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bio-hi-c-analysis-matrix-operations

Maintainer FreedomIntelligence · Last updated April 1, 2026

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

OpenClawNanoClawAnalysisReproductionbio-hi-c-analysis-matrix-operations🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinbalance

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: cooler.balance_cooler(clr), cooltools.expected_cis(clr).
Normalize my Hi-C contact matrix" → Apply iterative correction (ICE/KR balancing), compute distance-decay expected values, and generate observed/expected ratio matrices. Python: cooler.balance_cooler(clr), cooltools.expected_cis(clr).
Balance, normalize, and transform contact matrices.
cooler.balance_cooler('matrix.cool', store=True, cis_only=True).

Source Doc

Excerpt From SKILL.md

The balanced weights are stored in the 'weight' column

clr = cooler.Cooler('matrix.cool') weights = clr.bins()['weight'][:] print(f'Balanced weights range: {weights.min():.4f} - {weights.max():.4f}')


## Balance using cooler CLI

cooler balance matrix.cool --cis-only --force

## Check balance status

cooler info matrix.cool | grep "weight"

Use cases

Use when normalizing or transforming Hi-C matrices.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

hic-data-io - Load and access cooler files
compartment-analysis - Use O/E matrices for compartments
hic-visualization - Visualize processed matrices

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