y for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:47 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pXm6m-0007i4-OH for guix-patches@gnu.org; Thu, 02 Mar 2023 11:48:46 -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=1677775711; x=1679590112; bh=oii7NA4gPGIAQcf Ip4urfDRritU6hfyWTIAMRrsMw9Q=; b=at5OFq2Y44aDsh5ERlakzrNDHaATXxc n6bCI/QkLOTeHOdDjh+fmkGjNJjapEdYuFdXpngDbO5vhFiFs4nRJduz5szBRDwD cHvehTRfDpjrO87oVbTE3/zjqpPTBtjwFvpZMEe2JiwayDS+fNMgC2xIv6apUuOq peY4c+ONSEUU= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1DE6BA0268 for ; Thu, 2 Mar 2023 17:48:30 +0100 (CET) Received: from localhost (141.80.218.27) 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; Thu, 2 Mar 2023 17:48:30 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-oscope. Date: Thu, 2 Mar 2023 16:48:03 +0000 Message-ID: <20230302164803.71966-1-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: [141.80.218.27] 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-14.0.0.3092-9.0.1002-27480.001 X-TM-AS-Result: No-10--7.627800-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIyd mby1eQX7K1OIo1kOJjPuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/F0kjYVlocoaY5ZGw7wyeHm1L VbqyavHICBvE1eIcYKmIE2wu8D/s4xGoL6ZNDLbNT3j6uyvUYPA47FdvA20VAD2veI3/hwm9KfR F/WYdhbn0tCKdnhB58I/9UW5M5dRMpg5yOcdoVgvcUt5lc1lLgoGRyAacnhab3j9qEHCD2WKGUz 541wQvAVEps1bJtZAbBdtWJkhAMBH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.627800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.001 X-TM-SNTS-SMTP: 7E733F6A764EAE22DC12745819A03181531DBDA77CF03C29DD2AD6A3BE59ACA22002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 Cc: Navid Afkhami 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 | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bfca85bbc..c4fb44f7b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1702,6 +1702,37 @@ (define-public r-curatedtcgadata across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-oscope + (let ((commit "32e0ea72236128731f35a60fb5abcde5b5d35433") + (revision "1")) + (package + (name "r-oscope") + (version (git-version "1.29.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.bioconductor.org/packages/Oscope") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02929i7zd4fwdhxi0h2i7y3sn6v1k3srahn5a6v9wvihp5nmgcig")))) + (properties `((upstream-name . "Oscope"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) + (home-page "https://git.bioconductor.org/packages/Oscope") + (synopsis + "Oscillatory 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-parathyroidse (package (name "r-parathyroidse") -- 2.34.1 ------------=_1677844742-13014-1--