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Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 Aug 2023 10:40:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 65493 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65493@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169287355427106 (code B ref -1); Thu, 24 Aug 2023 10:40:01 +0000 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 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-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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Spam-Score: -4.01 X-Spam-Score: -4.01 X-Migadu-Queue-Id: F156E45641 X-Migadu-Scanner: mx1.migadu.com X-TUID: iO3WbFj9+qC9 * 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