bio-clinical-databases-polygenic-risk

npx skills add BioTender-max/awesome-bio-agent-skills --skill polygenic-risk --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: bigsnpr 1.12+ (LDpred2; Privé 2020), PRSice-2 2.3.5+, PRS-CS 1.0.0+ (Ge 2019), gctb 2.5+ (SBayesR/SBayesS/SBayesRC; Zheng 2024), LDAK 6.0+ (MegaPRS; Zhang 2021), pgsc_calc 2.0+ (nf-core; Lambert 2024), Hail 0.2.130+, numpy 1.26+, pandas 2.2+. No general FDA PRS guidance document exists as of May 2026; the operative regulatory text is the August 2025 Federal Register notice on Cancer Predisposition Risk Assessment Systems (Class II device with special controls). 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` - 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. The LDpred2-auto `snp_ldpred2_auto()` signature changed in bigsnpr 1.11+; pin `allow_jump_sign = FALSE` and `shrink_corr = 0.95` explicitly. # Polygenic Risk Scores; