Package: karioCaS
Title: Kraken Confidence Scores for Reliable Domain-Specific Microbiota
        Inference and Discovery
Version: 0.99.0
Authors@R: 
    person("Thiago", "Parente", , email = "thiago.parente@fiocruz.br", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7501-726X"))
Description: Provides a comprehensive framework for analyzing Kraken2 metagenomic 
    classification using multiple confidence scores. karioCaS implements a 
    robust comparative approach to evaluate taxonomic stability across different 
    stringency levels, facilitating the identification of reliable microbiota 
    components and the discovery of potentially novel or unrepresented species. 
    A key innovation is its domain-specific analysis, separately processing 
    Bacteria, Archaea, Eukaryota, and Viruses to ensure balanced visibility 
    of all biological domains. Includes high-quality visualization tools for 
    retention rates, shared taxa (Upset plots), and stability heatmaps.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports: ggplot2, patchwork, UpSetR, dplyr, readr, stringr, tidyr,
        purrr, scales, ggtext, SummarizedExperiment,
        TreeSummarizedExperiment, S4Vectors, forcats, fs, tibble,
        methods, rlang
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Metagenomics, Microbiome, Software
URL: https://github.com/thiagoparentefiocruz/karioCaS
BugReports: https://github.com/thiagoparentefiocruz/karioCaS/issues
NeedsCompilation: no
Packaged: 2026-05-18 18:05:38 UTC; pkgbuild
Author: Thiago Parente [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7501-726X>)
Maintainer: Thiago Parente <thiago.parente@fiocruz.br>
