bio-hi-c-analysis-tad-detection
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-tad-detection --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. # TAD Detection **"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. ## Required Imports ```python import cooler import cooltools import numpy as np import pandas as pd import matplotlib.pyplot as plt import bioframe ``` ## Compute Insulation Score ```python clr = cooler.Cooler('matrix.mcool::resolutions/10000') view_df = bioframe.make_viewframe(clr.chromsizes) # Compute insulation score insulat
- Version Compatibility
- Required Imports
- Compute Insulation Score
- Call TAD Boundaries
- Extract TAD Regions
- Using HiCExplorer (CLI)
- Using HiCExplorer in Python
- TAD Statistics
- Plot Insulation Score
- Compare TAD Boundaries Between Conditions
- Hierarchical TADs
- Export TADs
- Related Skills
Compute TADs with HiCExplorer hicFindTADs \ Output files: tads_domains.bed - TAD intervals tads_boundaries.bed - Boundary positions tads_score.bedgraph - Insulation score track
What does the bio-hi-c-analysis-tad-detection skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-hi-c-analysis-tad-detection --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.