From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id OItRCYLbxmO9nAAAbAwnHQ (envelope-from ) for ; Tue, 17 Jan 2023 18:31:46 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id aK1QCILbxmO+mgAAG6o9tA (envelope-from ) for ; Tue, 17 Jan 2023 18:31:46 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id CEC0E2B721 for ; Tue, 17 Jan 2023 18:31:45 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHpnd-0003t3-Nl; Tue, 17 Jan 2023 12:31:05 -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 1pHpnc-0003rk-3g for guix-patches@gnu.org; Tue, 17 Jan 2023 12:31:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pHpna-0007qG-JT for guix-patches@gnu.org; Tue, 17 Jan 2023 12:31:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHpna-0002Rv-Ez for guix-patches@gnu.org; Tue, 17 Jan 2023 12:31:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60885] [PATCH 4/4] gnu: Add r-numbat. Resent-From: Simon Tournier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 17 Jan 2023 17:31:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60885 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60885@debbugs.gnu.org Cc: Simon Tournier Received: via spool by 60885-submit@debbugs.gnu.org id=B60885.16739766599386 (code B ref 60885); Tue, 17 Jan 2023 17:31:02 +0000 Received: (at 60885) by debbugs.gnu.org; 17 Jan 2023 17:30:59 +0000 Received: from localhost ([127.0.0.1]:38132 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnX-0002RE-6i for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:59 -0500 Received: from mail-wm1-f46.google.com ([209.85.128.46]:55158) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnS-0002QW-Qt for 60885@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:55 -0500 Received: by mail-wm1-f46.google.com with SMTP id m15so1669866wms.4 for <60885@debbugs.gnu.org>; Tue, 17 Jan 2023 09:30:54 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=/X+/LHDa7Yb9jGbbBOa4e67Jq5mj9Rtl/wS0sIduITM=; b=MqxIvnfSV7ifs5RWvfWZxeSdfgRwlE2AXnEJPNrLImLe1xg8xwHh0xCiVupGQl4zUh rIO9U/ACV+elY3uTUaOjSUtIYdDR1a08xrKlJMQPzwI1sRvAIZaoEqwqZ0ydfiRBUaMy F5Y+JTaV3oxTA7HqIsjjZym6ehiv8W5hq9H0hqq3aHOkIu8nPMQud4OB1OOelXtx5J7k 6JkrJ2X9BJBKJ4X6i3t1b1InAVP9NNs8bpEpOX4Q4j/ihW/0oVVeGi7dYAlo+sXxs7Di Iud3uXaWVY7g4U97r+gDT8R86jsOFieewhPdaQfRRLIGCymYzOi1nJuCP77blV86DAxM rwug== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=/X+/LHDa7Yb9jGbbBOa4e67Jq5mj9Rtl/wS0sIduITM=; b=EscBRxiKDldx/FhneQpjZsAdzFHMUwiuCnpRwbKW7NzYpT66RqZAw4kFNnRIgtSoau bL3fw0fZ9ABbXmlEhCZSRP3zgl2stquHCecq3gPM/xA4UDo/b+I4V0SN3s7JtJRs/kzM RJ262TZPvINTN4MDgtehWSkK7ODwv+YGnXQOOKOdJ3+LXzz6XevmSmvIeKuuIHO0qiJb dQL6wbgAXuZGRW4D3NGKg2aaCdJNi4zUGTLum3u/y5DMiPzFw2dKerUaq4RrL+fu/bTO PFccNe2RJ7wuuzYJhBZpobZolv94IKjJa3wEJPWf6AeCOBZJwu1HPhxYSoh/oZ/ZZjUQ hBSw== X-Gm-Message-State: AFqh2krqQKgIVdjWsawCNV9DqI3uHQ2KG10NobzSqNTWWdVkVo2Grdvg Xwl1lhvpoAy5DGY0HKEx+s7ArY8pY6M= X-Google-Smtp-Source: AMrXdXvz5/ZeGdruWZutzHAMh1Pch9TtssID0V+ZKURAHLAB7gnDbcosmdDchMhvnMWJgTRaY4kgUg== X-Received: by 2002:a05:600c:3b05:b0:3d3:4f99:bb14 with SMTP id m5-20020a05600c3b0500b003d34f99bb14mr923791wms.0.1673976648947; Tue, 17 Jan 2023 09:30:48 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t12-20020a05600c198c00b003d9de0c39fasm47637107wmq.36.2023.01.17.09.30.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 17 Jan 2023 09:30:48 -0800 (PST) From: Simon Tournier Date: Tue, 17 Jan 2023 18:30:41 +0100 Message-Id: <20230117173041.1851206-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20230117173041.1851206-1-zimon.toutoune@gmail.com> References: <20230117173041.1851206-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1673976705; a=rsa-sha256; cv=none; b=Pftd1sqbWdVrgGrsGDpiFHLZuA5QDWCPHp8Mm1R+KTxzD/ecpWQMcz2vT0wwM3HgUgN8OU bd//jlerBtK8zXB/fn+9HKHAqkv2PDjeuRi1v/YMZgTPR5bfbKCzuxD6JRr9QCkQRlI+D6 iZs7qaei39AlLPgUsso1rMRxpYYVUUMPhoEPnpK/SYCZnOCBqGqy0kuLhg8YU5MqhQfkfc XqgrlRMVAUvUDZuJCY1w/l9q4eDijldUzDN4v30Wfn7I92mwy2Qvzz+V7bGu9BUSJN4sjB jVh8mFuny1jGa4yd/bcGKnjXxL3rQFcrNkg+sKSUmtYOJjSU9/33kCyaeIdzPw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MqxIvnfS; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1673976705; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=/X+/LHDa7Yb9jGbbBOa4e67Jq5mj9Rtl/wS0sIduITM=; b=ubMqExOJjO4tnuZ6BfOekOwx6FtTzlTfnBKscP4faGw2O0Hlyaa4CxCySF92fZrl3m5gfG 2WM/Ht//5kTBB4iXQR2LrmrcWGn9xX8ceHSGbvhRXcjFqINRW6zP0IDpk/qCc95J3OemG8 Pg6aLJHlYKrgy4ekPiCBgBXECSqfuE4c29igMhfHX7QT1La2jmpak7p969DM9gIb4VIWx+ kGHMtQWvaIfPxuUGjelSEttBwi+mdWzXJd8NaVBSTCNxsVaIv/RPcb/XFCx7q4whdbMhAO cmapzquepbRFym67U2x+Ac1PEBUXLzoOhLoNgcqAGZI9DrE8ia4cBXB09ZGRJw== X-Migadu-Scanner: scn0.migadu.com X-Migadu-Spam-Score: -2.03 X-Spam-Score: -2.03 X-Migadu-Queue-Id: CEC0E2B721 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MqxIvnfS; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-TUID: Urqqd1WZ6OfA * gnu/packages/bioconductor.scm (r-numbat): New variable. --- gnu/packages/bioconductor.scm | 67 +++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3511bfd81a..2d6093b238 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6696,6 +6696,73 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. It does not require +tumor/normal-paired DNA or genotype data, but operates solely on the donor +scRNA-data data (for example, 10x Cell Ranger output). It can be used to: + +@enumerate +@item detect allele-specific copy number variations from single-cells +@item differentiate tumor versus normal cells in the tumor microenvironment +@item infer the clonal architecture and evolutionary history of profiled tumors +@end enumerate + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") -- 2.38.1