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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: Thu, 16 Jun 2022 15:58:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56021 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56021@debbugs.gnu.org> Received: via spool by 56021-submit@debbugs.gnu.org id=B56021.16553950672742 (code B ref 56021); Thu, 16 Jun 2022 15:58:02 +0000 Received: (at 56021) by debbugs.gnu.org; 16 Jun 2022 15:57:47 +0000 Received: from localhost ([127.0.0.1]:42944 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsQ-0000i5-Nf for submit@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:47 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50129) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsO-0000hf-0M for 56021@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 8E660160304 for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:38 +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= 1655395057; x=1657209458; bh=GZFt1MbwOPSpPLHyHaawaKjcLCYO5JVrlyL G90SjITA=; b=PfUVJ09q/EzVXLTTFhBwqBnp38eWY8XROVgYHmVuNdMtOtJXsDg ZcwalEzYa7MH84JRVpCmesG8Qgr78yIbQUniXU/kecr3+oHYyDHmQxfwUPxvMZYN 7A5LsZw2mQzqhkxr1ztWjh2VF7zm+q7Rqufnzl1ZjuMQfVGSSXYZLXkQ= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id wf9LdgFI3d0x for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +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; Thu, 16 Jun 2022 17:57:35 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 16 Jun 2022 17:57:21 +0200 Message-ID: <20220616155721.23547-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> References: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 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-14.0.0.3092-9.0.1002-26958.007 X-TM-AS-Result: No-10--0.286500-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZEyi1T9AUgUbsUh +OkaOhpfN57BJxyhEO3wBfyL06jKAmv0Xhs8HK808o3fwIs8rQQwMqNovfwOoaGL2D7wHkbXizy 75l6H5qX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85RKzQhmWmrAKFISmIp7fCMIURQi Zjlai/4Yoani0CN60UElhXQWrfGQLdTLbLmr7KW7krrHdP6mXxDNMCPzHf5Y95nfdZUf8KIdAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.286500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-SNTS-SMTP: 1388152BD02AA69B6028D12098BE6B695F2BEB632E64CD7B466FD7E57173F6D52002: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-aldex2): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..3abd57359d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,48 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aldex2 + (package + (name "r-aldex2") + (version "1.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ALDEx2" version)) + (sha256 + (base32 + "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + (properties `((upstream-name . "ALDEx2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ggloor/ALDEx_bioc") + (synopsis + "Analysis Of differential abundance taking sample variation into account") + (description + "This package provides a differential abundance analysis for the comparison +of two or more conditions. Useful for analyzing data from standard RNA-seq or +meta-RNA-seq assays as well as selected and unselected values from in-vitro +sequence selections. Uses a Dirichlet-multinomial model to infer abundance from +counts, optimized for three or more experimental replicates. The method infers +biological and sampling variation to calculate the expected false discovery +rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test +(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear +model (via aldex.glm), or a correlation test (via aldex.corr). All tests report +p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates +expected standardized effect sizes for paired or unpaired study designs.") + ;; The code for the function "rdirichlet" which is from the "R" package + ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball + ;; LICENSE specifies GPL-3. + (license (list license:agpl3+ license:gpl2+ license:gpl3)))) + (define-public r-aneufinder (package (name "r-aneufinder")