From patchwork Fri Oct 28 02:53:52 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 44164 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id E506427BBEB; Fri, 28 Oct 2022 03:56:17 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5375427BBEA for ; Fri, 28 Oct 2022 03:56:17 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ooFWU-0004zG-La; Thu, 27 Oct 2022 22:55:06 -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 1ooFWR-0004vA-CK for guix-patches@gnu.org; Thu, 27 Oct 2022 22:55:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ooFWR-0001jU-4j for guix-patches@gnu.org; Thu, 27 Oct 2022 22:55:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ooFWQ-0005VF-Vf; Thu, 27 Oct 2022 22:55:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58827] [PATCH 1/2] gnu: Add r-dama. References: <91ee903b139e44e9a75ec5fd17386b0c@mdc-berlin.de> In-Reply-To: <91ee903b139e44e9a75ec5fd17386b0c@mdc-berlin.de> 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: Fri, 28 Oct 2022 02:55:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58827 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <58827@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 58827-submit@debbugs.gnu.org id=B58827.166692566121091 (code B ref 58827); Fri, 28 Oct 2022 02:55:02 +0000 Received: (at 58827) by debbugs.gnu.org; 28 Oct 2022 02:54:21 +0000 Received: from localhost ([127.0.0.1]:59862 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooFVl-0005U3-C6 for submit@debbugs.gnu.org; Thu, 27 Oct 2022 22:54:21 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:37993) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooFVj-0005Th-0V for 58827@debbugs.gnu.org; Thu, 27 Oct 2022 22:54:19 -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=1666925652; x=1668740053; bh=2CIawY83lXBQN+a jB2yz/XFktLAzrIQ/c+dSmgzmCzU=; b=G67S2mw/HF30yL2DYPZHSGSsdAxSmmc B51FFTKwcmVXDvrkumbsGl3zl4vO5dUEJaGGwcyhDZlfijBNlMB4gkmNcDjXvkW6 Nz13ecwer7ugVGzyq/vRROlcbGWOOWCxXyoLupJyfnIbYm/tujNto5qEJelQUm1r CUu0RQoR37ys= 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 id 937C7A02E4 for <58827@debbugs.gnu.org>; Fri, 28 Oct 2022 04:54:12 +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; Fri, 28 Oct 2022 04:54:09 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 28 Oct 2022 04:53:52 +0200 Message-ID: <20221028025353.2281-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27228.004 X-TM-AS-Result: No-10--1.804400-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2s6Rp8jBh2MVQrcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9r9+Kgn2XgeKe69x2ASyOme0Q UacIGnqW0RW6ZL06RRR8Cr9lHU/NX4Mu+9Uvd4HjGL//8mlodAxDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt8dWDYdvqmp9zw4lzv7RUn3FLeZXNZS4CiM3WUt6LtFH71YiKW2JewB6J/di7xc+jsOz JgtAnyMrfK6Pw2vAo6YRqZGT6NIrURlOr94Wh3XpihDO+CMxNeCmo1G5P+nhJNv+ktFXpG3WSgm pbFZnEI1kD2KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.804400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27228.004 X-TM-SNTS-SMTP: B38566F029CCEAC022FDBF5C8A7117B0A369F921C97E4B216F62D8342BDF455B2002: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-dama): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8535250f9..9f79954d8d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3013,6 +3013,29 @@ (define-public r-cummerbund used visualizations.") (license license:artistic2.0))) +(define-public r-dama + (package + (name "r-dama") + (version "1.68.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "daMA" version)) + (sha256 + (base32 + "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m")))) + (properties `((upstream-name . "daMA"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html") + ;; http://www.microarrays.med.uni-goettingen.de - domain not found + (synopsis + "Efficient design and analysis of factorial two-colour microarray data") + (description + "This package contains functions for the efficient design of factorial two- +colour microarray experiments and for the statistical analysis of factorial +microarray data.") + (license license:gpl2+))) + (define-public r-dearseq (package (name "r-dearseq") From patchwork Fri Oct 28 02:53:53 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 44163 