From patchwork Fri Mar 24 23:18:47 2023 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: 48648 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 C566F16FFB; Fri, 24 Mar 2023 23:21:35 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 86F5016FC9 for ; Fri, 24 Mar 2023 23:21:33 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhf-0002uK-9h; Fri, 24 Mar 2023 19:20:11 -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 1pfqhX-0002o5-Vx for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -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 1pfqhW-000210-Ra for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhW-0005nh-MR for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 01/14] gnu: Add r-anota2seq. References: <4619c49d-2e96-49a5-7bf1-81877eb94696@mdc-berlin.de> In-Reply-To: <4619c49d-2e96-49a5-7bf1-81877eb94696@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969996322089 (code B ref 62428); Fri, 24 Mar 2023 23:20:02 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:23 +0000 Received: from localhost ([127.0.0.1]:41649 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgs-0005kB-Oe for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:50233) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jN-JQ for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:21 -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=1679699953; x=1681514354; bh=MeVX0Bk2E57msnI jWHtuPIhXbDV9yLTMYv2EeRFgdXM=; b=dGDh2OSPcLACrSpUwKQ8ExkSxLKTtid AhMPjIcE5wC2DrETo98GXigRRtFet6cbFD5aOR4QdeFeugcrCn60hwO4ryAySyUi R0VUoJO1SXFmx2FGRsog7bfxfgb6+QkSCdywtNkWKUFefdcs8XeZfuESg3CPDcJ4 6p6SZwbFoJd8= 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 id B1C9D30016F for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:13 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:47 +0100 Message-ID: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--3.933000-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6ioK033WJkCkXjfR3d0weRm1/OiWPM9c7S+M w9GmoCTDtaS19CA2mWOa/i9HRzI0fYPVPAaE1AIJWeFNzK1vl0gK0ZgbTOeKUyiLz1Vtc/pWYDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85RGD4IDogaaVheJvX5hLxeooPQc Y4aTupiEFp+wBUhesaUw5xlhHUTSWyIjC0aI4hlUUzqxHl9/abO2k5GG6pBKvZpzWIFGCbEdAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.933000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 33682B79A758EC4CEB62BF7610614F1883192248AB2F951E94D1D54EE7EE1BE92002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-anota2seq): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) base-commit: ef71e3290916583973724316e815cee840c1b6d8 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe446df67a..37b649a7d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12069,6 +12069,42 @@ (define-public r-anota the data set is suitable for such analysis.") (license license:gpl3))) +(define-public r-anota2seq + (package + (name "r-anota2seq") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "anota2seq" version)) + (sha256 + (base32 "14ggggfa6mdqcb2hfvann9mb66s7a9nxlnh31zblb3mrrjizg1x3")))) + (properties `((upstream-name . "anota2seq"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-edger + r-limma + r-multtest + r-qvalue + r-rcolorbrewer + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/anota2seq") + (synopsis "Transcriptome-wide analysis of translational efficiency") + (description + "The anota2seq package provides analysis of translational efficiency and +differential expression analysis for polysome-profiling and ribosome-profiling +studies (two or more sample classes) quantified by RNA sequencing or +DNA-microarray. Polysome-profiling and ribosome-profiling typically generate +data for two RNA sources, translated mRNA and total mRNA. Analysis of +differential expression is used to estimate changes within each RNA source. +Analysis of translational efficiency aims to identify changes in translation +efficiency leading to altered protein levels that are independent of total mRNA +levels or buffering, a mechanism regulating translational efficiency so that +protein levels remain constant despite fluctuating total mRNA levels.") + (license license:gpl3))) + (define-public r-sigpathway (package (name "r-sigpathway") From patchwork Fri Mar 24 23:18:48 2023 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: 48651 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 8B6AD16FF1; Fri, 24 Mar 2023 23:21:47 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 E127516FC9 for ; Fri, 24 Mar 2023 23:21:46 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhd-0002sd-3O; Fri, 24 Mar 2023 19:20:09 -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 1pfqhY-0002oY-UW for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -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 1pfqhY-0002C3-MQ for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhY-0005o6-HW for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 02/14] gnu: Add r-repmis. