hi-c-analysis

Overview

Analyze Hi-C and chromosome conformation capture data using cooler, cooltools, pairtools, and HiCExplorer.

Tool type: mixed | Primary tools: cooler, cooltools, pairtools, HiCExplorer

Skills

Skill	Description
hic-data-io	Load, convert, and manipulate Hi-C matrices in cooler format
contact-pairs	Process Hi-C read pairs with pairtools
matrix-operations	Balance, normalize, and transform contact matrices
compartment-analysis	Detect A/B compartments from Hi-C data
tad-detection	Call topologically associating domains (TADs)
loop-calling	Detect chromatin loops and point interactions
hic-visualization	Visualize contact matrices and genomic features
hic-differential	Compare Hi-C between conditions, differential contacts

Example Prompts

• "Load my Hi-C contact matrix"
• "Convert .hic to cooler format"
• "Process Hi-C read pairs with pairtools"
• "Balance my Hi-C matrix"
• "Call compartments from my Hi-C data"
• "Detect TADs in my contact matrix"
• "Find chromatin loops"
• "Plot a Hi-C contact matrix"
• "Show interactions around this gene"
• "Compare Hi-C matrices between conditions"
• "Find differential contacts between treatment and control"
• "Identify compartment switches between conditions"

Requirements

# Python tools
pip install cooler cooltools bioframe matplotlib

# CLI tools (via conda)
conda install -c bioconda pairtools hicexplorer fanc

Related Skills

• genome-intervals - Work with genomic coordinates
• chip-seq - Integrate with ChIP-seq peaks
• atac-seq - Integrate with accessibility data