From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 16 12:35:28 2022 Received: (at submit) by debbugs.gnu.org; 16 Jun 2022 16:35:28 +0000 Received: from localhost ([127.0.0.1]:42980 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1sSt-00067i-LT for submit@debbugs.gnu.org; Thu, 16 Jun 2022 12:35:28 -0400 Received: from lists.gnu.org ([209.51.188.17]:38772) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1sSo-00067X-Nl for submit@debbugs.gnu.org; Thu, 16 Jun 2022 12:35:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42616) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1sSo-0003nc-GH for guix-patches@gnu.org; Thu, 16 Jun 2022 12:35:22 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:36893) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1sSk-0005Vu-RJ for guix-patches@gnu.org; Thu, 16 Jun 2022 12:35:22 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 5C97EA01EE for ; Thu, 16 Jun 2022 18:35:15 +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=1655397314; x=1657211715; bh=yAyX6j/zXBiynszSVGlG5FkLinBuYlKmxrURKEI3c0I=; b=L5pzl+7lwoc3 pOa64gvtedBzYA2NgFhsG/1Z+6n0gQdF+WcJkagrxicqedfQrSYjo0OFRF242NEP VAQ/UZ5XiIicUfc1wywIb+v9uA+eJBXWwqjZUlChXnqPbLs/iNq5iv058ffypJDA kDlkTLtJ/o06jRAR1whhDOyGct2Fl/c= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 2o3AnmFH6MuW for ; Thu, 16 Jun 2022 18:35:14 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Thu, 16 Jun 2022 18:35:14 +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; Thu, 16 Jun 2022 18:35:13 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-alphabeta. Date: Thu, 16 Jun 2022 18:35:02 +0200 Message-ID: <20220616163502.27554-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-14.0.0.3092-9.0.1002-26958.007 X-TM-AS-Result: No-10--2.594400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH60oH2iw13V7uiNCtus+nPOqY5ZGw7wyeHcJs 6p08L6d8CBvE1eIcYKsign5HsLTCTuJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGnGI6k+tMbXs7Z0sHKZkFAcrNz0KrBTyxDJwziTXCB2JO1Ds0aTjB4/LK0/A6lb2lHOx9 mXozrqRT/9/oRkaRwMN/oZfeA3QfWHkKCDQJqBctOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.594400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-SNTS-SMTP: D9ACF57C21571E48595223E0C34E60DC12070761BB607B3307F01E6589846FA52002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@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, 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-alphabeta): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..cd9923a946 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,46 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-alphabeta + (package + (name "r-alphabeta") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlphaBeta" version)) + (sha256 + (base32 + "1ikdrigma02gnl6ggrc89bjsiqmd7knpb9kw7nqyrdnv3qjd9iag")))) + (properties `((upstream-name . "AlphaBeta"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AlphaBeta") + (synopsis + "Estimating epimutation rates and spectra from DNA methylations in plants") + (description + "The package @code{AlphaBeta} is a computational method for estimating +epimutation rates and spectra from high-throughput DNA methylation data in plants. +The method has been specifically designed to: +@itemize +@item +analyze @emph{germline} epimutations in the context of multi-generational mutation +accumulation lines; +@item +analyze @emph{somatic} epimutations in the context of plant development and aging. +@end itemize") + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 24 09:21:07 2022 Received: (at 56023-done) by debbugs.gnu.org; 24 Nov 2022 14:21:07 +0000 Received: from localhost ([127.0.0.1]:57804 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyD6A-0006Bj-UM for submit@debbugs.gnu.org; Thu, 24 Nov 2022 09:21:07 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21103) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyD67-0006BO-2T for 56023-done@debbugs.gnu.org; Thu, 24 Nov 2022 09:21:06 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1669299661; cv=none; d=zohomail.com; s=zohoarc; b=WpEHhJpo7e3rOJ4la+1PYTj+R1XTd4hWNOOgkOMm+LiEcM5gGkSRU3W8LphtYWePIa1UWAbWXll/nmzDcgKsry7QBRwuYqfac40Fe00JEoEdEpI3SyrvHzpK8pnAePa8RfULQ8khIkQ4w4GCuA6nL63Y5ADAWUWrpYZAR4qJHmA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1669299661; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=IM1CCrS3UK+hRJqioc2amRe0mhh5UfMT2Og1xGIIC2ccvpT7Pcrg8wRrEYKjcbz+4vnJUoe9IXw+dKDThMUj3L1EcMGnxHN+NUKzYL706IAuQ/AU1tmh1GwrbTPebjYa8FkxGa6v2VFEJnocYsBb0jHbVyrcjEqJUdlSUJS1Cfk= 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=1669299661; 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=jFRBW2Hgn+pQyDKQfU6OlX2f7no3WJdY0SpD12xMebzg8gRiiE15iKskQ1qP06n7 RMYAmNScN42wOJ9o+KBUCLyLzcgDRuOh2r1DJ0kDM07VeActkAeEhCvTx+tJhFK/pLs MwuBgqpEDAfVf5NWNznbjgRwmtonjEqpxsfpecbQ= Received: from localhost (145-109-142-46.pool.kielnet.net [46.142.109.145]) by mx.zohomail.com with SMTPS id 1669299659037182.91857774544894; Thu, 24 Nov 2022 06:20:59 -0800 (PST) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56023-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-alphabeta. 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