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997822183 (code B ref 62428); Fri, 24 Mar 2023 23:20:04 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:38 +0000 Received: from localhost ([127.0.0.1]:41664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lh-Th for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54915) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgr-0005jS-Px for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:23 -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=1679699955; x=1681514356; bh=CjbdIC2YgyjHhETMPd4Q/uY+u80g6JyEB0+EyFn4Omg=; b=GpgZofnEJUTk IWVmhal/d80lsZlPGUZnOhPIAmFZEY3u/IJflBtrirG+MbwluJzu13fpwITKntH/ 6Llo78kKWsTK3oBpthiQy6uPY3PyrlbTD/TP3YsU9L3UG6tcVbhj8kZ2Edmba308 5xfwNRv808pUQ0FFxNwmYCOs9YfD0yY= 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 id F41F2300195 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:14 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:48 +0100 Message-ID: <20230324231900.28367-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10-0.932600-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYnvkzitR82DjQYcH09cOokpqhcdnP91eXFxXefgn/TNQ8IubEPSkNnJ5t3 2Pj5vqMiNrUz3M8EKMuPRJuyjz/feJVNtzAuihDwG7bNEJKsuNheN9Hd3TB5GhJsTo2dS2dnW9n uzdghUMnAdP2YpewALYd00a6+9/yijxYyRBa/qJV/Hpl/zcOjl5MIx11wv+CPKayT/BQTiGrZ7H WIEiikzBZIh8P50cNSX3Q5VMTahXVsKjK9NtYcbNtVqZ3FwrtNvmoSVQVMCNAF/0QPCBPrEN4uK bQVHLmOFf9wsEfX1HgAQiNUjB8O8tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.932600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 41A586DFA3E013FE9B3D1ED95B2A0C4D57338DD53D28C99F1B7E4BDD82A55E072002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-repmis): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a36c845479..325fec402b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2894,6 +2894,40 @@ (define-public r-selectr package is a port of the Python package @code{cssselect}.") (license license:bsd-3))) +(define-public r-repmis + (package + (name "r-repmis") + (version "0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "repmis" version)) + (sha256 + (base32 "0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5")))) + (properties `((upstream-name . "repmis"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-data-table + r-digest + r-httr + r-plyr + r-r-cache)) + (home-page "http://cran.r-project.org/package=repmis") + (synopsis "Miscellaneous tools for reproducible research") + (description + "This package is a colletion of tools to load R packages and automatically +generate BibTeX files citing them as well as load and cache plain-text and Excel +formatted data stored on GitHub, and from other sources.") + (license license:gpl3+))) + (define-public r-reprex (package (name "r-reprex") From patchwork Fri Mar 24 23:18:49 2023 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: 48646 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 6820C16FF1; Fri, 24 Mar 2023 23:21:30 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 C499A16FC9 for ; Fri, 24 Mar 2023 23:21:29 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhf-0002uc-FK; Fri, 24 Mar 2023 19:20:11 -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 1pfqhY-0002oX-Ss for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -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 1pfqhY-00025t-IB for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhX-0005np-Cz for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 03/14] gnu: Add r-hybridmtest. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997722169 (code B ref 62428); Fri, 24 Mar 2023 23:20:03 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:37 +0000 Received: from localhost ([127.0.0.1]:41660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lT-8M for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:37 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53385) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jL-JP for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:22 -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=1679699953; x=1681514354; bh=fT/IP6SUdlhubV7MYpVcfcjYz93/M00yNla37OGKLNU=; b=XeSagMK7mleN d1LNH0y9JOAEmw/5uHY63byzq9P260QqvPVDc941eicYqtRJQ+iNPo6Q8PYfkWV8 vzmu7oWxJ9g9s8BAnKTNL21Ggm2ugaht/YDN929CI8HkSmewGdl1dzVW5odyO6Jd fEQnYjD0Lch/UOfLnEvd7IgxRC1iTC4= 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 id 07E14300124 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:12 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:49 +0100 Message-ID: <20230324231900.28367-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--8.986600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIsD mFQEq0bLRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRqfMsy2bxlLv52/ 4Ak+0YK9gYGRmZe/Y+yEmqTfXa4IG25Xh6o1JmN87lKkz03w06+uLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWwCaCpZCqUcISz66hnNxSIiNGiaV/yFEEITVtlcPR/glWfxhTlCdaPQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.986600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 0B508CB8FEEAD6F11E0CD4157CEB03D8FB5138BCC90945482FFDF3DD58CCED912002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-hybridmtest): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37b649a7d6..c58613bea3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16248,6 +16248,36 @@ (define-public r-rsbml validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (license license:artistic2.0))) +(define-public r-hybridmtest + (package + (name "r-hybridmtest") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HybridMTest" version)) + (sha256 + (base32 "0mv092lq8548l306ghgvh8yka1fnyvs7w1yzfjzcchj8vlsb0qns")))) + (properties `((upstream-name . "HybridMTest"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-fdrtool + r-mass + r-survival)) + (home-page "https://bioconductor.org/packages/HybridMTest") + (synopsis "Hybrid multiple testing") + (description + "This package performs hybrid multiple testing that incorporates method +selection and assumption evaluations into the analysis using @acronym{EBP, +empirical Bayes probability} estimates obtained by Grenander density estimation. +For instance, for 3-group comparison analysis, Hybrid Multiple testing considers +EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test +of normality as weigth. Instead of just using EBPs from F-test only or using H- +test only, this methodology combines both types of EBPs through EBPs from Shapiro +Wilk test of normality. This methodology uses then the law of total EBPs.") + (license license:gpl2+))) + (define-public r-hypergraph (package (name "r-hypergraph") From patchwork Fri Mar 24 23:18:51 2023 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: 48650 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 B4B1616FEF; Fri, 24 Mar 2023 23:21:44 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 6613316FC9 for ; Fri, 24 Mar 2023 23:21:43 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhd-0002tG-4v; Fri, 24 Mar 2023 19:20:09 -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 1pfqhZ-0002ov-7T for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:05 -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 1pfqhY-0002Ah-QG for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhX-0005nw-Tu for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 05/14] gnu: Add r-org-sc-sgd-db. