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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 13 Apr 2022 12:06:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54907 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54907@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.164985150523931 (code B ref -1); Wed, 13 Apr 2022 12:06:01 +0000 Received: (at submit) by debbugs.gnu.org; 13 Apr 2022 12:05:05 +0000 Received: from localhost ([127.0.0.1]:51927 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nebk9-0006Dv-5b for submit@debbugs.gnu.org; Wed, 13 Apr 2022 08:05:05 -0400 Received: from lists.gnu.org ([209.51.188.17]:60560) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nebk7-0006Dk-49 for submit@debbugs.gnu.org; Wed, 13 Apr 2022 08:05:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50902) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nebk6-0005LO-Un for guix-patches@gnu.org; Wed, 13 Apr 2022 08:05:02 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:58919) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nebk3-0007wa-SU for guix-patches@gnu.org; Wed, 13 Apr 2022 08:05:02 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 87BAF160177 for ; Wed, 13 Apr 2022 14:04:55 +0200 (CEST) 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:received:received; s=mdc; t=1649851494; x=1651665895; bh=j37ZHDE0TiHgz8wttOUKpIZlT/NvHvrE0RI7BvuWjeM=; b=jHdy95X2+OdS opb/aLIvcq9C5UFJJ10UbMq1QVkOOUxN+tFUGZvZbXEjwNgkW6bDfg3DkU+DQ3ua WloDysCs7ww7mCrUmFIIEJzQ8nPuRa9ewWhkN+DAl4cbpNijc7xWA6tt5qK+EBEm vsiWFgkdjvzkYroSw02A0A7qWU8YMlw= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id W71S6lEkQObK for ; Wed, 13 Apr 2022 14:04:54 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 13 Apr 2022 14:04:54 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2375.24; Wed, 13 Apr 2022 14:04:54 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Wed, 13 Apr 2022 14:04:42 +0200 Message-ID: <20220413120442.28226-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26830.007 X-TM-AS-Result: No-10--5.212300-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6kYD8wAZKsSCp/958oU3WcKY5ZGw7wyeHxyz d3izIESnSK2SElTaHRoIZ90W1XMTOqkRlB2fqw8ZURfNbW2avkFG/eE72T0NCU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+8re9IPyYdQjDUa09XgljsZAqhlNR/oB1640W 4zgHoKkw0T5V9UEEFY= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.212300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26830.007 X-TM-SNTS-SMTP: 06EF1DA8B5D4EE15613E7EF007B9351AD2C20AB55E5CCC51F58A2BE27E0DFA6F2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action 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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-ace): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..ffa442ee1b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11642,6 +11642,35 @@ (define-public r-universalmotif motifs, and others.") (license license:gpl3))) +(define-public r-ace + (package + (name "r-ace") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACE" version)) + (sha256 + (base32 + "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6")))) + (properties `((upstream-name . "ACE"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tgac-vumc/ACE") + (synopsis + "Absolute copy number estimation from low-coverage whole genome sequencing") + (description + "This package uses segmented copy number data to estimate tumor cell +percentage and produce copy number plots displaying absolute copy numbers. For +this it uses segmented data from the @code{QDNAseq} package, which in turn uses +a number of dependencies to turn mapped reads into segmented data. @code{ACE} +will run @code{QDNAseq} or use its output rds-file of segmented data. It will +subsequently run through all samples in the object(s), for which it will create +individual subdirectories. For each sample, it will calculate how well the +segments fit (the relative error) to integer copy numbers for each percentage +of @dfn{tumor cells} (cells with divergent segments).") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs