From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id aGyAKCFrfWEjQwEAgWs5BA (envelope-from ) for ; Sat, 30 Oct 2021 17:56:17 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id 2HAzJCFrfWFiYwAAB5/wlQ (envelope-from ) for ; Sat, 30 Oct 2021 15:56:17 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 6DD401C085 for ; Sat, 30 Oct 2021 17:56:17 +0200 (CEST) Received: from localhost ([::1]:54574 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mgqiO-0001Pl-IF for larch@yhetil.org; Sat, 30 Oct 2021 11:56:16 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:45358) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001N1-TR for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:46699) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mgqiA-0001Jm-IZ for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mgqiA-00086h-Ib for guix-patches@gnu.org; Sat, 30 Oct 2021 11:56:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51513] [PATCH 3/3] gnu: Add r-xina. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 30 Oct 2021 15:56:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 51513 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <51513@debbugs.gnu.org> Cc: rekado@elephly.net, =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 51513-submit@debbugs.gnu.org id=B51513.163560935031127 (code B ref 51513); Sat, 30 Oct 2021 15:56:02 +0000 Received: (at 51513) by debbugs.gnu.org; 30 Oct 2021 15:55:50 +0000 Received: from localhost ([127.0.0.1]:58243 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhx-00085y-KP for submit@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:49 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:55881) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgqhv-00085T-BE for 51513@debbugs.gnu.org; Sat, 30 Oct 2021 11:55:47 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9DAE53000FE; Sat, 30 Oct 2021 17:55:41 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1635609341; x=1637423742; bh=kRKHD/RFu2vioRhUFWKdfOVlpKlo5W59t1V TGnrTtHQ=; b=nwWVr5gfD1r3KQmMZTR9gzN+iMwWuyi1rRbtN07a1Er7cWam1Rz NC+kh+Cr79eVlBQea8wkZOEpevIetDUEBiI008rtt8IUul++q/GjyrKL7oZ4bdfu DXvQgKGAs/65XGeG8ZBiRKGLB1+2hLy88D0A0ZY4XDcFnZM1jSlk+V8k= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 4s598y_FdpzC; Sat, 30 Oct 2021 17:55:41 +0200 (CEST) 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; Sat, 30 Oct 2021 17:55:41 +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 15.1.2308.15; Sat, 30 Oct 2021 17:55:40 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Sat, 30 Oct 2021 17:55:06 +0200 Message-ID: <20211030155506.28269-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 In-Reply-To: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> References: <20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-AS-Result: No-10--2.051700-8.000000 X-TMASE-MatchedRID: 0a+qS+HYqZUsaaYlMvaOHAPZZctd3P4BC//1TMV5chPIFck3f6fvyNN0 iv48FC5C7IvvzMgzLKZM7FV2jxGQluvd6Sh4AjN/nVTWWiNp+v/iTXBy70TaRHOaOgNxEZiuV3U Ws/brCBOp4L5MAnrh2A5Q7W8dBYFUjoR5DwlwBUdX7UpJhGB2Ym3wyFHQiRIJfcujmki2WQLFgy mj9DufconFJ5/U720jPKzpbpsDIY7/dJCaqb+IPN0KiTeJteVB64sVlliWKx8fE8yM4pjsDwtuK BGekqUpOlxBO2IcOBZw6NzqqA359tjB/Q6kjIicYHk8PLD2vOqdxsJWP1Y5ii0eWCYV6MytEC5J Je9+pPXFTmyhZfwo6Hn78542H/LROxqMmHhhomO3ShAi6P5JV4URV9DGzc3pkOCa3xB6S8HmZoJ 42/8sjNUZB2rCwOIS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.051700-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.001 X-TM-SNTS-SMTP: 6137070EA08315EDD2961CF1C2A998FD2D284246411F0CDAC0A98BCC6052A54C2000: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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1635609377; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=9qIW8FZWs8I300lNQIZP/1jlSZxyuQx8QnTdbIjLbfM=; b=khwvkMCVOurEcHJQXgi29ZRWCnT9FZe2UrYtp7kFR4c2c5kzVVxnfIyBx06RxGAysm761s 2AfvvPRdt3DBugNwILyRqzkUL9r7LiLVNmcQ/x25+HattsJIfuzAbWOis7psOIThORW5P8 MyT2HuzpIpNOyJCDr5TRDLgW4ueixwh77bHVjnaP7fpKRwKhLob7ImMehl3nWxlTzoHJ/4 6EZWecS6c/fQqKGfFkm80hfK9A3YKWu16GeQiuqnu0sxwMgV6RcpC6YpfHLhzPAbO5Rfe+ OHvQEADBEIlhKwDH8J9VbcCCyJWtnS2oeT84lxhgn6k/dPsCpRCkuhXuIpUe4g== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1635609377; a=rsa-sha256; cv=none; b=pPXtf9m7CS0Z10vjuo/ElIPAp7csgmkvMpATBO+k5I3ZUUn3j5jBVoVHlzhwbrymkdZvhA BYoolfjSlPIQwjUcDNdXKeZG8Wt2mfaP8hvqXK8gpIw1370jK/j0CmG7pWAue8zwFdAjoD N4QCu00BKzDQyNiO5/HZJMjH7uGNUV6dk9imLHfsh83mhhNm30FhXpwf2UxeXatSB3/pi0 kJk8xXMbU3AYgQ0C5aoQ/5N5TNg+PAFpwnUWsWbcKUa9oO1y/zM7y40LU1GWfEx4LT02/W kwiPiFI8Sdkcbc/FWS4O2ln+++pRDmQNT9btp+NtWB63TJcWHSSFmRMxruIIgQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=nwWVr5gf; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.18 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=nwWVr5gf; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 6DD401C085 X-Spam-Score: 2.18 X-Migadu-Scanner: scn0.migadu.com X-TUID: uuYAUeqG6Jfx * gnu/packages/bioconductor.scm (r-xina): 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 f82427f831..a232c3fe61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4660,6 +4660,42 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xina + (package + (name "r-xina") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XINA" version)) + (sha256 + (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (properties `((upstream-name . "XINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alluvial" ,r-alluvial) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-mclust" ,r-mclust) + ("r-plyr" ,r-plyr) + ("r-stringdb" ,r-stringdb))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://git.bioconductor.org/packages/XINA") + (synopsis "Identifying proteins that exhibit similar patterns") + (description + "The aim of @code{XINA} is to determine which proteins exhibit similar +patterns within and across experimental conditions, since proteins with +co-abundance patterns may have common molecular functions. @code{XINA} imports +multiple datasets, tags dataset in silico, and combines the data for subsequent +subgrouping into multiple clusters. The result is a single output depicting +the variation across all conditions. @code{XINA}, not only extracts +coabundance profiles within and across experiments, but also incorporates +protein-protein interaction databases and integrative resources such as +@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and +molecular functions, respectively, and produces intuitive graphical outputs.") + (license license:gpl3))) + (define-public r-xvector (package (name "r-xvector") -- 2.33.0