bio-clinical-databases-polygenic-risk
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-polygenic-risk --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: LDpred2 1.14+, PRSice-2 2.3+, numpy 1.26+, 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 - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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. # Polygenic Risk Scores **"Calculate polygenic risk scores for my cohort"** → Compute genome-wide risk scores from GWAS summary statistics and individual genotypes to predict disease susceptibility. - CLI: `PRSice_linux --base gwas.txt --target genotypes --out prs_results` - R: `bigsnpr::snp_ldpred2_auto()` for LDpred2 Bayesian PRS ## PRSice-2 Workflow **Goal:** Calculate polygenic risk scores from GWAS summary statistics using clumping and thresholding. **Approach:** Run PRSice-2 with GWAS summary stats and target genotypes, applying LD clumping and multiple p-value thresholds. ### Basic PRS Calculation ```bash # PRSice-2
- Version Compatibility
- PRSice-2 Workflow
- Basic PRS Calculation
- PRSice-2 with Covariates
- GWAS Summary Statistics Format
- LDpred2 (R)
- Setup and Run
- LDpred2 Grid Model
- PRS-CS
- Score Normalization
- Risk Stratification
- PGS Catalog Integration
- Validation Metrics
- Related Skills
PRSice-2 with clumping and thresholding PRSice_linux \ PRS-CS with external LD reference python PRScs.py \ Score with plink plink --bfile target \
What does the bio-clinical-databases-polygenic-risk skill do?
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-polygenic-risk --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.