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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 63803 in the body.
You can then email your comments to 63803 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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-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

Message #10 received at 63803-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: 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

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.