From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 13 12:15:30 2023 Received: (at submit) by debbugs.gnu.org; 13 Oct 2023 16:15:30 +0000 Received: from localhost ([127.0.0.1]:47291 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKp0-00048H-9X for submit@debbugs.gnu.org; Fri, 13 Oct 2023 12:15:30 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55984) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKox-0003mS-Mt for submit@debbugs.gnu.org; Fri, 13 Oct 2023 12:15:29 -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 1qrKoU-0005Wv-4F for guix-patches@gnu.org; Fri, 13 Oct 2023 12:14:58 -0400 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 1qrKoR-0002cm-Hi for guix-patches@gnu.org; Fri, 13 Oct 2023 12:14:57 -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=1697213691; x=1699028092; bh=HfYhUIjw5FeeRkH VC4S/Kdhmw3HLO6DOHjGRTP5LrT4=; b=P1aSebImQvD8/8wxqF1cwBJeMKu8s9/ aLIRKuXjQDYXDiK8d6SbbSeQFiAUpzoJ1pKxza5ye4bor+QmJ4H3UfEuuDLzw4HJ +wAqeTDBEdKJnWuCrFRdYk3L/dZFBV4/Tq7nZAoIXHa9vM7bLo4kMIn/ZKIE/woC 2hAJy+owJ9aQ= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 3D23E160167 for ; Fri, 13 Oct 2023 18:14:51 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 13 Oct 2023 18:14:50 +0200 From: "Afkhami, Navid" To: Subject: [PATCH] gnu: Add r-metacell. Date: Fri, 13 Oct 2023 16:14:43 +0000 Message-ID: <5cf244a75edf748f180e87b4607a67126260115f.1697213683.git.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-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-AS-Result: No-10--5.200400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJsUh +OkaOhpcV5MniPWJBrQAdOkL0w2geKgAlgjPhYpZvTnqYKYXTRhDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG73Yq8RVaZivWmLEn9syYec2jmviYAnAO9CXZSV0MUS2SyFL5xqNseSUsu3 c/ceBs0 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.200400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-SNTS-SMTP: 3099E1870F2B3C238980E2BB68A0E9A8CD1DFD5B914B073A915DB8393EFF00922000: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: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: "Afkhami, Navid" 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/bioinformatics.scm (r-metacell): New variable. --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb0bdf766e..45afde699d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10285,6 +10285,66 @@ (define-public r-markdownreports discovered.") (license license:gpl3)))) +(define-public r-metacell + (let ((commit "d6a6926d103ee0cb34a611c753572429c94a53d9") + (revision "1")) + (package + (name "r-metacell") + (version (git-version "0.3.41" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/metacell/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zrsckr3y35x37mj3ibm6scyqx925s84wzrz1i42fnm9n3msc265")))) + (properties `((upstream-name . "metacell"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster + r-cowplot + r-data-table + r-dbscan + r-domc + r-dplyr + r-entropy + r-ggplot2 + r-graph + r-igraph + r-kernsmooth + r-magrittr + r-matrix + r-matrixstats + r-pdist + r-pheatmap + r-plyr + r-rcolorbrewer + r-rcurl + r-rgraphviz + r-slam + r-singlecellexperiment + r-svglite + r-tgconfig + r-tgstat + r-tgutil + r-tidyr + r-umap + r-umap + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tanaylab/metacell/") + (synopsis "Meta cell analysis for single cell RNA-seq data") + (description + "This package facilitates the analysis of single-cell RNA-seq UMI matrices. +It does this by computing partitions of a cell similarity graph into +small homogeneous groups of cells, which are defined as metacells (MCs). +The derived MCs are then used for building different representations of +the data, allowing matrix or 2D graph visualization forming a basis for +analysis of cell types, subtypes, transcriptional gradients,cell-cycle +variation, gene modules and their regulatory models and more.") + (license license:expat)))) + (define-public r-snapatac (package (name "r-snapatac") base-commit: dcfd4d9c4827ca6bfebeec46fe6bb8373c425a1c prerequisite-patch-id: 8b3f1b30e7ca1f6ddb21bf801faad91cce276dfd prerequisite-patch-id: 86f04eb38885c80e1fa302cec734581778e62c26 prerequisite-patch-id: d5cebe9646097c611915c8b796a94ff0d1831343 prerequisite-patch-id: 675ed63512dcf5b145a929d0097b1bb7e7f1c389 prerequisite-patch-id: 8a7046dfe2c6c18892fed37a877f66be5be7f96e -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 17 08:32:19 2023 Received: (at control) by debbugs.gnu.org; 17 Oct 2023 12:32:19 +0000 Received: from localhost ([127.0.0.1]:58796 