ALDEx3: Linear Models for Sequence Count Data

Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data. Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.

Version:	1.0.0
Depends:	R (≥ 3.5)
Imports:	purrr, lme4, lmerTest, parallel, MASS, nlme, abind, matrixStats, methods, stats
Suggests:	rBeta2009, testthat (≥ 3.0.0), lmtest, sandwich, knitr, rmarkdown
Published:	2026-01-31
DOI:	10.32614/CRAN.package.ALDEx3
Author:	Justin Silverman [aut, cre], Greg Gloor [aut], Kyle McGovern [aut, ctb]
Maintainer:	Justin Silverman <JustinSilverman at psu.edu>
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	ALDEx3 results [issues need fixing before 2026-02-15]

Documentation:

Reference manual:	ALDEx3.html , ALDEx3.pdf
Vignettes:	ALDEx3-Quickstart (source)

Downloads:

Package source:	ALDEx3_1.0.0.tar.gz
Windows binaries:	r-devel: not available, r-release: ALDEx3_1.0.0.zip, r-oldrel: ALDEx3_1.0.0.zip
macOS binaries:	r-release (arm64): ALDEx3_1.0.0.tgz, r-oldrel (arm64): ALDEx3_1.0.0.tgz, r-release (x86_64): ALDEx3_1.0.0.tgz, r-oldrel (x86_64): ALDEx3_1.0.0.tgz

Linking:

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