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

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Documentation for package ‘karioCaS’ version 0.99.16

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

group_upset	Cross-Sample UpSet: Core vs Unique Taxa per Biological Group (Step 008)
heatmaps_karioCaS	Generate Heatmaps of Taxa Abundance with Extinction Patterns (Step 006)
import_karioCaS	Import Kraken MPA Reports to TreeSummarizedExperiment (Step 001)
kariocas_result	Result of a karioCaS analysis step
print.kariocas_result	Result of a karioCaS analysis step
reads_per_taxa	Read Cutoff Saturation Analysis & Optimal Minimum Reads (Step 003)
retrieve_selected_taxa	Retrieve Selected Taxa with Domain-Specific Thresholds (Step 004)
taxa_resolution	Generate Taxa Resolution Analysis (Step 007)
taxa_retention	Run Confidence Score Retention & Optimization (Step 002)
upset_kariocas	Generate UpSet Plots per Sample and Domain (Step 005)