Package: ALDEx2
Type: Package
Title: Analysis Of Differential Abundance Taking Sample and Scale
        Variation Into Account
Version: 1.42.0
Date: 2023-02-09
Author: Greg Gloor, Andrew Fernandes, Jean Macklaim, Arianne Albert,
        Matt Links, Thomas Quinn, Jia Rong Wu, Ruth Grace Wong, Brandon
        Lieng, Michelle Nixon
Maintainer: Greg Gloor <ggloor@uwo.ca>
biocViews: DifferentialExpression, RNASeq, Transcriptomics,
        GeneExpression, DNASeq, ChIPSeq, Bayesian, Sequencing,
        Software, Microbiome, Metagenomics, ImmunoOncology, Scale
        simulation, Posterior p-value
Description: 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 predicted p-values and posterior
        Benjamini-Hochberg corrected p-values. ALDEx2 also calculates
        expected standardized effect sizes for paired or unpaired study
        designs. ALDEx2 can now be used to estimate the effect of scale
        on the results and report on the scale-dependent robustness of
        results.
License: GPL (>=3)
URL: https://github.com/ggloor/ALDEx_bioc
BugReports: https://github.com/ggloor/ALDEx_bioc/issues
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Depends: methods, stats, zCompositions, lattice, latticeExtra
Imports: Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors,
        SummarizedExperiment, multtest, directlabels
Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern,
        ggplot2, cowplot, tidyverse, magick
Remotes: coolbutuseless/ggpattern
Config/pak/sysreqs: make libjpeg-dev libpng-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:21:46 UTC
RemoteUrl: https://github.com/bioc/ALDEx2
RemoteRef: RELEASE_3_22
RemoteSha: 4f9241417d12122a603cdbe89e75413e24ab5f01
NeedsCompilation: no
Packaged: 2026-02-23 09:43:30 UTC; root
Built: R 4.5.2; ; 2026-02-23 09:45:26 UTC; windows
