From unknown Sun Jun 22 07:57:04 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#62881] [PATCH] gnu: Add r-demuxmix. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 16 Apr 2023 10:11:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 62881 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 62881@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.168163982331019 (code B ref -1); Sun, 16 Apr 2023 10:11:02 +0000 Received: (at submit) by debbugs.gnu.org; 16 Apr 2023 10:10:23 +0000 Received: from localhost ([127.0.0.1]:50624 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pnzKw-00084F-LJ for submit@debbugs.gnu.org; Sun, 16 Apr 2023 06:10:23 -0400 Received: from lists.gnu.org ([209.51.188.17]:41152) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pnzKu-000845-G8 for submit@debbugs.gnu.org; Sun, 16 Apr 2023 06:10:21 -0400 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 1pnzKu-0003Cn-9b for guix-patches@gnu.org; Sun, 16 Apr 2023 06:10:20 -0400 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 1pnzKs-00039Y-3H for guix-patches@gnu.org; Sun, 16 Apr 2023 06:10:20 -0400 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=1681639800; x=1683454201; bh=3ihJVrL8wHzzhQh yKGmIcH5gRbdPJcL4M+j3RVcG+lc=; b=Xyzyr/RR8V461DeD1IBFVux18/7KVLD EO7OM7/YOUpFCsVyjqOGESiKH9OkTBt57+bgCyrU0Dei6rTfxHq5aWUfXYzYkotK mDUKUJx2Mj0BHLUjFHW5hzmd193pK+vUQsTJsfI4v6wUul8oFx8jCxD9lKZ6Q+sR F1sNGchL4UeM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 8DF80A0144 for ; Sun, 16 Apr 2023 12:10:00 +0200 (CEST) Received: from localhost.localdomain (10.84.128.6) 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 15.1.2507.23; Sun, 16 Apr 2023 12:09:59 +0200 From: Navid Afkhami Date: Sun, 16 Apr 2023 12:09:48 +0200 Message-ID: <20230416100948.59730-1-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: [10.84.128.6] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27568.007 X-TM-AS-Result: No-10--5.003900-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiJ6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJwFC Vfj8B4z7klvPIaBvBZQp3Fx4qZRwngBfp8CCuth77yUNHgaQS/f+PhkHLJnPiYDnmdMm9y0eUg5 UD6AlF0sX4oKkYTfsImyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1l3+bAt/YFVQYy9Xd3fYxwrnmG hOk8lBfdh+fkbqdmkXTOTnDb5Jeuh/BXqwE9HSW X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.003900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27568.007 X-TM-SNTS-SMTP: D58CDEB21090EFE8DECDA1F578C5A0F9568BC3CE9A0F3A2D16272C2D9DA71D742002: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/bioinformatics.scm (r-demuxmix): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99cc056f9f..b5442dd0ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9632,6 +9632,36 @@ (define-public r-centipede information as possible.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-demuxmix + (let ((commit "09a7918ca6e0cd23e6bbaed2b97388bc499e248e") + (revision "1")) + (package + (name "r-demuxmix") + (version (git-version "1.1.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/huklein/demuxmix") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03kfnns7m2447jsc3xplyv9qx8hvvdjmii7j837g3bb6smyxss96")))) + (properties `((upstream-name . "demuxmix"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gridextra r-mass r-matrix)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/huklein/demuxmix") + (synopsis + "Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models") + (description + "This package is used for demultiplexing single-cell sequencing experiments of pooled cells. +These cells are labeled with barcode oligonucleotides. The package +implements methods to fit regression mixture models for a probabilistic +classification of cells, including multiplet detection. Demultiplexing error +rates can be estimated, and methods for quality control are provided.") + (license license:artistic2.0)))) + (define-public r-demultiplex (let ((commit "6e2a1422c8e6f418cfb271997eebc91f9195f299") (revision "1")) -- 2.34.1 From unknown Sun Jun 22 07:57:04 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#62881: closed (gnu: Add r-demuxmix.) Message-ID: References: <87edoisw5d.fsf@elephly.net> <20230416100948.59730-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 62881 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 62881@debbugs.gnu.org Date: Mon, 17 Apr 2023 09:21:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1681723262-32592-1" This is a multi-part message in MIME format... ------------=_1681723262-32592-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #62881: [PATCH] gnu: Add r-demuxmix. 