GNU bug report logs - #61891
[PATCH] gnu: Add r-biglm, r-cplm, r-som, r-chemometrics, r-metagenomeseq, r-maaslin2, r-mmuphin.

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <61891 <at> debbugs.gnu.org>
Subject: [bug#61891] 
Date: Wed, 1 Mar 2023 08:23:42 +0100

Date: Wed, 1 Mar 2023 04:17:48 +0100
Subject: [PATCH 6/7] gnu: Add r-maaslin2.

* gnu/packages/bioconductor.scm (r-maaslin2): 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 7de5750e09..c7f623343e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6533,6 +6533,57 @@ (define-public r-limma
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-maaslin2
+  (package
+    (name "r-maaslin2")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Maaslin2" version))
+       (sha256
+        (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89"))))
+    (properties `((upstream-name . "Maaslin2")))
+    (build-system r-build-system)
+    (arguments (list #:tests? #f)) ;test suite is non-deterministic :(
+    (propagated-inputs
+     (list r-biglm
+           r-car
+           r-chemometrics
+           r-cplm
+           r-data-table
+           r-dplyr
+           r-edger
+           r-ggplot2
+           r-glmmtmb
+           r-hash
+           r-lme4
+           r-lmertest
+           r-logging
+           r-lpsymphony
+           r-mass
+           r-mumin
+           r-metagenomeseq
+           r-optparse
+           r-pbapply
+           r-pcapp
+           r-pheatmap
+           r-pscl
+           r-rmarkdown
+           r-robustbase
+           r-vegan))
+    (native-inputs (list r-knitr))
+    (home-page "http://huttenhower.sph.harvard.edu/maaslin2")
+    (synopsis
+     "Multivariable association discovery in population-scale meta-omics studies")
+    (description
+     "MaAsLin2 is comprehensive R package for efficiently determining multivariable
+association between clinical metadata and microbial meta'omic features.  This
+package relies on general linear models to accommodate most modern epidemiological
+study designs, including cross-sectional and longitudinal, and offers a variety
+of data exploration, normalization, and transformation methods.")
+    (license license:expat)))
+
 (define-public r-made4
   (package
     (name "r-made4")
-- 
2.39.1

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