Package: maaslin3
Title: "Refining and extending generalized multivariate linear models
        for meta-omic association discovery"
Year: 2025
Version: 1.0.0
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: 2025-04-16 01:51:20 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: 7584c46
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
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 4.5.0; ; 2025-04-16 14:47:50 UTC; windows
