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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=B56098.16556713434093 (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]:53302 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o31kV-00013r-0n for submit@debbugs.gnu.org; Sun, 19 Jun 2022 16:42:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44253) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o31kT-00013W-6j 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 4CAF9300366 for <56098@debbugs.gnu.org>; Sun, 19 Jun 2022 22:42:15 +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= 1655671334; x=1657485735; bh=oeGI+mXSP+NN8EDwkinDBMARlwIXxpSHfjS 15xc2LhM=; b=V7IwL2Nywkil6mi8IDIKxJK1+pIxBohv6Z4kmvwydGXwn0HJmMC UX4zMvKngn+b4YfYKzawk/TOgW8n3skiowTH3yKusLlkraxk6TFiV+MOcCWeefNp L8yPa3GM3q5iXkTwTlvUJkBUzfBe97Y9DalLsgm55lHenkuG3/0igLcI= 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 3E4CFrhBuXvw for <56098@debbugs.gnu.org>; Sun, 19 Jun 2022 22:42:14 +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 22:42:14 +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 22:42:13 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 19 Jun 2022 22:42:01 +0200 Message-ID: <20220619204201.18713-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20220619204201.18713-1-madalinionel.patrascu@mdc-berlin.de> References: <20220619204201.18713-1-madalinionel.patrascu@mdc-berlin.de> 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-10-0.341600-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkeNJPnASfMqtG5/ZtK3riSnVTWWiNp+v9K2HFvXNxwFGr4ZkmDx/8HJMJ XDJjkqdQ7a2CBzeQZMBJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgjMejjvPkBr4jnd Af9Yd7wQIdlpDus0JkjVJS0iZOAjEEgwtGZKLmbC3VKopdTE8nEolKSW3NXzStzSPY4I6CS+XPu ETt3k+cDzTqiufNz0RZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn4WKraKEh/oMPINhwTXBeZ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.341600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26966.002 X-TM-SNTS-SMTP: 2BDCD4B35D1AB456CA82171965C27274A69C55F77F1103D485A97DD5DB359BDA2002: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-ancombc): New variable. --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 54280a26f6..a9b19bfadd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,52 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (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")