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ALDEx3  

Linear Models for Sequence Count Data
View on CRAN: Click here


Download and install ALDEx3 package within the R console
Install from CRAN:
install.packages("ALDEx3")

Install from Github:
library("remotes")
install_github("cran/ALDEx3")

Install by package version:
library("remotes")
install_version("ALDEx3", "1.0.1")



Attach the package and use:
library("ALDEx3")
Maintained by
Justin Silverman
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-02-18
Latest Update: 2026-02-18
Description:
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>.
How to cite:
Justin Silverman (2026). ALDEx3: Linear Models for Sequence Count Data. R package version 1.0.1, https://cran.r-project.org/web/packages/ALDEx3. Accessed 06 Jun. 2026.
Previous versions and publish date:
1.0.0 (2026-01-31 20:10), 1.0.1 (2026-02-03 09:30)
Other packages that cited ALDEx3 R package
View ALDEx3 citation profile
Other R packages that ALDEx3 depends, imports, suggests or enhances
Complete documentation for ALDEx3
Functions, R codes and Examples using the ALDEx3 R package
Full ALDEx3 package functions and examples
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