GNU bug report logs - #62428
gnu: Add r-anota2seq, r-hybridmtest, r-apalyzer, r-org-sc-sgd-db, r-apcomplex, r-mdqc, , r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray, r-arrayqualitymetrics, r-repmis, r-setrng..

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <62428 <at> debbugs.gnu.org.>
Subject: [bug#62428] [PATCH 09/14] gnu: Add r-arraymvout.
Date: Sat, 25 Mar 2023 00:18:55 +0100

* gnu/packages/bioconductor.scm (r-arraymvout): New variable.
---
 gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f43c42bee..62cd786842 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3215,6 +3215,42 @@ (define-public r-arrayexpress
 structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
     (license license:artistic2.0)))
 
+(define-public r-arraymvout
+  (package
+    (name "r-arraymvout")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "arrayMvout" version))
+       (sha256
+        (base32 "0g66s64n4qlvhkanp33bbvpi93rsdx5xq0mjr96d0195qbf6k156"))))
+    (properties `((upstream-name . "arrayMvout")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-affy
+           r-affycontam
+           r-biobase
+           r-lumi
+           r-mdqc
+           r-parody))
+    (home-page "https://bioconductor.org/packages/arrayMvout")
+    (synopsis "Multivariate outlier detection for expression array QA")
+    (description
+     "This package supports the application of diverse quality metrics to AffyBatch
+instances, summarizing these metrics via PCA, and then performing parametric
+outlier detection on the PCs to identify aberrant arrays with a fixed Type I
+error rate.")
+    (license license:artistic2.0)))
+
 (define-public r-asafe
   (package
     (name "r-asafe")
-- 
2.39.2

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