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Reply-To: bug#54985 <54985@debbugs.gnu.org> Date: Sun, 15 Jun 2025 01:05:15 +0000 retitle 54985 [PATCH] gnu: Add r-adam. reassign 54985 guix-patches submitter 54985 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 54985 normal tag 54985 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 17 04:14:29 2022 Received: (at submit) by debbugs.gnu.org; 17 Apr 2022 08:14:29 +0000 Received: from localhost ([127.0.0.1]:34957 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ng03A-0001Ua-VO for submit@debbugs.gnu.org; Sun, 17 Apr 2022 04:14:29 -0400 Received: from lists.gnu.org ([209.51.188.17]:47952) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ng039-0001UQ-6m for submit@debbugs.gnu.org; Sun, 17 Apr 2022 04:14:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40228) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ng038-0004je-Sf for guix-patches@gnu.org; Sun, 17 Apr 2022 04:14:26 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49345) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ng035-0000pX-Is for guix-patches@gnu.org; Sun, 17 Apr 2022 04:14:26 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id C58AB30020E for ; Sun, 17 Apr 2022 10:14:05 +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=1650183245; x=1651997646; bh=v34iwhowlHtJer1H4aqk5aevC33dTVZ1Dx6Hm8M0Ud4=; b=NF+GfRtkbTCw 6OtqFoRFgziiuofGcvK94AnVhAEQ/g/6BZYGHSubBvVVLxV2kvlZ4vKHROSPh7VW q2N74x9lNnSeB+1Xq97cjBY7MzwPDJoT+2c8aGhTnB4lD6agzh086iSjWB+bjLYu 94porav1mSYC2EKfHMfmFx9e964cIrk= 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 TGmSkvieQHJA for ; Sun, 17 Apr 2022 10:14:05 +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 ; Sun, 17 Apr 2022 10:14:04 +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; Sun, 17 Apr 2022 10:14:04 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-adam. Date: Sun, 17 Apr 2022 10:13:43 +0200 Message-ID: <20220417081343.29275-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-14.0.0.3092-9.0.1000-26838.006 X-TM-AS-Result: No-10--1.488000-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEK5d mdubuPz8rCCXG3Lpn8TuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIFWHu1aRUIwChCb CVX9l4V6QiwR2kNJwDZQbULRF1yO8wa31kdtmHsAJslazArifUpmYsOd3akjf64sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RT3v6 emmvS1R8llWHg3VpCwjVVGiFAcSNrybQiBQJsjzxCXESrfgCBagpi3ocXHg9PnKTIr+ES9tr9xS 2/WEx5OOnGAF+7VhBVkoJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.488000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26838.006 X-TM-SNTS-SMTP: F3C47758F84EF83FA6C48EFC9FC2D09A2A462B6B95360CEE69C28B955398CDDA2000: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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-adam): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bec3496057..cd28d3eb20 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1581,6 +1581,41 @@ (define-public r-absseq ranking by fold-change and visualization.") (license license:gpl3+))) +(define-public r-adam + (package + (name "r-adam") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAM" version)) + (sha256 + (base32 + "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5")))) + (properties `((upstream-name . "ADAM"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-dt + r-go-db + r-keggrest + r-knitr + r-pbapply + r-rcpp + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAM") + (synopsis "Gene activity and diversity analysis module") + (description + "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) +package created to group a set of genes from comparative samples (control +versus experiment) belonging to different species according to their respective +functions. The corresponding roles are extracted from the default collections +like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG). +@code{ADAM} show their significance by calculating the p-values referring to +gene diversity and activity. Each group of genes is called @dfn{Group of +functionally associated genes} (GFAG).") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 0c89fe9e17dc9e628c73959289464ac5f146c7cd -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 04:00:00 2022 Received: (at 54985-done) by debbugs.gnu.org; 26 Apr 2022 08:00:00 +0000 Received: from localhost ([127.0.0.1]:36914 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njG75-00005g-VX for submit@debbugs.gnu.org; Tue, 26 Apr 2022 04:00:00 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21138) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njG73-00005S-Cs for 54985-done@debbugs.gnu.org; Tue, 26 Apr 2022 03:59:58 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1650959996; cv=none; d=zohomail.com; s=zohoarc; b=cy+3A6AHGV1wFHTbNj5JXJ8A8xLFgz8FrLvj69BmNngBlLyI6SmFJxMqhaumhJMmBccd9C3TfJAmY4o49tXiGKT33T6ahFjwaR+BHaS8pPa96wgkz8Wf983DaohhcxSGqAWFYH3WgwQe+ZmX9KHqlxDy6Zk4U+XT1JRiPKf0i9k= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1650959996; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=BvqSAbYmF/PLWoqUlFRjc5yM9/WXrbAkB3wYtJWeI7+U/ljwex8Tc+Ig5SG1H+j6j8lTg2vYQGa30wvx20SYWzcgCbj0F3yz0ye3VQX+mz/jcHtF4sF5uqm4PkXiksTSWuXor5O5Jb8edxJD5wDUfDUVyjrmfbMLGbbviNK8/fU= 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=1650959996; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=TXPtMk0wIGK8B4fmb7PikUIU+YefOyc2UnSGNYonKugHcIWufqSApM9B5u/RWLVn T+KqNtNzjX9afUKFRvS7wkvHIxPd5FAHCWsdb8kU5DGcVxQKhOYVyhailJkbmsjWdQn ERlDU3lyiKaSivzQIPHJ+8LmypNjaDW/nIK62nbI= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1650959994861597.3107491585388; Tue, 26 Apr 2022 00:59:54 -0700 (PDT) User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: 54985-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-adam. 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