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: | 1.0.2 |
| 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: | 2026-02-05 |
| 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 |
| Reference manual: | ALDEx3.html , ALDEx3.pdf |
| Vignettes: |
ALDEx3-Quickstart (source) |
| Package source: | ALDEx3_1.0.2.tar.gz |
| Windows binaries: | r-devel: ALDEx3_1.0.2.zip, r-release: ALDEx3_1.0.2.zip, r-oldrel: ALDEx3_1.0.2.zip |
| macOS binaries: | r-release (arm64): ALDEx3_1.0.2.tgz, r-oldrel (arm64): ALDEx3_1.0.2.tgz, r-release (x86_64): ALDEx3_1.0.2.tgz, r-oldrel (x86_64): ALDEx3_1.0.2.tgz |
| Old sources: | ALDEx3 archive |
Please use the canonical form https://CRAN.R-project.org/package=ALDEx3 to link to this page.
Need a high-speed mirror for your open-source project?
Contact our mirror admin team at info@clientvps.com.
This archive is provided as a free public service to the community.
Proudly supported by infrastructure from VPSPulse , RxServers , BuyNumber , UnitVPS , OffshoreName and secure payment technology by ArionPay.