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Reply-To: bug#55146 <55146@debbugs.gnu.org> Date: Fri, 15 Aug 2025 09:05:17 +0000 retitle 55146 [PATCH] gnu: Add r-aggregatebiovar. reassign 55146 guix-patches submitter 55146 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 55146 normal tag 55146 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 27 07:44:57 2022 Received: (at submit) by debbugs.gnu.org; 27 Apr 2022 11:44:57 +0000 Received: from localhost ([127.0.0.1]:41367 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njg6L-0000Ei-FW for submit@debbugs.gnu.org; Wed, 27 Apr 2022 07:44:57 -0400 Received: from lists.gnu.org ([209.51.188.17]:43270) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njg6J-0000EW-QG for submit@debbugs.gnu.org; Wed, 27 Apr 2022 07:44:56 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:46372) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njg6J-00082c-6S for guix-patches@gnu.org; Wed, 27 Apr 2022 07:44:55 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:42583) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njg6G-0003Ko-FA for guix-patches@gnu.org; Wed, 27 Apr 2022 07:44:54 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id A9F6DA017D for ; Wed, 27 Apr 2022 13:44:48 +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 :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1651059887; x=1652874288; bh=ENov4OuL6Id6hhUHKwirGKpD7lGI7iDLgZ3+k54t2X0=; b=bGleAnWryjHT VWCQwQ8RUHU65RVEH51vFJbfdiLXxcw/Y6TsHgiBi6dxRcTDDlin4v0hI01AQUOS l9zk8VEldz2JobYwT5cYpCoaSGF0xqrJmXTmKut2AipuG29TM//aJyltk296pZmM VnKltE+kGR104ANiezsdMKW1wFqVqDc= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id xTM0oGZ5a7C2 for ; Wed, 27 Apr 2022 13:44:47 +0200 (CEST) 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 for ; Wed, 27 Apr 2022 13:44:47 +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; Wed, 27 Apr 2022 13:44:47 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-aggregatebiovar. Date: Wed, 27 Apr 2022 13:44:36 +0200 Message-ID: <20220427114436.26482-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net 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-14.0.0.3092-9.0.1000-26858.006 X-TM-AS-Result: No-10--2.809400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJw6 tnDgS/8FRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8ZskwWqoib3KY5ZGw7wyeHqmO ixP08tcG4ZfkBlKsszY18A+G850MxjbcgpFl911rGL//8mlodA0LixrsCJ1jTlCkt7JatNPWeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DMu0nYNEK4kPCNOcUYQTlLezMaRdsck+80KMQ +LAxDKzx2WiBS8j7CFGsY2uVwcPsqxCCLRk5RCrHxcctPhZ0lwR6lbwep5oBdxSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.809400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26858.006 X-TM-SNTS-SMTP: 1776AA02F710E2882A12A19C7CFF3F7D0784FDC6F914050ACD2D8122BBA3645A2000: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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) * gnu/packages/bioconductor.scm (r-aggregatebiovar): 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 67ee6079c6..8f76324330 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1664,6 +1664,40 @@ (define-public r-adamgui the @code{GFAGpathUi} function.") (license license:gpl2+))) +(define-public r-aggregatebiovar + (package + (name "r-aggregatebiovar") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "aggregateBioVar" version)) + (sha256 + (base32 + "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk")))) + (properties `((upstream-name . "aggregateBioVar"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/jasonratcliff/aggregateBioVar") + (synopsis + "Differential gene expression analysis for multi-subject scRNA-seq") + (description + "This package @code{aggregateBioVar} contains tools to summarize single +cell gene expression profiles at the level of subject for single cell RNA-seq +data collected from more than one subject (e.g. biological sample or technical +replicates). A @code{SingleCellExperiment} object is taken as input and +converted to a list of @code{SummarizedExperiment} objects, where each list +element corresponds to an assigned cell type. The @code{SummarizedExperiment} +objects contain aggregate gene-by-subject count matrices and inter-subject +column metadata for individual subjects that can be processed using downstream +bulk RNA-seq tools.") + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76 -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 27 10:32:12 2022 Received: (at 55146-done) by debbugs.gnu.org; 27 Apr 2022 14:32:13 +0000 Received: from localhost ([127.0.0.1]:43888 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njiiC-0003ap-NH for submit@debbugs.gnu.org; Wed, 27 Apr 2022 10:32:12 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njiiA-0003Z4-Nn for 55146-done@debbugs.gnu.org; Wed, 27 Apr 2022 10:32:11 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1651069928; cv=none; d=zohomail.com; s=zohoarc; b=SO2MolI3A58iGGOqqCFDMPx2khfjKjC/p40rPFgyErQlzEgyP++d168Dc3H7Fyud3f1sWoDv7450+dk9jmg11IdmqojpaCoC8Eykm0wXVsDZAGmyrL+HjrZS4fj1khp3xLrhxiV8M/xSV0p8ipM1jr3tD+Pd7MuDkBRHBqsdGGg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1651069928; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=L1pakJQc8/gaLwrhXntiBcgOxmSh0bPV1IxONex8goE=; b=Q2GUXzXg6A9fMr64+mfAO2e/QqdsbEazIePyV22H/eZj/Kh0g8O7XHDkmRmEYbs4GRZrOFanXjjl1d2DK3y2AB0u8PZMybNZVGG16i1phLriU5+TwVcHrAGxrezKj2gqoIgSbBlSvxUo7EOmZ4cIFMZxe9xt3JnJF5f8yPRJV5c= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1651069928; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=L1pakJQc8/gaLwrhXntiBcgOxmSh0bPV1IxONex8goE=; b=UeyxVKONVAAifvt4A9gK4E1iF+DRVLp3igZKKqIoR5VJ471NznD63cbOhNGITS+1 jiIF5v00+4fZ8BTtM7zqd5i5Ib9U9Oi+0qQNddPvTebbnb5xSKd+qv9YRgxlUOSMe3J bCxSgZU68tdZ0L8aMgIaev+NbwZluQDYg88Jdiww= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1651069928017671.8209322134221; Wed, 27 Apr 2022 07:32:08 -0700 (PDT) References: <20220427114436.26482-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#55146] [PATCH] gnu: Add r-aggregatebiovar. Date: Wed, 27 Apr 2022 16:31:46 +0200 In-reply-to: <20220427114436.26482-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <877d7a4mxm.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55146-done Cc: 55146-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioconductor.scm (r-aggregatebiovar): New variable. Applied with minor stylistic changes. Thanks! --=20 Ricardo From unknown Fri Aug 15 02:05:17 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 26 May 2022 11:24:09 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator