DESCRIPTION

Type: Package
Package: zAMPExplorer
Title: A Versatile Shiny App for Microbiota Profiling in Clinical
    Microbiology
Version: 0.1.0
Authors@R: c(
    person("Sedreh", "Nassirnia", , "Sedreh.Nassirnia@chuv.ch", role = c("aut", "cre"),
    comment = c(ORCID = "0009-0008-7012-6983")),
    person("Violeta", "Castelo-Szekely", role = "aut"),
    person("Farid", "Chaabane", role = "aut"),
    person("Valentin", "Scherz", role = "aut"),
    person("Trestan", "Pillonel", role = "aut"),
    person("Gilbert", "Greub", role = "aut"),
    person("Claire", "Bertelli", role = "aut")
  )
Description: A Shiny web application offering a user-friendly, accessible,
    and reproducible platform for downstream analysis of 16S rRNA-based
    metagenomics data.  Key features include quality control
    visualizations (e.g., rarefaction curves), community composition
    plots, and statistical analyses for alpha- and beta-diversity.  The
    app integrates advanced features like community typing with Dirichlet
    multinomial modeling (DMM) and metadata-driven redundancy analysis
    (RDA) to explore microbial associations with clinical and experimental
    variables.
License: GPL-3
URL: https://github.com/metagenlab/zAMPExplorer
BugReports: https://github.com/metagenlab/zAMPExplorer/issues
SystemRequirements: microViz (install separately from R-universe or GitHub; see INSTALL file)
Imports: 
    dplyr,
    DT,
    forcats,
    reshape2,
    ggplot2,
    ggvenn,
    golem,
    graphics,
    grDevices,
    magrittr,
    microbiome,
    MicrobiotaProcess,
    phyloseq,
    shiny,
    shinydashboard,
    shinyFiles,
    shinyWidgets,
    stats,
    tidyr,
    UpSetR,
    utils,
    vegan,
    writexl,
    fs,
    scales,
    RColorBrewer,
    plotly,
    gridExtra,
    tibble,
    htmlwidgets,
    ComplexHeatmap,
    InteractiveComplexHeatmap
Depends:
    microViz,
    DirichletMultinomial,
    Maaslin2
Suggests: 
    config,
    spelling,
    webshot,
    ggside,
    grid,
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    shinytest2
biocViews: ShinyApps, StatisticalMethod, Metagenomics, Visualization, Sequencing, Microbiome
Config/ci-settings: lint_free: true
Config/ci-tools: testthat
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr