Package: maaslin3
Title: "Refining and extending generalized multivariate linear models
        for meta-omic association discovery"
Year: 2025
Version: 1.3.0
Authors@R: c(
  person("William", "Nickols", email = "willnickols@g.harvard.edu", role = c("aut", "cre"), comment=c(ORCID="0000-0001-8214-9746")), 
  person("Jacob", "Nearing", email = "nearing@broadinstitute.org", role = "aut")
  )
Depends: R (>= 4.4)
Description: 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.
License: MIT + file LICENSE
Imports: dplyr, plyr, pbapply, lmerTest, parallel, lme4, optparse,
        logging, multcomp, ggplot2, RColorBrewer, patchwork, scales,
        rlang, tibble, ggnewscale, survival, methods, BiocGenerics,
        SummarizedExperiment, TreeSummarizedExperiment
Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra
VignetteBuilder: knitr
Collate: fit.R utility_scripts.R viz.R maaslin3.R
URL: http://huttenhower.sph.harvard.edu/maaslin3
biocViews: Metagenomics, Software, Microbiome, Normalization,
        MultipleComparison
BugReports: https://github.com/biobakery/maaslin3/issues
NeedsCompilation: no
Packaged: 2026-01-09 21:36:11 UTC; root
Config/pak/sysreqs: cmake make libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:33:46 UTC
RemoteUrl: https://github.com/bioc/maaslin3
RemoteRef: HEAD
RemoteSha: b274055f30d65b3eff5b0768a01effc512d1d0fd
Author: William Nickols [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8214-9746>),
  Jacob Nearing [aut]
Maintainer: William Nickols <willnickols@g.harvard.edu>
Built: R 4.6.0; ; 2026-01-09 21:39:30 UTC; windows
