OGRE

OGRE computes overlaps between user-defined genomic regions and publicly available genomic annotations to enable systematic analysis of regulatory elements and genomic associations.

Key Features:

• Automated Overlap Calculation: Automates calculation of overlaps between user-defined genomic regions such as genes, SNPs, or sequencing reads and genomic annotations.
• Comprehensive Data Mining: Mines publicly available genomic databases to gather annotations for overlap analysis.
• Visualization and Result Tables: Generates visualizations and result tables summarizing locations, types, and counts of overlapping regulatory elements and annotations.
• Reproducibility and Insight Generation: Demonstrated reproducibility in application to recent studies and enabled identification of new genomic associations related to gene regulation.
• Benchmarked Performance: Benchmarked against similar tools for running time and output quality.
• Compatibility with Sequencing Outputs: Functions are designed to be compatible with most genomic sequencing outputs.
• Local Overlap Calculation Scope: Covers local genomic overlap calculation and associated visualization steps.

Scientific Applications:

• Gene Regulation Studies: Associate input regions with regulatory elements to investigate mechanisms of gene regulation.
• Genomic Association Analysis: Analyze overlaps between regions such as SNPs and annotations to study genomic associations and potential disease-related elements.
• Regulatory Element Mapping: Identify the location, type, and number of regulatory elements associated with input regions.

Methodology:

Automated overlap calculation between user-defined regions and public genomic annotations, mining publicly available databases for annotations, and generating visualizations and result tables.