STAMP

STAMP performs statistical analysis of metagenomic taxonomic and functional profiles to identify differences in microbial community composition and function.

Key Features:

• Profile support: Accepts taxonomic profiles (marker gene abundances across taxonomic units) and functional profiles (sequences assigned to biological subsystems or pathways).
• Statistical hypothesis testing: Performs hypothesis tests for pairwise comparisons and multi-group comparisons organized into multiple treatment categories.
• Effect sizes and confidence intervals: Calculates effect sizes and confidence intervals to evaluate biological relevance alongside statistical significance.
• Exploratory plots: Generates exploratory plot types to visualize patterns and trends within metagenomic datasets.

Scientific Applications:

• Comparative community analysis: Compare microbial community composition across different environments or experimental conditions.
• Functional profiling: Detect shifts in functional potential by comparing subsystem or pathway abundance between samples or groups.
• Treatment impact assessment: Assess the impact of treatments on microbial diversity and functional profiles.

Methodology:

Performs statistical hypothesis testing on metagenomic profiles, computes effect sizes and confidence intervals, and generates exploratory visualizations of taxonomic and functional abundance data.