CHiCANE

CHiCANE analyzes Capture Hi-C (CHi-C), including region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C), to identify regulatory chromatin interactions and support interpretation of spatial genome organization.

Key Features:

• Data Processing: Processes Capture Hi-C data from rCHi-C and pCHi-C libraries and harmonizes disparate input/output formats for analysis.
• Interaction Calling: Identifies regulatory chromatin interactions, including distal contacts mediated by risk loci.
• Quality Assessment: Performs quality assessment of interaction peaks to evaluate reliability of detected contacts.
• Downstream Analysis: Supports downstream analyses specific to rCHi-C and pCHi-C libraries to facilitate functional interpretation of interactions.

Scientific Applications:

• Spatial Genome Organization: Enables analysis of chromatin architecture from CHi-C datasets to study three-dimensional genome organization.
• Gene Regulation: Facilitates mapping of regulatory interactions to investigate mechanisms underlying gene expression regulation.
• Risk Locus Interpretation: Supports linking risk loci to target genes to identify potential genetic risk factors associated with disease.

Methodology:

Integrates data processing and interaction calling into a cohesive protocol, standardizes input/output formats, and employs statistical modeling assumptions for interaction detection.