Package: karioCaS 0.99.15

karioCaS: Kraken Confidence Scores for Reliable Domain-Specific Microbiota Inference and Discovery

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.

Authors:Thiago Parente [aut, cre], Fiocruz [fnd], IOC-Fiocruz [fnd], CAPES [fnd]