ALDEx3

MaRDI QIDQ7372461CRANFDO

Authors Justin Silverman, Greg Gloor, Kyle McGovern

Last update 26 August 2026

Copyright license MIT license, File License

Software version identifier 1.0.0, 1.0.1, 1.0.2, 1.2.0, PACKAGES.rds, 1.3.1

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>.

Cites work

• Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization
• Scale Reliant Mixed Effects Models Enhance Microbiome Data Analysis

This page was built for software: ALDEx3