Hi-C A/B Compartment Analysis

About

This skill provides a standardized, automated workflow for identifying A/B compartments from Hi-C data in .mcool, .cool, or .hic formats. It guides the user through the entire process, including genome alignment, chromosome renaming, PCA-based compartment score extraction, and the generation of visualization-ready BigWig tracks and interaction saddle plots. By leveraging specialized MCP tools, it ensures a reproducible and normalized analysis pipeline for studying large-scale chromatin organization and spatial genome architecture.

Key Features

• Automatic generation of interaction saddle plots and compartment distribution PDFs
• Built-in GC content normalization and chromosome-arm view definition
• 2 GitHub stars
• Standardized output of BigWig tracks for genome browser visualization
• Automated PCA-based A/B compartment calling and PC1 score extraction
• Multi-format support for .mcool, .cool, and .hic genomic data files

Use Cases

• Visualizing long-range interaction preferences using saddle plot analysis
• Identifying global chromatin organization patterns from Hi-C contact maps
• Generating normalized compartment tracks for comparative genomic studies