@@ -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")