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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 17 Jun 2022 09:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 56034 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56034@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.165545819231398 (code B ref -1); Fri, 17 Jun 2022 09:30:02 +0000 Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 09:29:52 +0000 Received: from localhost ([127.0.0.1]:43744 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o28Ia-0008AM-Bi for submit@debbugs.gnu.org; Fri, 17 Jun 2022 05:29:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:53386) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o28IW-0008AA-G8 for submit@debbugs.gnu.org; Fri, 17 Jun 2022 05:29:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36024) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o28IW-0005eD-7W for guix-patches@gnu.org; Fri, 17 Jun 2022 05:29:48 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53113) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o28IT-0008W5-Bl for guix-patches@gnu.org; Fri, 17 Jun 2022 05:29:47 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 44040300370 for ; Fri, 17 Jun 2022 11:29:41 +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=1655458180; x=1657272581; bh=dqVSR48DBza5Vg32CzbE+CFKY6UYYmhIOsYfse8k49Q=; b=qS2XbgYsRzeT 4f5L3wbv09sRcH7t/Wa2toWOYrxoKXi0cfVBsG7triSJTt63bl8tZXCdaH49PM6E UwBOABGtN1DtijmHB1/D9KnigJf+Uw/mCpgBorIlueBdL2Fx+KXAeD1sNB7090sc v91RCGNtOTlt61zUhlHnUoQ3ypqi48Y= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 8cihlrlp0_2s for ; Fri, 17 Jun 2022 11:29:40 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Fri, 17 Jun 2022 11:29:40 +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 15.1.2507.9; Fri, 17 Jun 2022 11:29:39 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 17 Jun 2022 11:29:29 +0200 Message-ID: <20220617092929.353-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26960.006 X-TM-AS-Result: No-10--6.897400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9DbojwkwY92nLGuXj0Sbso8/33pXlm91Fv1IpvL/Dm1nUPdkXjfR3d0weRtodkNYFbOrOe9Q KgtmmT7F8FOHDsv49Nz2FT75yDfBlWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWxfIVs4QjZ1xabmiIVZgQ7uFYSnIZ/Eam3jcWFjLbXS3r7RTBZjMGZg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.897400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.006 X-TM-SNTS-SMTP: 1C2317CBFE9EBE87A04C23F8DA116A706D554359E424D3994B22F93186DE92982002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.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 base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..a78ceb2de5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-amaretto + (package + (name "r-amaretto") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AMARETTO" version)) + (sha256 + (base32 + "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + (properties `((upstream-name . "AMARETTO"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocfilecache + r-callr + r-circlize + r-complexheatmap + r-curatedtcgadata + r-doparallel + r-dplyr + r-dt + r-foreach + r-ggplot2 + r-glmnet + r-gridextra + r-httr + r-impute + r-knitr + r-limma + r-matrix + r-matrixstats + r-multiassayexperiment + r-rcpp + r-readr + r-reshape2 + r-rmarkdown + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AMARETTO") + (synopsis "Regulatory network inference and driver gene evaluation") + (description + "This package @code{AMARETTO} represents an algorithm that integrates copy +number, DNA methylation and gene expression data to identify a set of driver +genes by analyzing cancer samples and connects them to clusters of co-expressed +genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer +setting to identify cancer driver genes and their modules on multiple cancer +sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle +and EMT, and modules that accurately predict survival and molecular subtypes. +This allows @code{AMARETTO} to identify novel cancer driver genes directing +canonical cancer pathways.") + (license license:asl2.0))) + (define-public r-aneufinder (package (name "r-aneufinder")