Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-hi-c-analysis-tad-detection

Maintainer FreedomIntelligence · Last updated April 1, 2026

Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.

OpenClawNanoClawAnalysisReproductionbio-hi-c-analysis-tad-detection🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatincall

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-hi-c-analysis-tad-detection

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: cooltools.insulation(clr, window_bp) then threshold boundary strength.
CLI: hicFindTADs (HiCExplorer).
Call TADs from my Hi-C data" → Identify topologically associating domain boundaries using insulation score minima or other boundary-detection algorithms. Python: cooltools.insulation(clr, window_bp) then threshold boundary strength CLI: hicFindTADs (HiCExplorer).
Call topologically associating domains from Hi-C contact matrices.
insulation = cooltools.insulation( clr, window_bp=[100000, 200000, 500000], # Multiple window sizes ignore_diags=2, ).

Source Doc

Excerpt From SKILL.md

Compute Insulation Score

clr = cooler.Cooler('matrix.mcool::resolutions/10000')
view_df = bioframe.make_viewframe(clr.chromsizes)

## Find boundaries (local minima in insulation score)

boundaries = cooltools.find_insulation(
    clr,
    window_bp=200000,  # Single window
    ignore_diags=2,
    min_dist_bad_bin=0,
)

## Filter significant boundaries

boundaries['is_boundary'] = boundaries['boundary_strength'] > 0.1
strong_boundaries = boundaries[boundaries['is_boundary']]
print(f'Found {len(strong_boundaries)} TAD boundaries')