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qsjFD-0004Bi-JI for submit@debbugs.gnu.org; Tue, 17 Oct 2023 08:32:19 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21112) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qsjF8-0004BV-VE for control@debbugs.gnu.org; Tue, 17 Oct 2023 08:32:18 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1697545905; cv=none; d=zohomail.com; s=zohoarc; b=FXX7r1zccCNyD5GQy3z0iGtcvxr7yJ6xvXrNr2+Htm/VOjoJsa/5MSlnALmZEKkojfLzO65eDoC162Um9gAyo1v0HZrJfDOzx/eUjjMieMhQygTp59KDtRMkzRz4k7qv8RcZPPbdWvR8C/te6cfnwahqf4x7r76PUXGnEP72sT0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1697545905; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:To:To:Message-Id:Reply-To:Subject:Cc; bh=A2OFROw83Gp2jIHwpbID6odi5l7ESv9nuyixNi0h610=; b=P7/jvTg0E5CfnWdwzwYz7PBMfwCMbb8pzNm9Wi6fzOg93tRznFYkNCTTBgf+Sz1+nFh8b8l+E7Vcci9z2vOAaTxTbRKRzUiahqOEXAlGakB9I2JQOdsS27mXKvkuq+55UO/mDnT9EQWXf+epcTDWP6bamw4uP2X/uqgzYHaWhlc= 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=1697545905; 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=A2OFROw83Gp2jIHwpbID6odi5l7ESv9nuyixNi0h610=; b=YfAW6W94d+u5NhSferyiIDGo1FQamPbeLAMTGp6J1LiA4t+wGNAtX61SzffRSqKh 5NxC20QX2FItUz6Qs06foW18PphrmCkaP8tyq2Xb7MJXaJv38ntV+jaPKvdHRiXycLg E1fnMaUhJppHHRf9rNP5UuKHoponkxwlemUJLOgo= Received: from localhost (14-108-142-46.pool.kielnet.net [46.142.108.14]) by mx.zohomail.com with SMTPS id 1697545903741776.3236170423603; Tue, 17 Oct 2023 05:31:43 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: control@debbugs.gnu.org Subject: Date: Tue, 17 Oct 2023 14:30:42 +0200 Message-ID: <87r0ltjuqb.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 2.0 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. 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Content preview: merge 66524 66526 66527 66528 66529 66530 -- Ricardo Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record -0.0 SPF_PASS SPF: sender matches SPF record -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at https://www.dnswl.org/, no trust [136.143.188.51 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H5 RBL: Excellent reputation (+5) [136.143.188.51 listed in wl.mailspike.net] 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 2.0 BLANK_SUBJECT Subject is present but empty X-Debbugs-Envelope-To: control 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 (+) merge 66524 66526 66527 66528 66529 66530 -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 17 08:34:32 2023 Received: (at 66530-done) by debbugs.gnu.org; 17 Oct 2023 12:34:32 +0000 Received: from localhost ([127.0.0.1]:58801 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qsjHM-0004JM-0v for submit@debbugs.gnu.org; Tue, 17 Oct 2023 08:34:32 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21128) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qsjHJ-0004JC-Os for 66530-done@debbugs.gnu.org; Tue, 17 Oct 2023 08:34:30 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1697546042; cv=none; d=zohomail.com; s=zohoarc; b=ibUH62l+sJj5LzlR4Bvc+1KzkzzUyCBODratPt0eqUg449/fXBkcbwibagXQwdtSxtGA9lRAS9fFt6yx75myiGKVLPlQiqNvJ6SI5AJL39JPC+tB1GG74miReJzUzCwXh1qiMKl86RvjDbSqh/86TPiaPLrHooZMmKWpamIb9zI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1697546042; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=+OCiisPse9axQuNCuHLKujKS0hi5ftOUr++K3O8ZfnI=; b=m1Z0nzMwu2zJgfz6+mgXOPZM6efXOW8VyJ2iFy63r50QAfN3r8gXelpIt1IfpT5MREoNkj9quO/lLYtpUNlghia5RakmyQM8Glk22lufWrz27yor5jKyBM5q+xFNrKsFVfX0iLmKRMcxzyyw56kpiXahO9nAiMyopJEHshzEPpM= 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=1697546042; 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=+OCiisPse9axQuNCuHLKujKS0hi5ftOUr++K3O8ZfnI=; b=iXuEtg1Wkr0YxHQSV5P3peI2FQOW3rm5weACDHo2BoCvuKFd0Cj6AXq2+LkcNexA neFR5R9Urj2h0R+AoaOd4uIygfyJXh5KdoAsq1i6HtqSJ48cNhd6JhogGNFcFlir2of hQ2V3XK1nhUoIal8wc4URQIvaXVyjzqr6VNNkVr4= Received: from localhost (14-108-142-46.pool.kielnet.net [46.142.108.14]) by mx.zohomail.com with SMTPS id 169754604131222.911162218667414; Tue, 17 Oct 2023 05:34:01 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: 66530-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-metacell. Date: Tue, 17 Oct 2023 14:33:33 +0200 Message-ID: <87mswhjumh.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66530-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 patches. I applied them after some massaging. -- Ricardo From unknown Sun Sep 21 07:03:35 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 16 Nov 2023 12:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator