maaslin2

name	maaslin2
description	MaAsLin2 / MaAsLin3 — multivariable association discovery between metadata and meta-omic features (taxonomy, pathways, genes) with filtering, normalization, transforms, and FDR control. Use for differential abundance with covariates or longitudinal designs. Upstream: https://github.com/biobakery/Maaslin2 and https://github.com/biobakery/MaAsLin3. Route via research-analysis. Classic LDA biomarkers → lefse; figure workflows → microeco / visualization.
license	MIT
category	evaluation
tags	["MaAsLin2","MaAsLin3","differential-abundance","statistics","bioBakery"]
upstream	https://github.com/biobakery/Maaslin2
stage	report

MaAsLin2 / MaAsLin3

Upstream: biobakery/Maaslin2 · biobakery/MaAsLin3

Citation

Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021). https://doi.org/10.1371/journal.pcbi.1009442

MaAsLin 3: Nickols, W. A. et al. MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery. Nat. Methods (2025). https://doi.org/10.1038/s41592-025-02923-9

See also docs/references.md.

Analytical thinking

Default for covariate-adjusted associations on compositional meta-omics tables (MetaPhlAn, HUMAnN, MAG abundances, …). Pin normalization/transform, fixed/random effects, and q-value threshold. MaAsLin3 adds prevalence vs abundance association framing — cite the version you run.

vs	Prefer MaAsLin when
lefse	Multiple covariates / mixed models / modern FDR workflow
microeco	Need model coefficients vs exploratory diversity suite

How to run

# Bioconductor / GitHub install per upstream README for Maaslin2 or MaAsLin3
# library(Maaslin2)  # or Maaslin3
# Maaslin2(input_data, input_metadata, output, fixed_effects = c("phenotype","age"), ...)

Do not invent formula syntax — follow the installed package vignette.

Decision tree

Differential / association analysis?
├─ Covariates / longitudinal → maaslin2 (2 or 3)
├─ Classic two-class LDA biomarkers → lefse
├─ Explore diversity first → microeco
└─ Plot checklist → visualization

Related skills

research-analysis · ancombc · lefse · stamp · microeco · phyloseq · visualization · metaphlan · humann · study-design · tool-selection