From unknown Sat Aug 16 16:19:43 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#68368] [PATCH] gnu: Add r-dsb. Resent-From: nafkhamdc Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 10 Jan 2024 13:59:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 68368 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68368@debbugs.gnu.org Cc: nafkhamdc X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.170489509113231 (code B ref -1); Wed, 10 Jan 2024 13:59:03 +0000 Received: (at submit) by debbugs.gnu.org; 10 Jan 2024 13:58:11 +0000 Received: from localhost ([127.0.0.1]:39322 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNZ5u-0003RL-PZ for submit@debbugs.gnu.org; Wed, 10 Jan 2024 08:58:11 -0500 Received: from lists.gnu.org ([2001:470:142::17]:44900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNZ5s-0003Py-Es for submit@debbugs.gnu.org; Wed, 10 Jan 2024 08:58:09 -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 1rNYEI-0000IF-8W for guix-patches@gnu.org; Wed, 10 Jan 2024 08:02:46 -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 1rNYEF-0007nZ-S4 for guix-patches@gnu.org; Wed, 10 Jan 2024 08:02:45 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1704891759; x=1706706160; bh=0KttMCZ4djuBLnI fwyUGnSgzS+WnwpLNvJCgOp7oxyc=; b=ITzatXfQRKogk8/Op5QnF+JFk7ecpHb M1XkAz1OC5NUXSRxaK/4G+KuJhelXmL74+lT7WS2KQtEih2zAXdQfcImp5eJHNWF 1NljjALFU2btTOsnu8CdbtX6wDNSOK9WVQrV1aub+MTka93Igitxa8knZQDUqjuk 18ysX53wV2KA= 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 29EAEA013A for ; Wed, 10 Jan 2024 14:02:38 +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 15.2.1258.28; Wed, 10 Jan 2024 14:02:38 +0100 From: nafkhamdc Date: Wed, 10 Jan 2024 13:02:35 +0000 Message-ID: <79a84f556ed434e7a51f4fb87872872ef719719b.1704891744.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.218.27] 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-14.0.0.3152-9.1.1006-28110.006 X-TM-AS-Result: No-10--1.917300-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9AKgfO6jacGa9j7aNnpjtlxHY 45c6zrjduf5ur5byPpcign5HsLTCTuJXEeLLJ6+yrm7DrUlmNkF+24nCsUSFNjaPj0W1qn0TKay T/BQTiGovaJmMmOK99BB0kraAvZprTS0yYi/fuP8kH6nuYpMv9eadAIHhw3CgYWj6zHBWXQaliB dumkwMgGjtwb3HkLh0F99M1WxeaYRBUufKjLHzaeFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJ m2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.917300-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28110.006 X-TM-SNTS-SMTP: 902F6425284BCBF916219AAD048AEF9F9B928EEC9A782AE190ED12BDAC35AFB52000: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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-dsb): New variable. Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7af5c42ce..7c4272f8be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5599,6 +5599,34 @@ (define-public r-dropletutils pseudo-cells, and downsampling of the count matrix.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-limma from Bioconductor. +(define-public r-dsb + (package + (name "r-dsb") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dsb" version)) + (sha256 + (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) + (properties `((upstream-name . "dsb"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-magrittr r-mclust)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://github.com/niaid/dsb") + (synopsis + "Normalize & denoise droplet single cell protein data (CITE-Seq)") + (description + "R-dsb improves protein expression analysis in droplet-based single-cell studies. +The package specifically addresses noise in raw protein UMI counts from methods like +CITE-seq. It identifies and removes two main sources of noise—protein-specific noise +from unbound antibodies and droplet/cell-specific noise. The package is applicable to +various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform +data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor, +and using dsb in Python.") + (license license:cc0))) + (define-public r-dss (package (name "r-dss") base-commit: 537768018ee03a6a9a5562022a16b47ac287d131 -- 2.34.1 From unknown Sat Aug 16 16:19:43 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: nafkhamdc Subject: bug#68368: closed ([PATCH] gnu: Add r-dsb.) Message-ID: References: <87il415b7y.fsf@elephly.net> <79a84f556ed434e7a51f4fb87872872ef719719b.1704891744.git.navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 68368 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 68368@debbugs.gnu.org Date: Wed, 10 Jan 2024 17:51:05 +0000 Content-Type: multipart/mixed; boundary="----------=_1704909065-10892-1" This is a multi-part message in MIME format... ------------=_1704909065-10892-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #68368: [PATCH] gnu: Add r-dsb. 