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bug#36799: closed ([PATCH 10/11] gnu: Add r-mixomics.)

From: GNU bug Tracking System
Subject: bug#36799: closed ([PATCH 10/11] gnu: Add r-mixomics.)
Date: Fri, 21 Feb 2020 17:08:04 +0000

Your message dated Fri, 21 Feb 2020 18:07:33 +0100
with message-id <CAJ3okZ2GnkOKAPNwz8FwmRbZ+W+pYHiwB=address@hidden>
and subject line patches merged
has caused the debbugs.gnu.org bug report #36797,
regarding [PATCH 10/11] gnu: Add r-mixomics.
to be marked as done.

(If you believe you have received this mail in error, please contact

36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797
GNU Bug Tracking System
Contact address@hidden with problems
--- Begin Message --- Subject: [PATCH 10/11] gnu: Add r-mixomics. Date: Wed, 24 Jul 2019 20:22:03 +0200
* 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
+    (license license:gpl2+)))

--- End Message ---
--- Begin Message --- Subject: patches merged Date: Fri, 21 Feb 2020 18:07:33 +0100

All the patches are merged now; except r-flowpeaks. Because this
package use Artistic1.0 which is not enough clear to be considered
"free" [1,2] (GNU's point of view [3]) and upstream are not
responsive, let clean the bug tracker. :-)

[1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16
[2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html
[3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense

All the best,

--- End Message ---

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