linkSet

linkSet provides a comprehensive framework for representing, analyzing, and visualizing genomic interactions, particularly focusing on gene-enhancer relationships.

Key Features:

• Genomic Interaction Representation: Extends the GenomicRanges infrastructure to handle paired genomic regions with specialized methods for chromatin interaction data.
• Data Format Conversion: Converts from common interaction formats.
• Genomic Annotation: Annotates promoters and enhancers.
• Distance-Based Analyses: Performs distance-based analyses on genomic interactions.
• Interaction Strength Metrics: Computes interaction strength metrics.
• Statistical Modeling: Implements statistical modeling using CHiCANE methodology.
• Visualization: Provides tailored visualization tools for genomic interaction data.

Scientific Applications:

• Hi-C Data Analysis: Analyzes chromatin interaction data from Hi-C experiments.
• Promoter Capture Hi-C Analysis: Analyzes chromatin interaction data from PCHi-C experiments.
• Single-Cell ATAC-seq Analysis: Analyzes chromatin interaction data from single-cell ATAC-seq experiments.
• Gene-Enhancer Relationship Studies: Investigates gene-enhancer relationships through genomic interaction analysis.

Methodology:

Extends GenomicRanges infrastructure for paired genomic regions; uses CHiCANE methodology for statistical modeling.