GenomicInteractions

GenomicInteractions processes, analyzes, and visualizes chromosome conformation capture data, including Hi-C and ChIA-PET, to identify and annotate chromatin interactions and relate them to genomic annotations and gene regulation.

Key Features:

• Data processing and analysis: Handles large genome-wide datasets from chromosome conformation capture techniques and produces interaction-level and feature-set summaries.
• Visualization capabilities: Provides multiple plotting and statistical output methods for representing complex interaction patterns in chromatin data.
• Annotation tools: Annotates genomic features with interaction information to link regulatory elements to interaction partners and genomic context.

Scientific Applications:

• Gene expression regulation: Supports analysis of spatial chromatin organization to investigate regulatory interactions affecting gene expression.
• Cellular differentiation and homeostasis: Enables study of chromatin interaction changes associated with differentiation processes and maintenance of cellular states.

Methodology:

Processes and summarizes Hi-C and ChIA-PET interaction data, integrates interaction datasets with genomic annotations, and generates interaction-level summaries, visualizations, and statistics within the R/Bioconductor environment.