Package: LegATo
Title: LegATo: Longitudinal mEtaGenomic Analysis Toolkit
Version: 1.6.0
Authors@R: c(
    person("Aubrey", "Odom", , "aodom@bu.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7113-7598")),
    person("Yilong", "Zhang", , "elong0527@gmail.com", role = "ctb",
           comment = "Author of NMIT functions"),
    person("Jared", "Pincus", , "pincus@bu.edu", role = "csl",
           comment = c(ORCID = "0000-0001-6708-5262", other = "Naming consultant of package")),
    person("Jordan", "Pincus", , "pincus@bu.edu", role = "art",
           comment = "Artist of LegATo icon")
  )
Description: LegATo is a suite of open-source software tools for
        longitudinal microbiome analysis. It is extendable to several
        different study forms with optimal ease-of-use for researchers.
        Microbiome time-series data presents distinct challenges
        including complex covariate dependencies and variety of
        longitudinal study designs. This toolkit will allow researchers
        to determine which microbial taxa are affected over time by
        perturbations such as onset of disease or lifestyle choices,
        and to predict the effects of these perturbations over time,
        including changes in composition or stability of commensal
        bacteria.
License: MIT + file LICENSE
URL: https://wejlab.github.io/LegATo-docs/
BugReports: https://github.com/wejlab/LegATo/issues
Depends: R (>= 4.4.0)
Imports: animalcules, data.table, dplyr, ggplot2, magrittr,
        MultiAssayExperiment, plyr, rlang, S4Vectors, stringr,
        SummarizedExperiment, tibble, tidyr, tidyselect
Suggests: BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap,
        emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr,
        lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling,
        TBSignatureProfiler, testthat (>= 3.0.0),
        TreeSummarizedExperiment, usethis, vegan
VignetteBuilder: knitr
BiocType: Software
biocViews: MicrobiomeData, ReproducibleResearch, SequencingData
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev make
        libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3
        zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:37:40 UTC
RemoteUrl: https://github.com/bioc/LegATo
RemoteRef: RELEASE_3_23
RemoteSha: b9eabb97ebf21b1d9ef6a2ca7412a4a2ae86a811
NeedsCompilation: no
Packaged: 2026-10-10 11:20:37 UTC; root
Author: Aubrey Odom [aut, cre] (ORCID: <https://orcid.org/0000-0001-7113-7598>),
  Yilong Zhang [ctb] (Author of NMIT functions),
  Jared Pincus [csl] (ORCID: <https://orcid.org/0000-0001-6708-5262>,
    other: Naming consultant of package),
  Jordan Pincus [art] (Artist of LegATo icon)
Maintainer: Aubrey Odom <aodom@bu.edu>