From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id aBq4GqM6VGJrKQEAgWs5BA (envelope-from ) for ; Mon, 11 Apr 2022 16:26:43 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id 2DxgF6M6VGKjFgAAauVa8A (envelope-from ) for ; Mon, 11 Apr 2022 16:26:43 +0200 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 050ED3F635 for ; Mon, 11 Apr 2022 16:26:43 +0200 (CEST) Received: from localhost ([::1]:50608 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ndv06-0007zo-6v for larch@yhetil.org; Mon, 11 Apr 2022 10:26:42 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58780) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ndupn-0004Js-Ja for guix-patches@gnu.org; Mon, 11 Apr 2022 10:16:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51005) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ndupn-0000xC-9s for guix-patches@gnu.org; Mon, 11 Apr 2022 10:16:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ndupn-0008WN-5v for guix-patches@gnu.org; Mon, 11 Apr 2022 10:16:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54856] [PATCH] gnu: Add r-xcir. 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: Mon, 11 Apr 2022 14:16:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54856 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54856@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.164968651132664 (code B ref -1); Mon, 11 Apr 2022 14:16:02 +0000 Received: (at submit) by debbugs.gnu.org; 11 Apr 2022 14:15:11 +0000 Received: from localhost ([127.0.0.1]:44897 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nduox-0008Uh-8r for submit@debbugs.gnu.org; Mon, 11 Apr 2022 10:15:11 -0400 Received: from lists.gnu.org ([209.51.188.17]:35454) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nduou-0008UU-0U for submit@debbugs.gnu.org; Mon, 11 Apr 2022 10:15:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58078) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nduos-0002Is-PU for guix-patches@gnu.org; Mon, 11 Apr 2022 10:15:07 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49269) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ndue2-00076o-If for guix-patches@gnu.org; Mon, 11 Apr 2022 10:03:56 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 3B400300128 for ; Mon, 11 Apr 2022 16:03:50 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1649685829; x=1651500230; bh=p1iEEfzE1P/cCcAnHGJAu/7fJww4E6QxLnog1tur6wA=; b=hwdHmFGhwhn2 Ap8ucPXvyOE9vj/47SCDdgLHYyHmke1ia2d1+Adb6ffhuONS5Uyd/rZqMSmA9eEw v9xxi7COPp+CRPachJjI3tlGiVGuyH/AnL9KXBhZA/OOeel7v9T92JNX8mrvSBCZ d/oFvJlgTISTpZzfJbhH1lCLMRlXKIM= 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 j86t1wCG7c1c for ; Mon, 11 Apr 2022 16:03:49 +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 for ; Mon, 11 Apr 2022 16:03:49 +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 15.1.2375.24; Mon, 11 Apr 2022 16:03:48 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 11 Apr 2022 16:03:35 +0200 Message-ID: <20220411140335.16135-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26828.000 X-TM-AS-Result: No-10--3.018200-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOORg EMvCxuZnV5rd0mltHqQue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedJEb gebEoSmV7MSP7SLpuGBHNILZy7DXD5SB5uUeEexrdCok3ibXlQQseQVcTRnF2lwV2iaAfSWeDGx /OQ1GV8t0H8LFZNFG7doMssNsUwYV+5/TKfK5lL9IT+ne0rFYJhiEmX0SoKHhjl6JgA+lTKKR8k HWqAahfloLl4biwhap6ShW7FS0t0r4DwNwEhmu/fN8LTdB5+CDHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.018200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26828.000 X-TM-SNTS-SMTP: A06D7F2ED7AA33632C9DAFD8ED346C21827DFD1E7EDFAA766F7CAC7986908ED12000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-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 X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1649687203; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=Xk9unpsLWmkM4jsQrrp9gmMKdXfS+Iy6sjTXplssRgQ=; b=MbezrlzHL+BPAkorpj0gHIYYwZKpVDJFG/n+gpHIOD7nrF/d4sVMFqngzWFyx6F4x027KQ SLBSXQXhdOANCjwF+A1Au97AsFOI1okH5QiKQpx8Y+AkoAgNu58svo4nyosvjUKtqtUQh8 0v/e6e4cTOLAUD4uTz4sXPfFNKgloh61uaeD0ol3DpjrLTgst7Q8YQpzoz8Z/M2QQJP0IJ NqGrHE7/upXWj4dMmm5lOW7q5p0+SEp9qB4nomQWzVsH3u7XuDcnabrvXA8AqtePCTkcRB rPrGeKJRsSNyD2gnbV2yVFy088/HNR6+ZA0KkNos0gNa/hertx8GvIhv/EES6A== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1649687203; a=rsa-sha256; cv=none; b=UmaiiwY/4Vv/0+kLmG3dDagDTIkndQi+H74z6aPZChR1NwOPvWAjL6GCla9hzo/tB6H4EH uKOHdPEco5efVpmvsk7PXnBs020CAMawYTwYcvsVPW/tKF+RC1FhnPs/eLQ+ZTSZywIdeA f0Pk8Uw+zOKI8v0IqU6tkZJuf2lAA+JETRwra90HKnEdE+piezV3vrtrYzUkkB/ezQWdmq 7qFPyaj4nzyjuXjNQl8VXKkkkN2Fw4z5vVOeRTPaMOvPIU+lRfI/8rtw7ho3oWzjSzoo7+ qlSE6bJt7vW88KxaPogOe7PaJY5v1c3zUDPqdwXrKiqu+7SG4CpO1T9Hf/tCNg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=hwdHmFGh; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 4.93 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=hwdHmFGh; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 050ED3F635 X-Spam-Score: 4.93 X-Migadu-Scanner: scn0.migadu.com X-TUID: 8vcGmbErIWhy * gnu/packages/bioconductor.scm (r-xcir): New variable. --- gnu/packages/bioconductor.scm | 37 ++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ce1e23f0bf..d78fcdce32 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier ;;; Copyright © 2020 Peter Lo -;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu +;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes @@ -5100,6 +5100,41 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) +;; This package doesn't have a release yet. +(define-public r-xcir + (let ((commit "4e51efe9980056e7fe274224da0173fcfaf2edd7") (revision "1")) + (package + (name "r-xcir") + (version (git-version "1.7.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SRenan/XCIR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pb2fnpwlimw2p43ygy56pwj90h1l7yz2npqm3ypzp3bgld9b8n5")))) + (properties `((upstream-name . "XCIR"))) + (build-system r-build-system) + (propagated-inputs (list r-biomart + r-biostrings + r-data-table + r-ggplot2 + r-iranges + r-readxl + r-s4vectors + r-seqminer + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SRenan/XCIR") + (synopsis "Analysis of X chromosome inactivation") + (description + "This package @code{XCIR} is a R package that offers models and tools +for subject level analysis of X chromosome inactivation (XCI) and XCI-escape +inference.") + (license license:gpl2)))) + (define-public r-xina (package (name "r-xina") -- 2.34.0