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
Config/pak/sysreqs: cmake make libicu-dev libjpeg-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-28 19:20:14 UTC
RemoteUrl: https://github.com/BiocStaging/karioCaS
RemoteRef: HEAD
RemoteSha: f2bbabd144ef4c6428e1c42253f83231c592ce6c
NeedsCompilation: no
Packaged: 2026-09-28 22:20:32 UTC; root
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>