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997722175 (code B ref 62428); Fri, 24 Mar 2023 23:20:03 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:37 +0000 Received: from localhost ([127.0.0.1]:41662 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lX-JM for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:37 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:57329) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jQ-JT for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:22 -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=1679699954; x=1681514355; bh=nf70d9vCEAWj2gwaOpHDT+qRauHCZdNL0v1kdZRiuss=; b=A8q2tsMfky2v FMfPKFFygPAV929cjN5HBaKG8bqsP0UPWh+Ga+nX1tx6Io2RluaawXcrPK1HcNkp kVBvWNDW5J6BOr0dtH4d4GDvzF/GNHUQZYJbMRPeVPtSNYwgMg5dSbWTCx9PKDEv S/l0/RMokmb4ulvYmSyDeioCttwylNo= 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 id 8C36830018D for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:14 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:51 +0100 Message-ID: <20230324231900.28367-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--1.158400-5.000000 X-TMASE-MatchedRID: toN6SH028bX/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkELI5 /dPWFNfzRRa406V/YwyBUGewL2YXt8i5BCxh8k4DwLYk+NSxc5r4qCLIu0mtIPPlAor2K6GjmA0 yITMNzjl9LQinZ4QefCP/VFuTOXUTae6hIZpj4Mv3FLeZXNZS4CiM3WUt6LtFxZNFioJyRwIak6 XSr0vmNytcJiiFSX+h7LR8o9gyKs+36Q0ry+c9FZM8+496nWoci9fDe9jp4aCujf9ZG3IYiuGQ4 V+vGKrnWSgmpbFZnEI1kD2KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.158400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: DC62EA9B71D0FA5384704EB5C0AC4B81EB5778F2C9F776152DFF95878E01FDF42002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-org-sc-sgd-db): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3ae0dba919..21aa3476c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -116,6 +116,27 @@ (define-public r-org-bt-eg-db based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-org-sc-sgd-db + (package + (name "r-org-sc-sgd-db") + (version "3.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "org.Sc.sgd.db" version + 'annotation)) + (sha256 + (base32 "03b8m4p865kzhjj8zyhmc0ic0n4jyjdl4h8a8xny10b7xs6l0v9f")))) + (properties `((upstream-name . "org.Sc.sgd.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi)) + (home-page "https://bioconductor.org/packages/org.Sc.sgd.db") + (synopsis "Genome wide annotation for Yeast") + (description + "Genome wide annotation for Yeast, primarily based on mapping using ORF +identifiers from @acronym{SGD, Saccharomyces Genome Database}.") + (license license:artistic2.0))) + (define-public r-pd-mapping50k-xba240 (package (name "r-pd-mapping50k-xba240") From patchwork Fri Mar 24 23:18:52 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 48640 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 8AC6A16FEF; Fri, 24 Mar 2023 23:20:41 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 55FF116FC9 for ; Fri, 24 Mar 2023 23:20:41 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhi-0002v8-Vh; Fri, 24 Mar 2023 19:20:16 -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 1pfqha-0002qx-WD for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -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 1pfqha-0002CO-J4 for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhZ-0005oL-KY for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 06/14] gnu: Add r-apcomplex. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997922200 (code B ref 62428); Fri, 24 Mar 2023 23:20:05 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41668 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh8-0005ls-Ka for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44263) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgw-0005jj-Su for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:27 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699956; x=1681514357; bh=XxHUkNOZ4eokr5w3C7Vdx8hfZOifJOEAJSD8zOYbdY4=; b=Kjwwgl6rJoSJ UBaTu+HOOxVt1thB1WA2GlD/ac4r+Ep1h0pjxV5YuMtUX8MASR/vNaDWyTLGYvnF qjN054n3QtqmLyRxum2dyvIfnayNRUlrbD/PQSJmo8M+Fb9UHbcob1Z+NMX6GAe1 bMSWOJtrI0jJ8LXdq1SvztXfNAvMCKs= 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 id 6DF6A300199 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:16 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:52 +0100 Message-ID: <20230324231900.28367-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.320200-5.000000 X-TMASE-MatchedRID: toN6SH028bX/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6r7wPook7ivAXjfR3d0weRiVIhha/jkqK4s8 u+Zeh+al9LQinZ4QefGWCfbzydb0gae6hIZpj4Mv3FLeZXNZS4CiM3WUt6LtFrGDsRPeZEf+z+L gjubLYqBp3yx0YBAue/PiFAYGEEmRLzJcrSYqXy0sOVnOKQgxW6kow3BV0MJ7KWOak9EyEngHT4 s6XK+DNWSgmpbFZnEI1kD2KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.320200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 4C919D57CAD93EC0132E302B2BF625ECC1B70BD3A84178D48B98F3C3E494410F2002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-apcomplex): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21aa3476c0..71d65d64a5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9420,6 +9420,31 @@ (define-public r-apalyzer expression analysis using RNA-seq data.") (license license:lgpl3))) +(define-public r-apcomplex + (package + (name "r-apcomplex") + (version "2.