Subject: [PATCH 3/3] gnu: Add r-aldex2.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Thu, 16 Jun 2022 17:57:21 +0200

* gnu/packages/bioconductor.scm (r-aldex2): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..3abd57359d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,48 @@ (define-public r-agimicrorna
 objects are used so that other packages could be used as well.")
     (license license:gpl3)))
 
+(define-public r-aldex2
+  (package
+    (name "r-aldex2")
+    (version "1.28.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ALDEx2" version))
+              (sha256
+               (base32
+                "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"))))
+    (properties `((upstream-name . "ALDEx2")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-genomicranges
+           r-iranges
+           r-multtest
+           r-rfast
+           r-s4vectors
+           r-summarizedexperiment
+           r-zcompositions))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/ggloor/ALDEx_bioc")
+    (synopsis
+     "Analysis Of differential abundance taking sample variation into account")
+    (description
+     "This package provides a differential abundance analysis for the comparison
+of two or more conditions.  Useful for analyzing data from standard RNA-seq or
+meta-RNA-seq assays as well as selected and unselected values from in-vitro
+sequence selections.  Uses a Dirichlet-multinomial model to infer abundance from
+counts, optimized for three or more experimental replicates.  The method infers
+biological and sampling variation to calculate the expected false discovery
+rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test
+(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear
+model (via aldex.glm), or a correlation test (via aldex.corr).  All tests report
+p-values and Benjamini-Hochberg corrected p-values.  ALDEx2 also calculates
+expected standardized effect sizes for paired or unpaired study designs.")
+    ;; The code for the function "rdirichlet" which is from the "R" package
+    ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball
+    ;; LICENSE specifies GPL-3.
+    (license (list license:agpl3+ license:gpl2+ license:gpl3))))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.36.1