bio-hi-c-analysis-hic-differential
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-differential --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+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+, statsmodels 0.14+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures 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 Differential Analysis **"Compare Hi-C contacts between my conditions"** → Compute log2 fold-change contact maps, identify statistically significant differential interactions, and visualize changes in 3D genome organization. - Python: `cooltools` for expected values, custom differential analysis with `scipy.stats` Compare Hi-C contact matrices between conditions. ## Required Imports ```python import cooler import cooltools import numpy as np import pandas as pd import matplotlib.pyplot as plt from matplotlib.colors import TwoSlopeNorm from scipy import stats import bioframe ``` ## Load Two Conditions ```python # Load balanced cooler files at same resolution clr1 = cooler.Cooler('condition1.mcool::resoluti
- Version Compatibility
- Required Imports
- Load Two Conditions
- Compute Log2 Fold Change
- Plot Differential Contact Map
- Split View Comparison
- Depth Normalization
- Statistical Testing (Per-Pixel)
- FDR Correction
- Differential at Distance Bins
- Compare Compartment Changes
- Compare TAD Boundaries
- Differential Loop Analysis
- Export Differential Results
What does the bio-hi-c-analysis-hic-differential skill do?
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-differential --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.