From unknown Thu Aug 21 12:10:34 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#61254 <61254@debbugs.gnu.org> To: bug#61254 <61254@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-psupertime. Reply-To: bug#61254 <61254@debbugs.gnu.org> Date: Thu, 21 Aug 2025 19:10:34 +0000 retitle 61254 [PATCH] gnu: Add r-psupertime. reassign 61254 guix-patches submitter 61254 Navid Afkhami severity 61254 normal tag 61254 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 03 08:44:27 2023 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 13:44:27 +0000 Received: from localhost ([127.0.0.1]:36847 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNwMd-0005r1-Dl for submit@debbugs.gnu.org; Fri, 03 Feb 2023 08:44:27 -0500 Received: from lists.gnu.org ([209.51.188.17]:47972) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNwMX-0005qq-U6 for submit@debbugs.gnu.org; Fri, 03 Feb 2023 08:44:25 -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 1pNwMX-0000yZ-EZ for guix-patches@gnu.org; Fri, 03 Feb 2023 08:44:21 -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 1pNwMV-0006rc-6Y for guix-patches@gnu.org; Fri, 03 Feb 2023 08:44:21 -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=1675431853; x=1677246254; bh=A2l8zc+N7Hbp/kW al2y8bc3PcagkubS16n1HRFm9dSA=; b=ppg3Ef4YistDAdwUJU5Nu+heHZkbua9 lw/yFTkWls1CZTqaRe4vADnklzyD2vhBmHOmbI7XDoa8MlzJbCJAFZR740mBHdbw fcHk6zbf5mwJZlv+S8Vgq6EzIKD1tatLeXt47b9UpI18ULPghXVp9DBEKvLp4O5J f9DSsrp+8VPM= 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 9C3B7A03F7 for ; Fri, 3 Feb 2023 14:44:13 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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 15.1.2507.17; Fri, 3 Feb 2023 14:44:12 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-psupertime. Date: Fri, 3 Feb 2023 14:44:02 +0100 Message-ID: <20230203134402.100385-1-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: [10.84.128.45] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10--6.391400-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXR6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VGb6 PphVtfZgRKje09piqOwue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedJEb gebEoSmXXFQkvS/0viY2h2ZcIum9E0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV/5N/ S1zEq4ujmW1BhHs6tru+k+9jYTJ3WtEjv8Hy4f8xwyDcFz/j8p X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.391400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: 4C9D2036DA0421B15647B454C037C84062B75A1BDF0C079C5086025BAB5D82D42002: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: -2.3 (--) 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: -3.3 (---) * gnu/packages/bioinformatics.scm (r-psupertime): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8676b0ece..703d71fb68 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8229,6 +8229,50 @@ (define-public r-doubletcollection benchmark of those eight mentioned methods.") (license license:gpl3+)))) +(define-public r-psupertime + (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207") + (revision "1")) + (package + (name "r-psupertime") + (version (git-version "0.2.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wmacnair/psupertime") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh")))) + (properties `((upstream-name . "psupertime"))) + (build-system r-build-system) + (propagated-inputs (list r-cowplot + r-data-table + r-fastcluster + r-forcats + r-ggplot2 + r-glmnet + r-knitr + r-matrix + r-rcolorbrewer + r-scales + r-scran + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-topgo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wmacnair/psupertime") + (synopsis + "Psupertime is supervised pseudotime for single cell RNAseq data") + (description + "Psupertime uses single cell RNAseq data, where the cells have a known ordering. +This ordering helps to identify a small number of genes which place +cells in that known order. It can be used for discovery of relevant +genes, for identification of subpopulations, and characterization of +further unknown or differently labelled data.") + (license license:gpl3)))) + (define-public r-pando (package (name "r-pando") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 03 10:58:54 2023 Received: (at 61254-done) by debbugs.gnu.org; 3 Feb 2023 15:58:54 +0000 Received: from localhost ([127.0.0.1]:39840 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNySk-0003xj-B8 for submit@debbugs.gnu.org; Fri, 03 Feb 2023 10:58:54 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21148) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNySe-0003xV-Lc for 61254-done@debbugs.gnu.org; Fri, 03 Feb 2023 10:58:52 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675439926; cv=none; d=zohomail.com; s=zohoarc; b=R0zvHmW7RSWrfTfoOP3GgIOg+nTqMTgNWT8wqoMnwesaZHFedwYUyGvzWL2+h1DNg8HprlLEIX6RA8qvSfRYfws9uEemf/I9N6wtmXSIqhyorF1XGc9wBxrYkCP/cxdfAzq6fEtSJfW1Fn6lR7ujE052hkmz6SzK0PWXwYaZ6nc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675439926; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=Mpm2rfamMpeLkdv8wHv52RJaCDt7rEr5uLxmhHlq4gE=; b=gAPWxXWBTfpD/rkomTayAW/Zhzd4LK6NWxxfJXfqirEvF7BU0v/xw64Ce/YbVLU6WwpQvuw52yoOWyCVlagNC949UgoHtVgm2jLzZD3buE0EkRQOuQonYY5HIswuLeAfuL4xSIxlwBkgMDfGsyIvJ8mu9uTVRDqQNi21nu0Hpus= 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=1675439926; 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=Mpm2rfamMpeLkdv8wHv52RJaCDt7rEr5uLxmhHlq4gE=; b=ZmIunZEaqAO5DUFwc83Dj/mCp1m9c27H0tUY4VG+g3k5gnUoFJFDLwzQm31/hCo7 1Vf3g93KGxwEm2zFSBJmQBitRa3pKTMkSSvqiqls+3RcEZ7HakfbABw0e7G/Naly5PF gNBDSEgZERoqwsgq8/kmbGvgVHC2ATNAw9kFSRmQ= Received: from localhost (i5E862D0C.versanet.de [94.134.45.12]) by mx.zohomail.com with SMTPS id 1675439924638296.56279587624385; Fri, 3 Feb 2023 07:58:44 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61254-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-psupertime. Date: Fri, 03 Feb 2023 16:53:47 +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: <875yci91vx.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61254-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. Applied! -- Ricardo From unknown Thu Aug 21 12:10:34 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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