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 68368@debbugs.gnu.org. --=20 68368: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D68368 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1704909065-10892-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 68368-done) by debbugs.gnu.org; 10 Jan 2024 17:50:50 +0000 Received: from localhost ([127.0.0.1]:42918 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNcj3-0002oE-MS for submit@debbugs.gnu.org; Wed, 10 Jan 2024 12:50:49 -0500 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21828) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNcj1-0002o3-5O for 68368-done@debbugs.gnu.org; Wed, 10 Jan 2024 12:50:47 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1704909046; cv=none; d=zohomail.com; s=zohoarc; b=oBR7EsBpiJ1YO3O4zjqME54/eknlCjJqpunOzWZTE6vyPTAij8ZtzZO26Zp8hXJ0bIMDU8bpp8TeuezD0Z862PC3LMZ+g7tPBvghv7TixgosaPtK/rDLUIihPwX+EOXp5y8BOUvcl1ssdL/elEMWaZ/hirNjFJIZ1ooMOdNjjcM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1704909046; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=RB6qWQbAx0OW+Wk9JU61meGayd7VT7kwsRJPNcjZ7C303nTcYMv3wT1mbWkNA2cAEaftmTs5PgtSo1Pf8ig/AUL1GADCzKEQQlH5QZV7J7sCOY+6bdbTKawKgPsx2NteXJ7X4/ywR37dhm6lxMEIwWpVRXeIxSQoS7QcLSKW8Dw= 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=1704909046; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=bQ/78mala1DQlCXcMNwGPMIAOWYLUPcM5oBbr1Igg4BlNFoUaJAyW9jJOBu+kas4 /Y7NPZM41yshpqET+RZA/dM4rtFvYnlfZoG0cVzQmbPxdFl9rrp9430CmWpTNJ9/qqM 13oIgF4A4STurqJPcV+DS14Hdb4pGhJfbV2Tict8= Received: from localhost (103-108-142-46.pool.kielnet.net [46.142.108.103]) by mx.zohomail.com with SMTPS id 1704909043712384.89693937544564; Wed, 10 Jan 2024 09:50:43 -0800 (PST) User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 68368-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-dsb. Date: Wed, 10 Jan 2024 18:50:23 +0100 Message-ID: <87il415b7y.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 68368-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, thanks! -- Ricardo ------------=_1704909065-10892-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 10 Jan 2024 13:58:11 +0000 Received: from localhost ([127.0.0.1]:39322 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNZ5u-0003RL-PZ for submit@debbugs.gnu.org; Wed, 10 Jan 2024 08:58:11 -0500 Received: from lists.gnu.org ([2001:470:142::17]:44900) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rNZ5s-0003Py-Es for submit@debbugs.gnu.org; Wed, 10 Jan 2024 08:58:09 -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 1rNYEI-0000IF-8W for guix-patches@gnu.org; Wed, 10 Jan 2024 08:02:46 -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 1rNYEF-0007nZ-S4 for guix-patches@gnu.org; Wed, 10 Jan 2024 08:02:45 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1704891759; x=1706706160; bh=0KttMCZ4djuBLnI fwyUGnSgzS+WnwpLNvJCgOp7oxyc=; b=ITzatXfQRKogk8/Op5QnF+JFk7ecpHb M1XkAz1OC5NUXSRxaK/4G+KuJhelXmL74+lT7WS2KQtEih2zAXdQfcImp5eJHNWF 1NljjALFU2btTOsnu8CdbtX6wDNSOK9WVQrV1aub+MTka93Igitxa8knZQDUqjuk 18ysX53wV2KA= 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 29EAEA013A for ; Wed, 10 Jan 2024 14:02:38 +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 15.2.1258.28; Wed, 10 Jan 2024 14:02:38 +0100 From: nafkhamdc To: Subject: [PATCH] gnu: Add r-dsb. Date: Wed, 10 Jan 2024 13:02:35 +0000 Message-ID: <79a84f556ed434e7a51f4fb87872872ef719719b.1704891744.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.218.27] 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-14.0.0.3152-9.1.1006-28110.006 X-TM-AS-Result: No-10--1.917300-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9AKgfO6jacGa9j7aNnpjtlxHY 45c6zrjduf5ur5byPpcign5HsLTCTuJXEeLLJ6+yrm7DrUlmNkF+24nCsUSFNjaPj0W1qn0TKay T/BQTiGovaJmMmOK99BB0kraAvZprTS0yYi/fuP8kH6nuYpMv9eadAIHhw3CgYWj6zHBWXQaliB dumkwMgGjtwb3HkLh0F99M1WxeaYRBUufKjLHzaeFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJ m2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.917300-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28110.006 X-TM-SNTS-SMTP: 902F6425284BCBF916219AAD048AEF9F9B928EEC9A782AE190ED12BDAC35AFB52000: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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: nafkhamdc 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-dsb): New variable. Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7af5c42ce..7c4272f8be 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5599,6 +5599,34 @@ (define-public r-dropletutils pseudo-cells, and downsampling of the count matrix.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-limma from Bioconductor. +(define-public r-dsb + (package + (name "r-dsb") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dsb" version)) + (sha256 + (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) + (properties `((upstream-name . "dsb"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-magrittr r-mclust)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://github.com/niaid/dsb") + (synopsis + "Normalize & denoise droplet single cell protein data (CITE-Seq)") + (description + "R-dsb improves protein expression analysis in droplet-based single-cell studies. +The package specifically addresses noise in raw protein UMI counts from methods like +CITE-seq. It identifies and removes two main sources of noise—protein-specific noise +from unbound antibodies and droplet/cell-specific noise. The package is applicable to +various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform +data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor, +and using dsb in Python.") + (license license:cc0))) + (define-public r-dss (package (name "r-dss") base-commit: 537768018ee03a6a9a5562022a16b47ac287d131 -- 2.34.1 ------------=_1704909065-10892-1--