From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:41510) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLux-0003kA-Bg for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuw-00006D-1K for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57433) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuv-00005z-SU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuv-0005QO-NU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Subject: [bug#36799] [PATCH 10/11] gnu: Add r-mixomics. Resent-Message-ID: Received: from eggs.gnu.org ([2001:470:142:3::10]:41156) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JD-NB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuG-0007LN-E5 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x444.google.com ([2a00:1450:4864:20::444]:37543) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007KG-7w for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x444.google.com with SMTP id n9so22935346wrr.4 for ; Wed, 24 Jul 2019 11:22:28 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:03 +0200 Message-Id: <20190724182204.6818-11-zimon.toutoune@gmail.com> In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 36799@debbugs.gnu.org * gnu/packages/bioconductor.scm (r-mixomics): New variable. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd6570ed17..64625aedd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4959,3 +4959,57 @@ and to both short and long sequence reads.") "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") (license license:gpl2+))) +(define-public r-mixomics + (package + (name "r-mixomics") + (version "6.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mixOmics" version)) + (sha256 + (base32 + "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + (properties `((upstream-name . "mixOmics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-dplyr" ,r-dplyr) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.mixOmics.org") + (synopsis "Omics Data Integration Project") + (description + "Multivariate methods are well suited to large omics data sets where the +number of variables (e.g. genes, proteins, metabolites) is much larger than +the number of samples (patients, cells, mice). They have the appealing +properties of reducing the dimension of the data by using instrumental +variables (components), which are defined as combinations of all variables. +Those components are then used to produce useful graphical outputs that enable +better understanding of the relationships and correlation structures between +the different data sets that are integrated. mixOmics offers a wide range of +multivariate methods for the exploration and integration of biological +datasets with a particular focus on variable selection. The package proposes +several sparse multivariate models we have developed to identify the key +variables that are highly correlated, and/or explain the biological outcome of +interest. The data that can be analysed with mixOmics may come from high +throughput sequencing technologies, such as omics data (transcriptomics, +metabolomics, proteomics, metagenomics etc) but also beyond the realm of +omics (e.g. spectral imaging). The methods implemented in mixOmics can also +handle missing values without having to delete entire rows with missing data. +A non exhaustive list of methods include variants of generalised Canonical +Correlation Analysis, sparse Partial Least Squares and sparse Discriminant +Analysis. Recently we implemented integrative methods to combine multiple +data sets: N-integration with variants of Generalised Canonical Correlation +Analysis and P-integration with variants of multi-group Partial Least +Squares.") + (license license:gpl2+))) -- 2.21.0