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "apComplex" version)) + (sha256 + (base32 "0ycchrdhx7zh62f0p0gxm7g58m2w3c2lfkaasrwydspd3jx0rsna")))) + (properties `((upstream-name . "apComplex"))) + (build-system r-build-system) + (propagated-inputs + (list r-graph + r-org-sc-sgd-db + r-rbgl + r-rgraphviz)) + (home-page "https://bioconductor.org/packages/apComplex") + (synopsis "Estimate protein complex membership using AP-MS protein data") + (description + "This package provides functions to estimate a bipartite graph of protein +complex membership using @acronym{AP-MS, affinity purification–mass spectrometry} +data.") + (license license:lgpl2.0+))) + (define-public r-apeglm (package (name "r-apeglm") From patchwork Fri Mar 24 23:18:53 2023 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: 48645 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 AEB9316FF1; Fri, 24 Mar 2023 23:21:26 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 2579716FC9 for ; Fri, 24 Mar 2023 23:21:26 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhk-0002wA-Hi; Fri, 24 Mar 2023 19:20:16 -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 1pfqha-0002pQ-Vn for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -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 1pfqhZ-0002CI-V8 for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhZ-0005oD-5X for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 07/14] gnu: Add r-mdqc. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997822191 (code B ref 62428); Fri, 24 Mar 2023 23:20:05 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:38 +0000 Received: from localhost ([127.0.0.1]:41666 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh8-0005lk-7D for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44857) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgw-0005jl-TM for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:27 -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=1679699956; x=1681514357; bh=VSG4+KkSq6jiD0FEsbOvnZPaqRBFudG4XyhRcYjkyvk=; b=Ni8S4KitIbQ8 YpvqCyc5/vWrPacyiZ9U/umuxBDmgKiaiAGTtAvXVpKIQMZjmIRAqdoqkq39d5zu jKMo8klahKNC2qBlAZIyzjvdXSTufXlQmjIY9WkSvOxNW4Nwk/40r9wBOcrPiV7M Tllev5tORkixE+WVjlxzYYP71PNwHM4= 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 id D795430019D for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:16 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:53 +0100 Message-ID: <20230324231900.28367-7-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--0.722000-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0YXjfR3d0weRny/Hx1AgJrrI1v /+HUjidRh0YasV59YfxJTjjs9yT6Yo8WMkQWv6iV3LAytsQR4e42j49Ftap9Eymsk/wUE4hqOvG 6VW4FmOZpK2j+/zzAuH6HKqegP5nmZpHaT7Nk8h6AJfBeyyoLclTs224IdfsnBbgAOnvaIzWEKn YY64E5ZgyQTsnD1LuIAEIjVIwfDvLTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.722000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 9857609EAF0F6C011D707F19DD17F7CDD8795143DCC4564B051C7557ED3D1A192002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-mdqc): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 71d65d64a5..39367dd927 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6968,6 +6968,31 @@ (define-public r-maser and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-mdqc + (package + (name "r-mdqc") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mdqc" version)) + (sha256 + (base32 "1hn6m0z8q3jnzb0h8m29khgm0cx81cfs3s1j6hlg4wsrwkha1i3w")))) + (properties `((upstream-name . "mdqc"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-mass)) + (home-page "https://bioconductor.org/packages/mdqc") + (synopsis "Mahalanobis distance quality control for microarrays") + (description + "MDQC is a multivariate quality assessment method for microarrays based on +quality control (QC) reports. The Mahalanobis distance of an array's quality +attributes is used to measure the similarity of the quality of that array +against the quality of the other arrays. Then, arrays with unusually high +distances can be flagged as potentially low-quality.") + (license license:lgpl2.0+))) + (define-public r-metagenomeseq (package (name "r-metagenomeseq") From patchwork Fri Mar 24 23:18:54 2023 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: 48643 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 E79BD16FF1; Fri, 24 Mar 2023 23:21:21 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 5A61F16FC9 for ; Fri, 24 Mar 2023 23:21:21 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhf-0002ub-FO; Fri, 24 Mar 2023 19:20:11 -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 1pfqhb-0002s2-7y for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -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 1pfqha-0002CV-SL for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqha-0005oS-23 for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 08/14] gnu: Add r-parody. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997922207 (code B ref 62428); Fri, 24 Mar 2023 23:20:06 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41670 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005m1-0m for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:39 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45073) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jp-1T for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -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=1679699957; x=1681514358; bh=vllmIsZOEjk4QYNe9jsKDtc9mCmm2R8kT78Wa8FpiVg=; b=Zl2xG9U1y0E9 yK+NYhC3DRCUdw9z6DZ0M294uP0UjBW+V+iIo4IroOniAMC2ZzSi3g9l6f9wXPKD Ac7o7ao1gyAN6wwoBVb6up5OJdrnxo1jOI5ya5Tve7FJav/PffATT7QKmCOYpSeg C4/BnIaxlxX+hsJmtL+ZGxmiXrb63xA= 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 id 4A9503001A3 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:17 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:54 +0100 Message-ID: <20230324231900.28367-8-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--3.943400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZCWxD2S0xfx/OFG 8uiwVdY/F+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2KlfnlVv2XS+do85bE pzx6+0ruAFgmtvJJSFb83j9qM4FC18Tx4THFVLcE4sekoUOvVCECnJm2Z3T2S6sCZ0pbyKJJyxD 2EOkNO1b+P+STSeAJkoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.943400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 89469A79AD44A1C060B15D3027AAC540EDBC30629CF47D50C211061AFF5A3B7E2002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-parody): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39367dd927..9f43c42bee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18999,6 +18999,27 @@ (define-public r-spp other functional sequencing data.") (license license:gpl2))) +(define-public r-parody + (package + (name "r-parody") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "parody" version)) + (sha256 + (base32 "12i5g4ai7a0p81kvqvz1qw099cy3g71n69pij8w760r3jn0c9ilw")))) + (properties `((upstream-name . "parody"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/parody") + (synopsis "Parametric and resistant outlier dytection") + (description + "The parody package provides routines for univariate and multivariate outlier +detection with a focus on parametric methods, but support for some methods based +on resistant statistics.") + (license license:artistic2.0))) + (define-public r-pathview (package (name "r-pathview") From patchwork Fri Mar 24 23:18:55 2023 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: 48644 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 CBDD316FF1; Fri, 24 Mar 2023 23:21:22 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 3B17116FC9 for ; Fri, 24 Mar 2023 23:21:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhl-0002wf-0k; Fri, 24 Mar 2023 19:20:17 -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 1pfqhd-0002u0-BH for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:09 -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 1pfqhc-0002DA-Ex for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhb-0005oq-Fl for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 09/14] gnu: Add r-arraymvout. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969998022229 (code B ref 62428); Fri, 24 Mar 2023 23:20:07 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41676 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mN-1u for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:43281) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jq-2Z for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -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=1679699957; x=1681514358; bh=6QcW3L17Rq4Y/u9pytApGq78a8H0WcCnye/qLVMz2TU=; b=myrlqTPnBtIh TFQ92KyGAnjtoxncFzwIlxQg/AcQ199sT8XvYHJhLIdl+sEY0mqJXHWzsS2/2Yta uV/xnvC9m8CA+zZBR1wxJqOj0QM2Lh1sijx02L3CG6NNt5HqbC35pjBIJNwC1u78 Ymq9H2kYCpvRrpWYG+YMnRQvBnaen94= 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 id A8F4B3001AD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:17 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:55 +0100 Message-ID: <20230324231900.28367-9-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--0.774700-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYnvkzitR82DjQYcH09cOokpqhcdnP91eXFxXefgn/TNQ8IubEPSkNnJR3V 9V6dMWSWKbindmE5bmEwECQaT0DBZIrDBDJBPVs6uG6vp8tkx53iZgkcDEaRzk5Oq0M3nL1DEvo wQGF7Hg4jQSOd69r3fmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5dahHHRNtA1e4Hhm lAwuGnTE41Ztc+fFvlZl6qaUBLo2cbJFAtk5vWZY17A/rrTegklfnzEqph9AAnEDrBhOrVryndM Ht5d/doNQSQFNny84vGXJMJdBHjGKgDk8Dh1C7G5iklHaSF5d37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.774700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 5C5409C88FEAE7475460F4219536FB1D5CA4863C88AD81CCC40751FD0D8036F42002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-arraymvout): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f43c42bee..62cd786842 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3215,6 +3215,42 @@ (define-public r-arrayexpress structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (license license:artistic2.0))) +(define-public r-arraymvout + (package + (name "r-arraymvout") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayMvout" version)) + (sha256 + (base32 "0g66s64n4qlvhkanp33bbvpi93rsdx5xq0mjr96d0195qbf6k156")))) + (properties `((upstream-name . "arrayMvout"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-affy + r-affycontam + r-biobase + r-lumi + r-mdqc + r-parody)) + (home-page "https://bioconductor.org/packages/arrayMvout") + (synopsis "Multivariate outlier detection for expression array QA") + (description + "This package supports the application of diverse quality metrics to AffyBatch +instances, summarizing these metrics via PCA, and then performing parametric +outlier detection on the PCs to identify aberrant arrays with a fixed Type I +error rate.") + (license license:artistic2.0))) + (define-public r-asafe (package (name "r-asafe") From patchwork Fri Mar 24 23:18:56 2023 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: 48649 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 D98B216FEF; Fri, 24 Mar 2023 23:21:36 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 BB00716FF1 for ; Fri, 24 Mar 2023 23:21:35 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhk-0002ve-6w; Fri, 24 Mar 2023 19:20:16 -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 1pfqhb-0002sJ-GE for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -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 1pfqhb-0002Cz-76 for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhb-0005oj-39 for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 10/14] gnu: Add r-arrayquality. