Package: microSTASIS
Title: Microbiota STability ASsessment via Iterative cluStering
Version: 1.11.0
Description: The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis
            of microbiota in a temporal framework by leveraging on iterative 
            clustering. Concretely, the core function uses Hartigan-Wong k-means
            algorithm as many times as possible for stressing out paired samples
            from the same individuals to test if they remain together for 
            multiple numbers of clusters over a whole data set of individuals. 
            Moreover, the package includes multiple functions to subset samples
            from paired times, validate the results or visualize the output.
Authors@R: c(
    person(given = "Pedro",
           family = "Sánchez-Sánchez",
           role = c("aut", "cre"),
           email = "bio.pedro.technology@gmail.com",
           comment = c(ORCID = "0000-0002-4846-1813")),
    person(given = "Alfonso",
           family = "Benítez-Páez",
           role = c("aut"),
           email = "alfbenpa@gmail.com",
           comment = c(ORCID = "0000-0001-5707-4340")))
License: GPL-3
Imports: 
    BiocParallel,
    ggplot2,
    ggside,
    grid,
    rlang,
    stats,
    stringr,
    TreeSummarizedExperiment
Suggests:
    BiocStyle,
    gghighlight,
    knitr,
    rmarkdown,
    methods,
    RefManageR,
    sessioninfo,
    SingleCellExperiment,
    SummarizedExperiment,
    testthat (>= 3.0.0)
biocViews: GeneticVariability, BiomedicalInformatics, Clustering, 
          MultipleComparison, Microbiome
BugReports: https://github.com/BiotechPedro/microSTASIS
URL: https://doi.org/10.1093/bib/bbac055
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
VignetteBuilder: knitr
Depends: 
    R (>= 4.2.0)
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/microSTASIS
git_branch: devel
git_last_commit: bd7c8a4
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
