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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: Sat, 29 Oct 2022 23:17:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58879 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <58879@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 58879-submit@debbugs.gnu.org id=B58879.166708539718239 (code B ref 58879); Sat, 29 Oct 2022 23:17:02 +0000 Received: (at 58879) by debbugs.gnu.org; 29 Oct 2022 23:16:37 +0000 Received: from localhost ([127.0.0.1]:36868 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oov49-0004k0-0S for submit@debbugs.gnu.org; Sat, 29 Oct 2022 19:16:37 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:36683) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oov41-0004jC-BS for 58879@debbugs.gnu.org; Sat, 29 Oct 2022 19:16:30 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1667085383; x=1668899784; bh=MCyD5h/YxxWmGordmKncozOCF1lxDu/5fXVLKitlz2Q=; b=Vzlc79lsBfhy +y0z9gvM9Fif2ltFR1VT/X9Hw0Hvf+cUAzlpauIyJkoWqvEzJ9jWPR22sFHkr9i/ WHp8NW/R1cxQxbbNNaibgwRhAdcLOUJZd3laS3+t8RzpW2btgJGeFKTq+ZSuoJI3 zExe2IMYlkSMv1vzO5J9zM8IDVuamis= 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 id 2904716029B for <58879@debbugs.gnu.org>; Sun, 30 Oct 2022 01:16:23 +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 15.1.2507.13; Sun, 30 Oct 2022 01:16:20 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 30 Oct 2022 01:16:06 +0200 Message-ID: <20221029231608.13909-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.0 In-Reply-To: <20221029231608.13909-1-madalinionel.patrascu@mdc-berlin.de> References: <20221029231608.13909-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27232.003 X-TM-AS-Result: No-10--3.859500-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOU8ftiyKjZrf3K 2YuhoY97RRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9lRzZAkKRGDa9j7aNnpjtlfIv PJGZ/sqeI0Ejneva935soi2XrUn/Jn6KdMrRsL14qtq5d3cxkNTkrFvPK8AqoFvyBafJ65+8O6M Az4PC+kHQcuIdj0AcEQw6NRcO5KWla1XM3GsFyNPfE4x4lcm5UfnLXRZ9cYIWSclNWa7K5guQe3 Rh0fyEQx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8odyTXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.859500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27232.003 X-TM-SNTS-SMTP: 71C31D2CFBE8C45CE80C2BBF02D2AEF069BC461DCE3B28BB23832AB6149ADF502002:F 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: , Sender: "Guix-patches" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 809ba69bc3..7f6ba37bf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3150,6 +3150,49 @@ (define-public r-decomplexdisease based on the shared signatures.") (license license:gpl3))) +(define-public r-decomptumor2sig + (package + (name "r-decomptumor2sig") + (version "2.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decompTumor2Sig" version)) + (sha256 + (base32 + "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + (properties `((upstream-name . "decompTumor2Sig"))) + (build-system r-build-system) + (inputs (list perl)) ;script/extractSpecColumns.pl + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-data-table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-matrix + r-plyr + r-quadprog + r-readxl + r-s4vectors + r-summarizedexperiment + r-txdb-hsapiens-ucsc-hg19-knowngene + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://rmpiro.net/decompTumor2Sig/") + (synopsis "Decomposition of individual tumors into mutational signatures") + (description + "The package uses quadratic programming for signature refitting, i.e., to +decompose the mutation catalog from an individual tumor sample into a set of given +mutational signatures (either Alexandrov-model signatures or Shiraishi-model +signatures), computing weights that reflect the contributions of the signatures +to the mutation load of the tumor.") + (license license:gpl2))) + (define-public r-deconvr (package (name "r-deconvr")