GNU bug report logs - #66915
[PATCH] gnu: Add r-methylaid.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-methylaid.
Date: Fri, 3 Nov 2023 14:51:17 +0100

* gnu/packages/bioconductor.scm (r-methylaid): New variable.

Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d79236ea26..c60f440f3f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8454,6 +8454,44 @@ (define-public r-metaneighbor
 profiles than cells of different types.")
     (license license:expat)))
 
+(define-public r-methylaid
+  (package
+    (name "r-methylaid")
+    (version "1.36.0")
+    (source
+    (origin
+      (method url-fetch)
+      (uri (bioconductor-uri "MethylAid" version))
+      (sha256
+        (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d"))))
+    (properties `((upstream-name . "MethylAid")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-ggplot2
+           r-gridbase
+           r-hexbin
+           r-matrixstats
+           r-minfi
+           r-rcolorbrewer
+           r-shiny
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://git.bioconductor.org/packages/MethylAid")
+    (synopsis
+     "Quality control of large Illumina DNA Methylation array data sets")
+    (description
+     "This package provides a visual and interactive web application using
+RStudio's shiny package.  Bad quality samples are detected using sample-dependent
+and sample-independent controls present on the array and user adjustable
+thresholds.  In depth exploration of bad quality samples can be performed using
+several interactive diagnostic plots of the quality control probes present on
+the array.  Furthermore, the impact of any batch effect provided by the user can
+be explored.")
+    (license license:gpl2+)))
+
 (define-public r-methylkit
   (package
     (name "r-methylkit")

base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d
-- 
2.41.0

Message #10 received at 66915-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 66915-done <at> debbugs.gnu.org
Subject: Re: [bug#66915] [PATCH] gnu: Add r-methylaid.
Date: Sat, 04 Nov 2023 16:14:43 +0100

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-methylaid): New variable.

Applied, thanks!

-- 
Ricardo

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