bio-hi-c-analysis-tad-detection - Call TADs and boundary structures from Hi-C data
Calls topologically associating domains (TADs) and domain boundaries from Hi-C contact matrices using insulation scores and HiCExplorer.
Tags
Updated: 2026-09-18Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Compute Hi-C insulation scores
- Call TAD domain boundaries
- Extract TAD region intervals
- Calculate TAD size statistics
- Plot insulation score tracks
- Compare TAD boundaries across conditions
- Analyze multi-scale hierarchical TADs
- Export TAD regions and boundaries
Inputs
- Hi-C contact matrix files
- Boundary BED files
- Chromosome viewframe annotations
Outputs
- TAD interval BED files
- Boundary position BED files
- Insulation score bedGraph files
- TAD size distribution plots
- Insulation score track plots
Requirements
- Python environment with cooler and cooltools
- HiCExplorer CLI tool
- bioframe, pandas, numpy, matplotlib libraries