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 62881@debbugs.gnu.org. --=20 62881: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D62881 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1681723262-32592-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 62881-done) by debbugs.gnu.org; 17 Apr 2023 09:20:16 +0000 Received: from localhost ([127.0.0.1]:53207 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1poL1w-0008Rn-Tu for submit@debbugs.gnu.org; Mon, 17 Apr 2023 05:20:16 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21717) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1poL1r-0008RZ-LP for 62881-done@debbugs.gnu.org; Mon, 17 Apr 2023 05:20:11 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1681723203; cv=none; d=zohomail.com; s=zohoarc; b=XWzgJFBhDOvNVAQ2vaD+TcNUmPOepeH8xXB2ZbCNqqzbjnscO8obdhTIP+VPQYr+W1ofCUHqWSN69CkCkhgQwPeX1orj1cCOJ6ZolNUC8UP0DMhVCkDQ0576iKkxj0Ra8ztNgbaoyjBt/uz+/fwMLYZTGSSRr+wWw9qAH2XdRuo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1681723203; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=CbAmXz1Edy8vDoj+1t5njMbOvZTvS91xHipnRpAIjQrG+IpK0BYirHO9gCMxoV6UWYzgUEkGHEe/3D/TFYuFY3q3p27pVbkY6vlXLCFCwEmDtdidcd49Zq+9KpAMXo6Jr8BqJF/RtaHirXO0koTzFcfBRc0M7BlmGZYDg+GzxyA= 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=1681723203; 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=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=PWQSE2NM5oiBp0PNfmlasnQOwRl0BC/HmxlqnTzA0jf5XJHA4iGT74AKs4kmLU8k 7hHAzTG8zcoF8OwZ/loUZEGItoOBlCr45PEFfdq6jr6JRbShFxyHBfIT9AabQQUTi5v b2JuGZa1zIRlP1va+63OxkA1+Lp6jGbUp+FJ2eHY= Received: from localhost (169-110-142-46.pool.kielnet.net [46.142.110.169]) by mx.zohomail.com with SMTPS id 1681723201423130.10254767262165; Mon, 17 Apr 2023 02:20:01 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 62881-done@debbugs.gnu.org Subject: gnu: Add r-demuxmix. Date: Mon, 17 Apr 2023 11:19:34 +0200 Message-ID: <87edoisw5d.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 62881-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 (-) Applied, thank you! -- Ricardo ------------=_1681723262-32592-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 16 Apr 2023 10:10:23 +0000 Received: from localhost ([127.0.0.1]:50624 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pnzKw-00084F-LJ for submit@debbugs.gnu.org; Sun, 16 Apr 2023 06:10:23 -0400 Received: from lists.gnu.org ([209.51.188.17]:41152) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pnzKu-000845-G8 for submit@debbugs.gnu.org; Sun, 16 Apr 2023 06:10:21 -0400 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 1pnzKu-0003Cn-9b for guix-patches@gnu.org; Sun, 16 Apr 2023 06:10:20 -0400 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 1pnzKs-00039Y-3H for guix-patches@gnu.org; Sun, 16 Apr 2023 06:10:20 -0400 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=1681639800; x=1683454201; bh=3ihJVrL8wHzzhQh yKGmIcH5gRbdPJcL4M+j3RVcG+lc=; b=Xyzyr/RR8V461DeD1IBFVux18/7KVLD EO7OM7/YOUpFCsVyjqOGESiKH9OkTBt57+bgCyrU0Dei6rTfxHq5aWUfXYzYkotK mDUKUJx2Mj0BHLUjFHW5hzmd193pK+vUQsTJsfI4v6wUul8oFx8jCxD9lKZ6Q+sR F1sNGchL4UeM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= 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 8DF80A0144 for ; Sun, 16 Apr 2023 12:10:00 +0200 (CEST) Received: from localhost.localdomain (10.84.128.6) 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 15.1.2507.23; Sun, 16 Apr 2023 12:09:59 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-demuxmix. Date: Sun, 16 Apr 2023 12:09:48 +0200 Message-ID: <20230416100948.59730-1-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: [10.84.128.6] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27568.007 X-TM-AS-Result: No-10--5.003900-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiJ6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJwFC Vfj8B4z7klvPIaBvBZQp3Fx4qZRwngBfp8CCuth77yUNHgaQS/f+PhkHLJnPiYDnmdMm9y0eUg5 UD6AlF0sX4oKkYTfsImyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1l3+bAt/YFVQYy9Xd3fYxwrnmG hOk8lBfdh+fkbqdmkXTOTnDb5Jeuh/BXqwE9HSW X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.003900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27568.007 X-TM-SNTS-SMTP: D58CDEB21090EFE8DECDA1F578C5A0F9568BC3CE9A0F3A2D16272C2D9DA71D742002: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 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/bioinformatics.scm (r-demuxmix): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99cc056f9f..b5442dd0ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9632,6 +9632,36 @@ (define-public r-centipede information as possible.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-demuxmix + (let ((commit "09a7918ca6e0cd23e6bbaed2b97388bc499e248e") + (revision "1")) + (package + (name "r-demuxmix") + (version (git-version "1.1.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/huklein/demuxmix") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03kfnns7m2447jsc3xplyv9qx8hvvdjmii7j837g3bb6smyxss96")))) + (properties `((upstream-name . "demuxmix"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gridextra r-mass r-matrix)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/huklein/demuxmix") + (synopsis + "Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models") + (description + "This package is used for demultiplexing single-cell sequencing experiments of pooled cells. +These cells are labeled with barcode oligonucleotides. The package +implements methods to fit regression mixture models for a probabilistic +classification of cells, including multiplet detection. Demultiplexing error +rates can be estimated, and methods for quality control are provided.") + (license license:artistic2.0)))) + (define-public r-demultiplex (let ((commit "6e2a1422c8e6f418cfb271997eebc91f9195f299") (revision "1")) -- 2.34.1 ------------=_1681723262-32592-1--