Package: karioCaS
Title: Kraken Confidence Scores for Reliable Domain-Specific Microbiota
        Inference and Discovery
Version: 0.99.16
Authors@R: c(
    person("Thiago", "Parente", , email = "thiago.parente@fiocruz.br", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7501-726X")),
    person("Fiocruz", role = "fnd"),
    person("IOC-Fiocruz", role = "fnd"),
    person("CAPES", role = "fnd"))
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)
Depends: R (>= 4.5.0)
Encoding: UTF-8
RoxygenNote: 8.1.0
Imports: ggplot2, patchwork, UpSetR, dplyr, readr, stringr, tidyr,
        scales, ggtext, SummarizedExperiment, TreeSummarizedExperiment,
        S4Vectors, forcats, tibble, methods, rlang, grid, grDevices,
        stats, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Metagenomics, Microbiome, DataImport, Software
URL: https://github.com/thiagoparentefiocruz/karioCaS
BugReports: https://github.com/thiagoparentefiocruz/karioCaS/issues
git_url: https://git.bioconductor.org/packages/karioCaS
git_branch: devel
git_last_commit: f2bbabd
git_last_commit_date: 2026-09-28
Repository: Bioconductor 3.24
Date/Publication: 2026-10-14
NeedsCompilation: no
Packaged: 2026-10-14 22:31:55 UTC; biocbuild
Author: Thiago Parente [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7501-726X>),
  Fiocruz [fnd],
  IOC-Fiocruz [fnd],
  CAPES [fnd]
Maintainer: Thiago Parente <thiago.parente@fiocruz.br>
