bio-tumor-fraction-estimation
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid biopsy or monitoring treatment response.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tumor-fraction-estimation --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: CNVkit 0.9+, ichorCNA 0.5+, 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 - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Tumor Fraction Estimation **"Estimate tumor fraction from my cfDNA data"** → Calculate the proportion of tumor-derived DNA in a liquid biopsy sample using copy number aberrations from shallow whole-genome sequencing. - R: `ichorCNA` for tumor fraction and CNA estimation from sWGS Estimate ctDNA tumor fraction from shallow whole-genome sequencing. ## ichorCNA Overview ichorCNA (GavinHaLab fork, v0.5.1+) detects copy number alterations and estimates tumor fraction from sWGS (0.1-1x coverage). **Sensitivity:** 97-100% detection at >= 3% tumor fraction (2024 validation) ## Input Requirements | Requirement | Specification | |-------------|---------------| | Data type | sWGS (NOT targeted panel) | | Cove
- Version Compatibility
- ichorCNA Overview
- Input Requirements
- Running ichorCNA
- Batch Processing
- Parsing Results
- Python Wrapper
- Interpretation
- Related Skills
What does the bio-tumor-fraction-estimation skill do?
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid biopsy or monitoring treatment response.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tumor-fraction-estimation --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.