GNU bug report logs - #63803
[PATCH] gnu: Add r-mbecs.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#63803: closed ([PATCH] gnu: Add r-mbecs.)
Date: Thu, 01 Jun 2023 07:22:02 +0000

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Your message dated Thu, 01 Jun 2023 09:18:22 +0200
with message-id <87a5xjtzp3.fsf <at> elephly.net>
and subject line Re: [bug#63803] [PATCH] gnu: Add r-mbecs.
has caused the debbugs.gnu.org bug report #63803,
regarding [PATCH] gnu: Add r-mbecs.
to be marked as done.

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help-debbugs <at> gnu.org.)


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63803: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=63803
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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-mbecs.
Date: Tue, 30 May 2023 15:37:50 +0200

* gnu/packages/bioconductor.scm (r-mbecs): New variable.
---
 gnu/packages/bioconductor.scm | 51 +++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 265a70cdd4..b75b9f1886 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10118,6 +10118,57 @@ (define-public r-ripseeker
 processing to visualization and annotation.")
     (license license:gpl2)))
 
+(define-public r-mbecs
+  (package
+    (name "r-mbecs")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MBECS" version))
+       (sha256
+        (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz"))))
+    (properties `((upstream-name . "MBECS")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-HOME
+          ;; Fontconfig needs an writable cache
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-cluster
+           r-dplyr
+           r-ggplot2
+           r-gridextra
+           r-limma
+           r-lme4
+           r-lmertest
+           r-magrittr
+           r-markdown
+           r-matrix
+           r-pheatmap
+           r-phyloseq
+           r-rmarkdown
+           r-ruv
+           r-sva
+           r-tibble
+           r-tidyr
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/rmolbrich/MBECS")
+    (synopsis
+     "Evaluation and correction of batch effects in microbiome data-sets")
+    (description
+     "The @acronym{MBECS, Microbiome Batch Effect Correction Suite} provides a
+set of functions to evaluate and mitigate unwated noise due to processing in
+batches.  To that end it incorporates a host of batch correcting algorithms
+(BECA) from various packages.  In addition it offers a correction and reporting
+pipeline that provides a preliminary look at the characteristics of a data-set
+before and after correcting for batch effects.")
+    (license license:artistic2.0)))
+
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")

base-commit: 3807876af4b53babdbc2f1d730e4763ff651f316
-- 
2.40.1

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 63803-done <at> debbugs.gnu.org
Subject: Re: [bug#63803] [PATCH] gnu: Add r-mbecs.
Date: Thu, 01 Jun 2023 09:18:22 +0200

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

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

Applied, thanks!

-- 
Ricardo

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