bio-hi-c-analysis-hic-visualization
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-visualization --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+ 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 Visualization **"Plot my Hi-C contact matrix"** → Create triangle heatmaps, virtual 4C profiles, and multi-track figures combining contact maps with genomic annotations. - Python: `matplotlib.pyplot.imshow()` on cooler matrices, `cooltools` for aggregate plots - CLI: `hicPlotMatrix` (HiCExplorer) Visualize Hi-C contact matrices and genomic features. ## Required Imports ```python import cooler import cooltools import cooltools.lib.plotting import numpy as np import matplotlib.pyplot as plt from matplotlib.colors import LogNorm import bioframe ``` ## Basic Contact Matrix Plot ```python clr = cooler.Cooler('matrix.mcool::resolutions/10000') # Get matrix for a region matrix =
- Version Compatibility
- Required Imports
- Basic Contact Matrix Plot
- Triangle (Upper Triangle) Plot
- Plot with TADs
- Plot with Loops
- Compare Two Matrices
- Split View (Upper/Lower Triangle)
- Virtual 4C
- Multi-Track Figure
- Using HiCExplorer Visualization
- Cooltools Pileup Plot
- Related Skills
Plot matrix with HiCExplorer hicPlotMatrix \ Plot with TADs hicPlotTADs \
What does the bio-hi-c-analysis-hic-visualization skill do?
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-hic-visualization --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.