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 1861D27BBEA; Fri, 28 Oct 2022 03:56:06 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 292AA27BBE9 for ; Fri, 28 Oct 2022 03:56:04 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ooFWU-00050G-SO; Thu, 27 Oct 2022 22:55:06 -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 1ooFWR-0004v9-EG for guix-patches@gnu.org; Thu, 27 Oct 2022 22:55:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ooFWR-0001i7-4J for guix-patches@gnu.org; Thu, 27 Oct 2022 22:55:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ooFWQ-0005V7-G4; Thu, 27 Oct 2022 22:55:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58827] [PATCH 2/2] gnu: Add r-damefinder. 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: Fri, 28 Oct 2022 02:55:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58827 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <58827@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 58827-submit@debbugs.gnu.org id=B58827.166692566121085 (code B ref 58827); Fri, 28 Oct 2022 02:55:02 +0000 Received: (at 58827) by debbugs.gnu.org; 28 Oct 2022 02:54:21 +0000 Received: from localhost ([127.0.0.1]:59860 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooFVl-0005Tz-0W for submit@debbugs.gnu.org; Thu, 27 Oct 2022 22:54:21 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:43485) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooFVi-0005Tf-Qm for 58827@debbugs.gnu.org; Thu, 27 Oct 2022 22:54:19 -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=1666925651; x=1668740052; bh=tdDTdnJDRMF/CTYI8/HAmUW1cnT6HaGzpIgaKuftzbs=; b=EBeOtQzd70c7 9FyepKZZTo7RBOc8C8c9ffxQDIOF+m+YkiktvDCw/aL9qNIrZ5p6fXPvdMX6YjCb kRS22cVzIrQc+mvxKWP/EYV0Fu2/00Ocn/BLRdv22zKSKQdlH0aE1XFiHbvhXp6C VvUFPINNCgds05z78nZrPr511492JW0= 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 id A506DA02DD for <58827@debbugs.gnu.org>; Fri, 28 Oct 2022 04:54:10 +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; Fri, 28 Oct 2022 04:54:09 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 28 Oct 2022 04:53:53 +0200 Message-ID: <20221028025353.2281-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.0 In-Reply-To: <20221028025353.2281-1-madalinionel.patrascu@mdc-berlin.de> References: <20221028025353.2281-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27228.004 X-TM-AS-Result: No-10-4.620600-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOkNS9uwltRRHqP d8i3AhBoRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v+EcPeBa3EClqY5ZGw7wyeHthf nRdJrUQbXLLhBS2gSrT1F1hMHmKU4oc50oBUFVx+eAiCmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP 1xgyx3DC0DfKHxag6w2H5FpDpktWLAZ481mZSVV/sNZRHhDxXglDsBl22dmpHrdf6rqzdzLs9Xt uazcTAjtKm2kb77IJ18HQ6LxlQQWdxSR7be7fnTFTs4ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl 0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-4.620600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27228.004 X-TM-SNTS-SMTP: D93924FDE42FAD6ED44BEEC6589EC70ED788EE0C0487A82C844A2D85297C2FEA2002: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-damefinder): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f79954d8d..81918e4fe6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3036,6 +3036,47 @@ (define-public r-dama microarray data.") (license license:gpl2+))) +(define-public r-damefinder + (package + (name "r-damefinder") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DAMEfinder" version)) + (sha256 + (base32 + "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf")))) + (properties `((upstream-name . "DAMEfinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bumphunter + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-plyr + r-readr + r-reshape2 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DAMEfinder") + (synopsis "Differential allelicly methylated regions") + (description + "This package offers functionality for taking methtuple or @code{bismark} +outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and compute +@acronym{DAMEs, Differential Allelicly MEthylated regions}. It also offers nice +visualization of methyl-circle plots.") + (license license:expat))) + (define-public r-dearseq (package (name "r-dearseq")