From patchwork Sun Jun 19 20:42:00 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 40184 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 55FE427BBE9; Sun, 19 Jun 2022 21:43:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 0D15727BBE9 for ; Sun, 19 Jun 2022 21:43:11 +0100 (BST) Received: from localhost ([::1]:50210 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o31lG-0006Um-5w for patchwork@mira.cbaines.net; Sun, 19 Jun 2022 16:43:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58234) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o31l8-0006UM-IQ for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59405) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o31l8-0005OB-AM for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o31l8-00014n-8Z for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56098] [PATCH 1/2] gnu: Add r-microbiome. References: In-Reply-To: Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 19 Jun 2022 20:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56098 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56098@debbugs.gnu.org> Received: via spool by 56098-submit@debbugs.gnu.org id=B56098.16556713434086 (code B ref 56098); Sun, 19 Jun 2022 20:43:02 +0000 Received: (at 56098) by debbugs.gnu.org; 19 Jun 2022 20:42:23 +0000 Received: from localhost ([127.0.0.1]:53300 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o31kU-00013p-Nu for submit@debbugs.gnu.org; Sun, 19 Jun 2022 16:42:22 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:37273) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o31kS-00013S-Pe for 56098@debbugs.gnu.org; Sun, 19 Jun 2022 16:42:21 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 95113300337 for <56098@debbugs.gnu.org>; Sun, 19 Jun 2022 22:42:14 +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=1655671333; x=1657485734; bh=q4lgaJ24tqMmfk6tKxjNEmiAlvFRFBm0U6G1/tpgIuc=; b=Jj/KEAscp9KJ 2NKjrF3Hasc6GyRhk3npKOxfa2Stg8pvksS6vd0VlmH4tWihoZIqGLsbv/v0HNcW sOj5MeaggEs2rSHlx9NA2tdKEY6hzBD36JGaN2SDUUetwabEzfxETAiTY4i8bzik iY02YpVEKPevzcSlJngNVGKxadCmpHk= 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 qo09z191gzFb for <56098@debbugs.gnu.org>; Sun, 19 Jun 2022 22:42:13 +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 <56098@debbugs.gnu.org>; Sun, 19 Jun 2022 22:42:13 +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; Sun, 19 Jun 2022 22:42:12 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 19 Jun 2022 22:42:00 +0200 Message-ID: <20220619204201.18713-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 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-14.0.0.3092-9.0.1002-26966.002 X-TM-AS-Result: No-10--8.138900-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiJBhSnhB8QHrArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9y4VFP6muDhqY5ZGw7wyeHY87 NwWBxSviLvSisHnAzk4LRPgDkKAntmZGvWTp76WBFdmLrX42PXAK0ZgbTOeKUyiLz1Vtc/pUjL8 WDWZGeoqEbr6VH4TuZmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1l3+bAt/YFVTGobSoBU+5DRkMm ApDmEfUfiDZlarXxj6szgvhE852huulxyHOcPoH X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.138900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26966.002 X-TM-SNTS-SMTP: A2EC108BC9BAF6FDF672CFE739479E5FECE245CDE6EF9C61C4D39F63A6EC7D682002: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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-microbiome): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..54280a26f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8100,6 +8100,44 @@ (define-public r-bumphunter studies.") (license license:artistic2.0))) +(define-public r-microbiome + (package + (name "r-microbiome") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "microbiome" version)) + (sha256 + (base32 + "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12")))) + (properties `((upstream-name . "microbiome"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-compositions + r-dplyr + r-ggplot2 + r-phyloseq + r-reshape2 + r-rtsne + r-scales + r-tibble + r-tidyr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://microbiome.github.io/microbiome/") + (synopsis "Tools for microbiome analysis") + (description + "The @code{microbiome} facilitates @code{phyloseq} exploration and analysis +of taxonomic profiling data. This package provides tools for the manipulation, +statistical analysis, and visualization of taxonomic profiling data. In addition +to targeted case-control studies, the @code{microbiome} facilitates scalable +exploration of population cohorts. This package supports the independent +@code{phyloseq} data format and expands the available toolkit in order to +facilitate the standardization of the analyses and the development of best +practices.") + (license license:bsd-2))) + (define-public r-minfi (package (name "r-minfi") From patchwork Sun Jun 19 20:42:01 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 40185 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id C5A1727BBE9; Sun, 19 Jun 2022 21:43:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3008627BBEA for ; Sun, 19 Jun 2022 21:43:11 +0100 (BST) Received: from localhost ([::1]:50214 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o31lG-0006V0-96 for patchwork@mira.cbaines.net; Sun, 19 Jun 2022 16:43:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58236) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o31l8-0006UV-VD for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59406) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o31l8-0005OH-NN for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o31l8-00014v-LL for guix-patches@gnu.org; Sun, 19 Jun 2022 16:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56098] [PATCH 2/2] gnu: Add r-ancombc. 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(license license:gpl3))) +(define-public r-ancombc + (package + (name "r-ancombc") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANCOMBC" version)) + (sha256 + (base32 + "1p9yryv85qk7m3hbflmpdffd3azpsifcw54x1rp8sb67yjmq3whq")))) + (properties `((upstream-name . "ANCOMBC"))) + (build-system r-build-system) + (propagated-inputs + (list r-desctools + r-doparallel + r-dorng + r-dplyr + r-energy + r-foreach + r-hmisc + r-magrittr + r-mass + r-microbiome + r-nlme + r-nloptr + r-phyloseq + r-rdpack + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FrederickHuangLin/ANCOMBC") + (synopsis "Analysis of compositions of microbiomes with bias correction") + (description + "@code{ANCOMBC} is a package containing @dfn{DA} (differential abundance) +and correlation analyses for microbiome data. Specifically, the package includes +@dfn{ANCOM-BC} (Analysis of Compositions of Microbiomes with Bias Correction) and +@dfn{ANCOM} (Analysis of Composition of Microbiomes) for DA analysis, and +@dfn{SECOM} (Sparse Estimation of Correlations among Microbiomes) for correlation +analysis. Microbiome data are typically subject to two sources of biases: +unequal sampling fractions (sample-specific biases) and differential sequencing +efficiencies (taxon-specific biases). Methodologies included in the @code{ANCOMBC} +package were designed to correct these biases and construct statistically +consistent estimators.") + (license license:artistic2.0))) + (define-public r-aneufinder (package (name "r-aneufinder")