bio-hi-c-analysis-matrix-operations
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-matrix-operations --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: cooler 0.9+, cooltools 0.6+, numpy 1.26+, pandas 2.2+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Hi-C Matrix Operations **"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. ## Required Imports ```python import cooler import cooltools import numpy as np import pandas as pd ``` ## Matrix Balancing (ICE) ```python # Balance a cooler file (iterative correction) cooler.balance_cooler('matrix.cool', store=True, cis_only=True) # The balanced weights are stored in the 'weight' column clr = cooler.Cooler('matrix.cool') weights = clr.bins()['weigh
- Version Compatibility
- Required Imports
- Matrix Balancing (ICE)
- Balance with CLI
- Access Balanced vs Raw Matrix
- Compute Expected Values
- Observed/Expected Matrix
- Using cooltools for O/E
- Log Transform
- Distance Decay Normalization
- Aggregate Multiple Replicates
- Smooth Matrix
- Downsample/Coarsen Matrix
- Correlation Matrix
Balance using cooler CLI cooler balance matrix.cool --cis-only --force Check balance status cooler info matrix.cool | grep "weight"
What does the bio-hi-c-analysis-matrix-operations skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-matrix-operations --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.