From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id sEk1CDn/kGLVCAAAbAwnHQ (envelope-from ) for ; Fri, 27 May 2022 18:41:29 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id UDwlCDn/kGJrEwEA9RJhRA (envelope-from ) for ; Fri, 27 May 2022 18:41:29 +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 1A168ACB4 for ; Fri, 27 May 2022 18:41:28 +0200 (CEST) Received: from localhost ([::1]:58216 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nud1i-0002yl-SM for larch@yhetil.org; Fri, 27 May 2022 12:41:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51344) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nud1K-0002xZ-9m for guix-patches@gnu.org; Fri, 27 May 2022 12:41:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41792) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nud1K-0004OZ-05 for guix-patches@gnu.org; Fri, 27 May 2022 12:41:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nud1J-0001s5-SP for guix-patches@gnu.org; Fri, 27 May 2022 12:41:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55679] [PATCH 2/2] gnu: Add r-scmap. 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: Fri, 27 May 2022 16:41:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55679 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <55679@debbugs.gnu.org> Received: via spool by 55679-submit@debbugs.gnu.org id=B55679.16536696467148 (code B ref 55679); Fri, 27 May 2022 16:41:01 +0000 Received: (at 55679) by debbugs.gnu.org; 27 May 2022 16:40:46 +0000 Received: from localhost ([127.0.0.1]:35687 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nud14-0001rE-CW for submit@debbugs.gnu.org; Fri, 27 May 2022 12:40:46 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:38997) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nud10-0001qr-U1 for 55679@debbugs.gnu.org; Fri, 27 May 2022 12:40:44 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 66DB6300225 for <55679@debbugs.gnu.org>; Fri, 27 May 2022 18:40:36 +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= 1653669635; x=1655484036; bh=pVyff+ZSIGyMf3joE9p+9LB71i+e25qk05y rTpb6neI=; b=eB6eNOImoKihnRuNWBxytxRYpPNBlBmXCQr8PGI+/z8mGpfpV3S L0mcxcoDCyYFNND71QyJkSSzzNMjQxhcOrv7dsCyDnqdyfyYY0ktQlCGrJLpf5A/ MhKn5JIvit855GARqLMF6UGUxDONqdYlaJAhUd2FNw2kumlCi0yHMyRc= 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 Y2DFHIbYHS_E for <55679@debbugs.gnu.org>; Fri, 27 May 2022 18:40:35 +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 <55679@debbugs.gnu.org>; Fri, 27 May 2022 18:40:35 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Fri, 27 May 2022 18:40:34 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 27 May 2022 18:40:13 +0200 Message-ID: <20220527164013.4195-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.0 In-Reply-To: <20220527164013.4195-1-madalinionel.patrascu@mdc-berlin.de> References: <20220527164013.4195-1-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-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-14.0.0.3092-9.0.1002-26920.000 X-TM-AS-Result: No-10-1.772600-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEOq1 eyR8QAGQRRa406V/YwyBUGewL2YXt+srvpo9o0SbwLYk+NSxc5r4qCLIu0mtIPZAgAXnySC8FfN /bCXGyd9CL0iaxKE1f0CHHH5mbTfBpSvuaUcwSJ87lKkz03w06+uLFZZYlisfHxPMjOKY7A9qHX ONfTwSQsRB0bsfrpPI0PU0TdJoUtej10rkD5kD4CXH5jcvc825RMynKF6EVr5Ed+dmkyqHlCTnC GhqgcMKM1Hlhyt3yJrX5BvfMAPPhjJd+ZjIOGUE1PgeRVwzA9zcUke23u350xU7OJY7bdPeD9iv /sJMsVc7Oyi/ulxQeIZB3RJBkOzT X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.772600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26920.000 X-TM-SNTS-SMTP: 4682A6ACE975982F8FE59C1EE934A1AC5D6ED6AE1A5EF3805ADF37908BAC8C4B2002: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 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=1653669689; 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:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=m4DTQWuwStPHH66G7EFFErhqHz7BkrZlR/QJyw+9Wqs=; b=OnSA1nZRVki5kle3NQwhLhWJneFaJ/qHqyyaaZY+xjI+y2UlKklcSa2pUIa6+aQTq+8tPT V3GhD5GJqkPrEKDe33nLmzS4u9uEMwzkyO3INapQcWowZOA3LkMBII+d9UPJ16COtrY8dC Rh0FBy+ND/3g/69PKmf9oQNRufbz7VX/ySyBoQ0wR3mc4OKHXrHJuFyo0AyS4i3W+WgSvq OZ4SeZGz1rK/J2npQQzgR+VMGOAKM7XSbrX5LsOGVea/T42UkQREgNHy2kPQLBpGSXw95t tafuL2Lcoqn1OYoyLBa2C5HkXeMDz/fyCi1nllomTk+Zodz9XMDGd578tLKGJQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1653669689; a=rsa-sha256; cv=none; b=DUFXelSDbOEPdQxsqvKiqNa56agEhZyGXm8AD3x/5m5qwIuEZp29iRKFAqz6zfdST/rU05 QrSOlKv+azTGp5C4202EWBdY6nMpZQIzdlS0NNRCN8MDo0tJAmKTbku1BSTRKZSvBXAoZT XYE/nB9yaRMXms7X2da0nRWclQ0qFgCpfawNnY+HGw9OOxB+a+4UfJsFDfgIXxGCwTrHSB IWftCm04GKucb2+TjpEmkVNCkq5E5VXcjDaiwqkCjC1h39J7uXl+7bfV9Lqy7CfgaBwlgq 1E5Qdz+CoAg5mNaBaV0Op/J3nqtT3wTdrl/xiiGBzbYXulsu9NROsp+jtkioSQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=eB6eNOIm; 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: 5.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=eB6eNOIm; 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: 1A168ACB4 X-Spam-Score: 5.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: rc9PHAa9lGXJ * gnu/packages/bioconductor.scm (r-scmap): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4baa80dcb1..9c6526331e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5049,6 +5049,47 @@ (define-public r-scdblfinder comprehensive scDblFinder method.") (license license:gpl3))) +(define-public r-scmap + (package + (name "r-scmap") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scmap" version)) + (sha256 + (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (properties `((upstream-name . "scmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dplyr + r-e1071 + r-ggplot2 + r-googlevis + r-matrixstats + r-proxy + r-randomforest + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hemberg-lab/scmap") + (synopsis "Tool for unsupervised projection of single cell RNA-seq data") + (description + "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the +composition of complex tissues since the technology allows researchers to define +cell-types using unsupervised clustering of the transcriptome. However, due to +differences in experimental methods and computational analyses, it is often +challenging to directly compare the cells identified in two different experiments. +@code{scmap} is a method for projecting cells from a scRNA-seq experiment onto +the cell-types or individual cells identified in a different experiment.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") -- 2.36.0