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This is the development version of ALDEx2; for the stable release version, see ALDEx2.

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Bioconductor version: Development (3.20)

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, 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.

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 at>

Citation (from within R, enter citation("ALDEx2")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ANOVA-Like Differential Expression tool for high throughput sequencing data HTML R Script
Incorporating Scale Uncertainty into ALDEx2 HTML R Script
Reference Manual PDF


biocViews Bayesian, ChIPSeq, DNASeq, DifferentialExpression, GeneExpression, ImmunoOncology, Metagenomics, Microbiome, Posterior p-value, RNASeq, Scale simulation, Sequencing, Software, Transcriptomics
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>=3)
Depends methods, stats, zCompositions, lattice, latticeExtra
Imports Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels
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Suggests testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick
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Depends On Me omicplotR
Imports Me benchdamic, microbiomeMarker, aIc, ggpicrust2
Suggests Me dar, pctax
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