annoLinker

annoLinker annotates genomic peaks using DNA interaction data by constructing interaction networks with igraph, where peaks overlapping any node in a connected subgraph are annotated with all genes in that subgraph.

Key Features:

• Network-based annotation: Constructs interaction networks with igraph to connect genomic peaks to genes through chromatin interaction links.
• Connected subgraph annotation: Peaks overlapping any node in a connected subgraph receive annotation with all genes in that subgraph.
• Network graph visualization: Annotation evidence can be visualized as a network graph.
• Genomic track visualization: Annotation evidence can be visualized as a genomic track integrated with gene annotation information.

Scientific Applications:

• Genomic peak annotation: Fast annotation of genomic regions using DNA interaction data and chromatin interaction links.

Methodology:

Constructs interaction networks with igraph; peaks overlapping any node in a connected subgraph are annotated with all genes in that subgraph.