PathoStat

PathoStat performs statistical analysis of microbiome data from metagenomic sequencing by leveraging PathoScope-generated report files to quantify taxa, assess diversity, detect differential abundance, and analyze temporal and core OTU patterns.

Key Features:

• PathoScope report integration: Parses and uses PathoScope-generated report files from metagenomic sequencing as input for downstream analyses.
• Relative Abundance Charts: Generates visualizations of relative taxonomic abundances across samples.
• Diversity Estimates and Plots: Computes and plots diversity indices, including richness and evenness, for comparing microbial biodiversity across datasets.
• Tests of Differential Abundance: Implements statistical tests to identify taxa with significant abundance differences between groups or conditions.
• Time Series Visualization: Visualizes longitudinal changes in microbial community composition over time.
• Core OTU Analysis: Identifies and analyzes core Operational Taxonomic Units (OTUs) consistently present across samples or conditions.

Scientific Applications:

• Microbiome studies in health and disease: Analyzes microbial community composition and associations with host physiology and disease states.
• Environmental microbiology: Assesses microbiome responses to environmental changes.
• Longitudinal studies: Supports analysis of temporal microbial dynamics in time series data.
• Microbial ecology and keystone taxa identification: Investigates microbial ecology and identifies stable or keystone taxa via core OTU analysis.

Methodology:

Implemented in R within the Bioconductor framework, with formal initial review and continuous automated testing.