From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms9.migadu.com with LMTPS id UOaoJWAYXWRnpgAASxT56A (envelope-from ) for ; Thu, 11 May 2023 18:31:28 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id CGLAJWAYXWRDKQEA9RJhRA (envelope-from ) for ; Thu, 11 May 2023 18:31:28 +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 43D9216044 for ; Thu, 11 May 2023 18:31:28 +0200 (CEST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1px9CL-0005lA-EU; Thu, 11 May 2023 12:31:21 -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 1px9C9-0005kf-4q for guix-patches@gnu.org; Thu, 11 May 2023 12:31:09 -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 1px9C2-0005V9-I9 for guix-patches@gnu.org; Thu, 11 May 2023 12:31:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1px9C2-00063V-3E; Thu, 11 May 2023 12:31:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63447] [PATCH] gnu: Add r-dropletutils. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Thu, 11 May 2023 16:31:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 63447 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63447@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.168382264123243 (code B ref -1); Thu, 11 May 2023 16:31:01 +0000 Received: (at submit) by debbugs.gnu.org; 11 May 2023 16:30:41 +0000 Received: from localhost ([127.0.0.1]:53247 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1px9Bg-00062p-QH for submit@debbugs.gnu.org; Thu, 11 May 2023 12:30:41 -0400 Received: from lists.gnu.org ([209.51.188.17]:46474) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1px9Bf-00062h-7k for submit@debbugs.gnu.org; Thu, 11 May 2023 12:30:39 -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 1px9Be-0005bD-Ur for guix-patches@gnu.org; Thu, 11 May 2023 12:30:38 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1px9Bc-0005KP-6q for guix-patches@gnu.org; Thu, 11 May 2023 12:30:38 -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=1683822630; x=1685637031; bh=Dt+bFKZWglZgpNl 7z0eAYqytFHwdg1dw3hFpoi+9Sfk=; b=h4bop4oHT2zyWW34JFKNOWpQA0yhRlx oDK0NYTySCvZo22hBNgHGRa3U3Z4psEDPYseK7fTvWfqpT8kK+CkXDdwVpSGhHDF SVqTMGSvFy2aiFh4zsEu9XeCqTbmh14XPRIredYMK0f7ZRb88dyk+yw6PzH3szhR IClGx5+yTlHM= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=madalinionel.patrascu@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 7CBFBA0142 for ; Thu, 11 May 2023 18:30:30 +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 15.1.2507.23; Thu, 11 May 2023 18:30:29 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Thu, 11 May 2023 18:30:16 +0200 Message-ID: <20230511163016.19814-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27620.000 X-TM-AS-Result: No-10--4.174300-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkENtL +zfrHC2wRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRhItcoSAIccJ0bT 1Y3RDNvRvzRCt0rfaa57nIUt1j4g83SWdjqTh/wrGL//8mlodAz5//buCv56OlwV2iaAfSWcURS Scn+QSXl1PyA7eE+Ph+gtHj7OwNO22utO5qEfOUWU1CkedNSO9nGCAFbBWQX+hsZid/8qdxh7hh hGUgR7xOAPxmxvpNm/tFw1H3ExvIQNd3ckJHT2QmlhBxy5C3TcUY0ri0HwrWnQJ88ZHP8DjvmJf 6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.174300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27620.000 X-TM-SNTS-SMTP: 4C8ED340AFCF5B2E036A95A1089B75C7F55127E56BEC84FE09BA24A1DB58022A2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.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-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1683822688; a=rsa-sha256; cv=none; b=AJ5YiBnwUIs5RiG4S8elQVEayKC02h0jD3A90lf4Xt/Ppr31hoojKVgulrtjFQC1ae0nKq /QVmWiTSKy0Do1eSQizvVTqNyOiBQWc/JJNRLIBZ8rXpFyTj5di0S1AmH5DGNDpRWXSiue ClCHgK0+YDnj6NXBwQVwHSAkGRzHrkSUzBn+iIvvyFTE3u4F0s/avdUPdMvdGohJTvcrz+ cMAwQTFKh1/Ht3MWbtCAr1JCjvf2Q62PIi2k+wQoQ4AxOFZo/4LiV2S4vNRD6GCWEOn4VU /L0NwxPVD07kLpB96Tp/89UdSb+Tx23+ziXAzcpuCIdWfDHyUQCASUnPhrbMsA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=h4bop4oH; 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" ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1683822688; 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:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=ZmDWMNDk+Zcj/IJPF1J6udzXSz+UpOZwMzjjOFl3KrU=; b=W+mh+a1WckYfKr1Xk0yNzjlCfTybQZDZvaU3sC+6/8x/hz0s3cJ5MZoUtAPdEcDzNwPJu6 2n/Gkj7vvazMxx67jNoNtHpw+x6wmRaJ02qyMBcqsz1IWPsKewMvE5Kmc02qVVbJMMZeau GqVsQ0Hc7l3bjwuYmqcrpyZ1m8ysW5P9P+iHKk28pl8lLl6jAVfMqhtcBgn//+l5wD1IJc 9N6baIu/peYyQe38aQKgjFoWeplqn1kxuCkT2IV9sARg7K1bhyrBndzdizeP0tENilTVzW WMrpNcAYkT0nwDNkyRLByoEyWAPhf+nWlpdNe8KcAlpW6t0luFIcwglS3wd+lw== X-Migadu-Spam-Score: -0.11 X-Spam-Score: -0.11 X-Migadu-Queue-Id: 43D9216044 X-Migadu-Scanner: scn0.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=h4bop4oH; 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-TUID: 6yrC+/pGIR/g * gnu/packages/bioconductor.scm (r-dropletutils): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb441655eb..b54585e97f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4897,6 +4897,50 @@ (define-public r-drimseq results.") (license license:gpl3+))) +(define-public r-dropletutils + (package + (name "r-dropletutils") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DropletUtils" version)) + (sha256 + (base32 "09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y")))) + (properties `((upstream-name . "DropletUtils"))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-genomicranges + r-hdf5array + r-iranges + r-matrix + r-r-utils + r-rcpp + r-rhdf5 + r-rhdf5lib + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DropletUtils") + (synopsis "Utilities for handling single-cell droplet data") + (description + "This package provides a number of utility functions for handling +single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. +This includes data loading from count matrices or molecule information files, +identification of cells from empty droplets, removal of barcode-swapped pseudo- +cells, and downsampling of the count matrix.") + (license license:gpl3))) + (define-public r-dss (package (name "r-dss") base-commit: e2eb43f945fd467e9b55a4b3c91cd186cf32e268 -- 2.39.2