GenomicInteractionNodes

GenomicInteractionNodes imports interactions from bedpe files and defines interaction nodes, the genomic interaction sites with multiple interaction loops that function as binding platforms regulating one or multiple genes, for annotation and downstream validation.

Key Features:

• Interaction Import: Imports genomic interactions from bedpe file format.
• Node Detection: Defines interaction nodes as genomic interaction sites with multiple interaction loops.
• Gene Regulation Annotation: Annotates detected interaction nodes that serve as binding platforms regulating one or multiple genes.

Scientific Applications:

• HiC Data Analysis: Detects interaction nodes from HiC chromatin conformation capture data.
• HiChIP Data Analysis: Detects interaction nodes from HiChIP data.
• HiCAR Data Analysis: Detects interaction nodes from HiCAR data.
• Downstream Validation: Supports annotation of interaction nodes for downstream experimental or computational validation.

Methodology:

The package imports interactions from bedpe files, defines interaction nodes as genomic interaction sites with multiple interaction loops, and annotates the detected nodes.