maaslin3
This is the development version of maaslin3; for the stable release version, see maaslin3.
All Bioconductor versions of maaslin3
3.24 (devel), 3.23 (release), 3.22, 3.21
"Refining and extending generalized multivariate linear models for meta-omic association discovery"
Bioconductor version: 3.24 · Package version: 1.5.7
MaAsLin 3 refines and extends generalized multivariate linear models for meta-omicron association discovery. It finds abundance and prevalence associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates, repeated measures, and ordered predictors), filtering, normalization, and transform options to customize analysis for your specific study.
Author: William Nickols [aut, cre] 
, Jacob Nearing [aut]
Maintainer: William Nickols <willnickols at g.harvard.edu>
Citation
From within R, enter citation("maaslin3"):
William Nickols, Jacob Nearing. maaslin3: "Refining and extending generalized multivariate linear models for meta-omic association discovery". doi:10.18129/B9.bioc.maaslin3, R package version 1.5.7, https://bioconductor.org/packages/maaslin3.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("maaslin3")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.5.7 |
| License | MIT + file LICENSE |
| URL | http://huttenhower.sph.harvard.edu/maaslin3 |
| Bug Reports | https://github.com/biobakery/maaslin3/issues |
| Last updated | 2026-09-15 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 901 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Metagenomics, Microbiome, MultipleComparison, Normalization, Software |
| Package Short Url | https://bioconductor.org/packages/maaslin3/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("maaslin3")| MaAsLin 3 User Manual | HTML | R Script |
| MaAsLin 3 Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | maaslin3_1.5.7.tar.gz |
| Windows binary (x86_64) | maaslin3_1.5.7.zip |
| macOS binary (arm64) | maaslin3_1.5.7.tgz |
| macOS binary (x86_64) | maaslin3_1.5.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/maaslin3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/maaslin3 |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4)
Imports: data.table, collapse (>= 2.1.0), lmerTest, lme4, optparse, mirai, multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang, ggnewscale, survival, methods, BiocGenerics, reformulas
Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra, dplyr, SummarizedExperiment, TreeSummarizedExperiment