ProOvErlap

ProOvErlap assesses feature proximity and overlap between genomic intervals in BED format and tests their statistical significance using a nonparametric randomization test.

Key Features:

• Proximity and overlap analysis: Quantitatively assesses the degree of proximity or overlap between genomic features represented in BED format.
• Statistical significance testing: Determines whether observed overlap or proximity differs from what would be expected by chance using a nonparametric randomization test.
• Visualization: Generates clear visualizations and publication-quality figures.

Scientific Applications:

• Gene regulation studies: Analyzes spatial relationships between promoters and the genes they regulate.
• Epigenetic studies: Evaluates overlap of regions enriched for specific epigenetic modifications or accessible chromatin to elucidate complex molecular phenotypes.
• Disease state research: Identifies biologically significant interactions between genomic features in healthy and disease states.

Methodology:

ProOvErlap uses a nonparametric randomization test to assess statistical significance of feature proximity and overlap.