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969998022222 (code B ref 62428); Fri, 24 Mar 2023 23:20:07 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41674 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005mG-Nq for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49865) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jx-Eo for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -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=1679699958; x=1681514359; bh=DWT3Cm/IROuXeaWMgtLwCbWTO96BayEuv2ZdTbIRG9k=; b=iUOyllIfAr8s 1d35KMOVlCgrlJ+UKf3/hL3XiyjAz8pTrJeez5vvX1qQ6BN/MVaDXF8JMiBXcWXu iLUF0OX2cekhGQ+keMI5UKdiLqmBcTVdEOsyqqBSIqkUWDOrG7Gz57tiKljHj5L3 2mWMLfWAT8uRDxxwyeTjS3xiWqZWrw8= 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 id 1202C3001B5 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:18 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:56 +0100 Message-ID: <20230324231900.28367-10-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--4.783700-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeM3ZbGC9oP/O7Wc X/fVk9aGRRa406V/YwyBUGewL2YXt8Z8zsjIitoJ71Wx2uUbPLclSmDuA9gjEVVMJlS9HCuzGg6 YSQd92h57MSP7SLpuGM+e/4CnFGik8f+64gLLEwLdCok3ibXlQeuLFZZYlisfHxPMjOKY7A9wK7 mZ44aKbi8z+bJ2nm9UKrauXd3MZDUal568aygjl6tO5InZNwbJJOSKosHSuiqJkErMcswT/X3GH u67ZOgPaUlfxqclV0qZ7Z76m2H8uz0zXC8ftXDbDxJaJjSdPyku41Tl3hgJxQ1BJAU2fLzi8Zck wl0EeMYqAOTwOHULsbmKSUdpIXl3ftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.783700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 22FF38CABA2830017324679FBF21F06C832E8F5EC7ED9518AA978C9084ECBA8A2002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-arrayquality): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 62cd786842..7a904d3d08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3251,6 +3251,31 @@ (define-public r-arraymvout error rate.") (license license:artistic2.0))) +(define-public r-arrayquality + (package + (name "r-arrayquality") + (version "1.76.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayQuality" version)) + (sha256 + (base32 "0b5q71bpl9ln26622jvchd4f9i4kwayqkm9b75yj0a69imbfcn4s")))) + (properties `((upstream-name . "arrayQuality"))) + (build-system r-build-system) + (propagated-inputs + (list r-gridbase + r-hexbin + r-limma + r-marray + r-rcolorbrewer)) + (home-page "http://arrays.ucsf.edu/") + (synopsis "Assessing array quality on spotted arrays") + (description + "This package provides functions for performing print-run and array level +quality assessment.") + (license license:lgpl2.0+))) + (define-public r-asafe (package (name "r-asafe") From patchwork Fri Mar 24 23:18:57 2023 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: 48641 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 B109716FF1; Fri, 24 Mar 2023 23:20:59 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 7DDE216FC9 for ; Fri, 24 Mar 2023 23:20:58 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhi-0002uv-BR; Fri, 24 Mar 2023 19:20:14 -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 1pfqhd-0002u1-FG for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:09 -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 1pfqhc-0002Ds-Oc for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhc-0005pD-Jz for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 11/14] gnu: Add r-setrng. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969998122252 (code B ref 62428); Fri, 24 Mar 2023 23:20:08 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:41 +0000 Received: from localhost ([127.0.0.1]:41682 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhB-0005mk-5n for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:41 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53231) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005k5-S3 for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -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=1679699959; x=1681514360; bh=bVqr6m5qcZ+cXnDU8yXpAzhBqNT3EtmHdB1s/jIDx+E=; b=D1Gvj3rhdABW FRcFqOqMCmpb5EbAgBJk0QvOAzcq3zzrBFm5XFCJuXhXvGP6eWQJP8/DiSxH0pMv gSAhwBFl5f+xwInzIE3s02QP0hceLqmPYQzefkYPNntoMdR3hG72j+oVyPEzZL+r U3iQ1rX51Ja4jtZFU/VHmodRWwKl8yc= 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 id 8C7CE3001C5 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:19 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:57 +0100 Message-ID: <20230324231900.28367-11-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.544200-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90Badv+F8ucSI031Nfxfj2zOp/958oU3WcKY5ZGw7wyeHiwO YVASrRss7RZ9SX+rqZS1h1eUc+p680N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jFnjKVTYbDMDEQd G7H66TyN+E/XGDLHcMWpoRm6v3svZWb0mb4EdHMQ3BXaA1V5BHBcpNiZN6sQLm0Ju/KvlWS9XVd ckExYCRAKR1s4zi9sJpV+rqK0DCKOBiOleQmdrd3FJHtt7t+dMVOziWO23T3g/Yr/7CTLFXOzso v7pcUHilIGXSGl4OHw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.544200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 7C79A6904B47EB2567C2FA24EAC0495D33F3A6C442B25B955939C0E2BA9C27252002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-setrng): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 325fec402b..bfcafea355 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20170,6 +20170,28 @@ (define-public r-bedr additional utilities for genomic regions processing.") (license license:gpl2))) +(define-public r-setrng + (package + (name "r-setrng") + (version "2022.4-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "setRNG" version)) + (sha256 + (base32 "09089vr5x8snwxh38kdhgpjl3jl7zrk056f6f9a2jg5lsrmnxh31")))) + (properties `((upstream-name . "setRNG"))) + (build-system r-build-system) + (home-page "http://distr.r-forge.r-project.org/") + (synopsis "Set (normal) random number generator and seed") + (description + "This package provides utilities to help set and record the setting of the +seed and the uniform and normal generators used when a random experiment is run. +The utilities can be used in other functions that do random experiments to simplify +recording and/or setting all the necessary information for reproducibility. See +the vignette and reference manual for examples.") + (license license:gpl2))) + (define-public r-sets (package (name "r-sets") From patchwork Fri Mar 24 23:18:58 2023 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: 48647 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 5ED2316FF8; Fri, 24 Mar 2023 23:21:35 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 BDF5016FEF for ; Fri, 24 Mar 2023 23:21:33 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqho-0002yb-BS; Fri, 24 Mar 2023 19:20:20 -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 1pfqhb-0002rz-6V for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -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 1pfqha-0002Cf-Jj for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqha-0005oa-Ev for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 12/14] gnu: Add r-beaddatapackr. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969997922215 (code B ref 62428); Fri, 24 Mar 2023 23:20:06 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41672 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005m8-BC for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:39 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34373) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jy-Fj for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -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=1679699958; x=1681514359; bh=1yoUsl/j9D3TJ0c0M+ccciUJ9kkLnbpVfVxmE0jGE64=; b=Hf7VSEtSk+wc csBt2zNu7SvcIcENRpf5XtWVps5FxhBZW8BOoL592YIS5M4+alMBrP29oAntiISO 1psIIjqd1u22LpbqjSRIX301C0D1wrZNt2+hCkblltLb1y6po4muckAd9BfyobXt jfekTnoUWQZLleXsJNURFru9nCsVkZM= 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 id A8A6E3001BD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:18 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:58 +0100 Message-ID: <20230324231900.28367-12-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--1.554600-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPODnR iQbMAyihJNe/yL58XWfuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHY87 NwWBxSvhBPQd6lWNwpDnWWI8LLh4D28TY4LGPyU0apIb9znReA7qGBW9J0Yqj/c/LnF3l7WqYDT IhMw3OOX0tCKdnhB58I/9UW5M5dRNp7qEhmmPgy/cUt5lc1lLgKIzdZS3ou0UrnHTI07mmi3JGW UoimBufc5o+WNeCB1ubGxGgnOsaIpEy59Ba2lVvNGQKI8Iqn28nHNBsPal2ED8X7/6KqlDFDQ51 p2D4IpRZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.554600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: B0AC5ED89D21E244F08D1D2561DD108F65967CD92B4BF077FAD0F81939C5C47B2002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-beaddatapackr): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7a904d3d08..e7ab9c983c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17963,6 +17963,26 @@ (define-public r-beadarraysnp performs copy number calculations and reports.") (license license:gpl2))) +(define-public r-beaddatapackr + (package + (name "r-beaddatapackr") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BeadDataPackR" version)) + (sha256 + (base32 "0309cvc9aq4nb06zysb7jvzd844pvw6jbjiqwhar6fg01cx255j0")))) + (properties `((upstream-name . "BeadDataPackR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BeadDataPackR") + (synopsis "Compression of Illumina BeadArray data") + (description + "This package provides functionality for the compression and decompression +of raw bead-level data from the Illumina BeadArray platform.") + (license license:gpl2))) + ;; This package includes files that have been taken from kentutils. Some ;; parts of kentutils are not released under a free license, but this package ;; only uses files that are also found in the free parts of kentutils. From patchwork Fri Mar 24 23:18:59 2023 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: 48653 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 86E5D16FF1; Fri, 24 Mar 2023 23:21:53 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 0935A16FC9 for ; Fri, 24 Mar 2023 23:21:53 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqho-0002zB-Rt; Fri, 24 Mar 2023 19:20:20 -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 1pfqhc-0002sa-BS for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:08 -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 1pfqhb-0002DL-VS for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhb-0005oy-RT for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 13/14] gnu: Add r-beadarray. