From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 24 06:39:13 2023 Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 10:39:14 +0000 Received: from localhost ([127.0.0.1]:36216 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZ7k9-000737-Ij for submit@debbugs.gnu.org; Thu, 24 Aug 2023 06:39:13 -0400 Received: from lists.gnu.org ([2001:470:142::17]:57580) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZ7k5-00072r-IM for submit@debbugs.gnu.org; Thu, 24 Aug 2023 06:39:12 -0400 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 1qZ7jw-0003NS-Bt for guix-patches@gnu.org; Thu, 24 Aug 2023 06:39:00 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qZ7jt-0001Ny-4t for guix-patches@gnu.org; Thu, 24 Aug 2023 06:39:00 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1692873523; x=1694687924; bh=O1Z0yxgnJqi+2h7 pIjS/h0Y9dDQtkcsZUj7i2z9RR60=; b=qrtQpJFaNAm0KX5SeOdJ55FTKY83Xyc 5fR+KGylW/Ay3s4TqGJEfXQXQuvLt5IikvY4zi1OtnSzqwFb/jvVxQ+vgIFTNUEE mZwpOipgz5NLP+0mWvuhJNQAACHdlpcuQlevIsJahrqLllRRqbspIr7IlmW40GAM 8Cz8ls3j08Os= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4C840A02B9 for ; Thu, 24 Aug 2023 12:38:43 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Thu, 24 Aug 2023 12:38:42 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-msigdb. Date: Thu, 24 Aug 2023 10:38:37 +0000 Message-ID: <0e1abe23554c0125ec623d0926c7eb7d274c38f0.1692873517.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.006 X-TM-AS-Result: No-10--10.450700-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEGf0 psGams1smUhH31Cro3rlFNVd1xwO6iq+GZ9ZHxIhuW77/y896siFzNNPDc6umMicqvB+icULKpd i3M+FP42jnl/fXbQ2QRf6uqcdjTP5HZVDA3E+C7uXVXMu1aPavNvhAz8PvMa364sf0Egj7iqsqx rFSI3/KcX4oKkYTfsImyiLZetSf8mfop0ytGwvXiq2rl3dzGQ14fElrjbaY/caMUyeC0staIoCV 2MAhQ2quhom19DzeJnp/lSo1zbI5eRb3dQntY1p9uPxkwCKmVSDI+7PTmom/g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--10.450700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.006 X-TM-SNTS-SMTP: 960446A16FE5038C3AAFE13C23C57A03AC7922389A26EA47839F0A76A47985002000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-msigdb): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74071900a3..5e323d11ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1754,6 +1754,39 @@ (define-public r-msdata files for various search engines.") (license license:gpl2+))) +(define-public r-msigdb + (package + (name "r-msigdb") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "msigdb" version + 'experiment)) + (sha256 + (base32 + "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby")))) + (properties `((upstream-name . "msigdb"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-experimenthub + r-gseabase + r-org-hs-eg-db + r-org-mm-eg-db)) + (native-inputs (list r-knitr)) + (home-page "https://davislaboratory.github.io/msigdb") + (synopsis "ExperimentHub package for the molecular signatures database") + (description + "R-msigdb provides the Molecular Signatures Database in a R accessible objects. +Signatures are stored in @code{GeneSet} class objects form +the GSEABase package and the entire database is stored in a +@code{GeneSetCollection} object. These data are then hosted +on the @code{ExperimentHub.} Data used in this package was +obtained from the @code{MSigDB} of the Broad Institute. +Metadata for each gene set is stored along with the gene +set in the @code{GeneSet} class object.") + (license license:cc-by4.0))) + (define-public r-pasilla (package (name "r-pasilla") base-commit: 160f78a4d92205df986ed9efcce7d3aac188cb24 -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 28 04:08:07 2023 Received: (at 65493-done) by debbugs.gnu.org; 28 Aug 2023 08:08:07 +0000 Received: from localhost ([127.0.0.1]:46851 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXI6-0002KN-Ej for submit@debbugs.gnu.org; Mon, 28 Aug 2023 04:08:06 -0400 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21886) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXHv-0002Jo-Jx for 65493-done@debbugs.gnu.org; Mon, 28 Aug 2023 04:08:04 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1693210066; cv=none; d=zohomail.com; s=zohoarc; b=efTmrVnpkLnferyP/OALbdCt9A9+/lc/u/UismElk3lZhbROLWWK4d8WnCtPMa/T+xHfhjVQ0UxcSCGYcOwbvrMNS7AWgQWw+6zuE/t9rn5/zbGLHf36tJLpfjgjV2Lorg3Q/lWBl1M1KMvyBI3jv7HOkU0L7mycJ3pGbSDUPHo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1693210066; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=Qvm42CCF96yw9rYcNSUFkJVBLMgQtnZ44WlHhs5Cw+s=; b=HVI0YpcbyocjN2bPTRJgUbs0P8kAOOP4CcwgVbJl3gFbG9BszTm6WsC3CAXRF3BPeqNoSrBy22qIMBUujV8kiAJuyEcdrYw8tmzMr0Xy6sBmLnoY7NWCPfUybzpmf3QWyELJtXwlAnWk8ZhaCIdUMey02wLMjHzXc08OYfSA2S8= 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=1693210066; 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=Qvm42CCF96yw9rYcNSUFkJVBLMgQtnZ44WlHhs5Cw+s=; b=XknrGznShe1LmAYijpLj4B8MbIWYc0U7dFbvyABbX7sMyQBZDGzSmuL6NQkcQK6o cvSXtnE9bDKfptR5FYv6UvWhBQf2ds24IBlnsKcmG9vOcg7lc6Bm6EHxqhWmzJRDEI6 q7a4gYrWgjs2zh4R6jq9iqNYuJffgycqr2qsYSAo= Received: from localhost (113-111-142-46.pool.kielnet.net [46.142.111.113]) by mx.zohomail.com with SMTPS id 1693210065224780.399587427601; Mon, 28 Aug 2023 01:07:45 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 65493-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-msigdb. Date: Mon, 28 Aug 2023 10:06:47 +0200 Message-ID: <87h6ojfv3l.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 65493-done 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: -1.0 (-) Applied with minor changes: - changed the home page because it is not reachable (guix lint complained) - reflowed the description Thanks! -- Ricardo From unknown Sun Jun 22 11:43:09 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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