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969998022237 (code B ref 62428); Fri, 24 Mar 2023 23:20:07 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41678 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mU-Dd for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:55909) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005k4-Rc for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -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=1679699959; x=1681514360; bh=uwmw+G5iWXE4KdKFMj79uywLHjdincbMT4gg1qislE8=; b=G9LEepANSeCR Ypr4tW6grGWnd/6T87oW7tMR0lm9E2dyNxmgZfX9NTaI3ci+QdRYxZqGxbqmTplq emP9yxjyx7FGBS4DKUaViNkxTu840qv8BHxrQcj2JlYHEV8qPaz6MsmpN8de1Epg uMCScmvD2DIAFklxs02aXxBXn7jnq7U= 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 id 1FAD13001C1 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:19 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:18:59 +0100 Message-ID: <20230324231900.28367-13-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.238000-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0ahHrZE2+S866Y5ZGw7wyeHEpM Y0o/BrKdyQB4UAGIVrzgELkIsyIqM0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV+i5u /VvsFaHR8XkxC85xWeJY6AKHAFL88yiOD9xnnZjT5/EAmAmUoaXxkIOPs/mxH9WYIiq13f/x88F JLWCwbOvNj0INejLTzinpP+yXTbVShCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.238000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: D5FBD11E844786B796B39C8CEC7464734CA73E13D4FF979A987272DDC2AE17742002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-beadarray): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7ab9c983c..6c114efd21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17943,6 +17943,40 @@ (define-public r-beachmat matrices.") (license license:gpl3))) +(define-public r-beadarray + (package + (name "r-beadarray") + (version "2.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beadarray" version)) + (sha256 + (base32 "0fr24gj6h2rr1r4l3n8myjaihjqi5yinwdsxqa5ih8m3v72dlrby")))) + (properties `((upstream-name . "beadarray"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-beaddatapackr + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-hexbin + r-illuminaio + r-iranges + r-limma + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/beadarray") + (synopsis + "Quality assessment and low-level analysis for Illumina BeadArray data") + (description + "The package is able to read bead-level data (raw TIFFs and text files) +output by BeadScan as well as bead-summary data from BeadStudio. Methods for +quality assessment and low-level analysis are provided.") + (license license:expat))) + (define-public r-beadarraysnp (package (name "r-beadarraysnp") From patchwork Fri Mar 24 23:19:00 2023 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: 48652 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 CA5DF16FF1; Fri, 24 Mar 2023 23:21:49 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=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 E413116FC9 for ; Fri, 24 Mar 2023 23:21:48 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pfqhk-0002vu-Bf; Fri, 24 Mar 2023 19:20:16 -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 1pfqhc-0002tI-SI for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:09 -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 1pfqhc-0002Di-Bs for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pfqhc-0005p5-7g for guix-patches@gnu.org; Fri, 24 Mar 2023 19:20:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62428] [PATCH 14/14] gnu: Add r-arrayqualitymetrics. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 24 Mar 2023 23:20:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62428 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <62428@debbugs.gnu.org> Received: via spool by 62428-submit@debbugs.gnu.org id=B62428.167969998122246 (code B ref 62428); Fri, 24 Mar 2023 23:20:08 +0000 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:41 +0000 Received: from localhost ([127.0.0.1]:41680 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mc-Pf for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:41 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44897) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgz-0005kP-2q for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -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=1679699960; x=1681514361; bh=hw63NtPPgj/cEoqZIlmcR95LDRQlFpJgL8NaL5NGHRE=; b=CsFiaK4V6J5B 1oTgNuCJQgf8PPyAfUdqANnluk2lubvHkjbEOFbU7qHP0TwbmUmdxtVSw6XhBNvZ RoezklMDT7YS/O00y0oM9fgTK+kNzI3+rCpiurinfw5os1gob1Jcz8Uv+LGBMdNJ HgnTka/quiQeQ3kQ2+IEcytYrXpSTPg= 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 id 1F0CC3001CD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:20 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 00:19:00 +0100 Message-ID: <20230324231900.28367-14-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.105400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0YXjfR3d0weRhh1mpCXNVC8qbd h+ZHR69rF+KCpGE37CJsoi2XrUn/J8m+hzBStansfRoCwBzgRYsK21zBg2KlfCQvlWYtoEBHLqa IYEBIRhIU3Gs62OX1uQndELcZsq4lJ7Z0rexjc6sOFCT51VwnScK6BPLcMIqcshzQkxO+/gdD1q km1QqYayBr8AT+uPPcoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.105400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 08CC6DD37CC7598EFEF6A3ECF6F2323DB216039CE3511D85806A3ED7182D40602002: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-arrayqualitymetrics): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6c114efd21..8792c94d29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3190,6 +3190,44 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayqualitymetrics + (package + (name "r-arrayqualitymetrics") + (version "3.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayQualityMetrics" version)) + (sha256 + (base32 "0jz9b3f8x1aal4sskq1a09jpavhm8alggwbj3ka42fb89xymrz33")))) + (properties `((upstream-name . "arrayQualityMetrics"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-affyplm + r-beadarray + r-biobase + r-genefilter + r-gridsvg + r-hmisc + r-hwriter + r-lattice + r-latticeextra + r-limma + r-rcolorbrewer + r-setrng + r-svglite + r-vsn + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/arrayQualityMetrics") + (synopsis "Quality metrics report for microarray data sets") + (description + "This package generates microarray quality metrics reports for data in +Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). +One and two color array platforms are supported.") + (license license:lgpl2.0+))) + (define-public r-arrayexpress (package (name "r-arrayexpress")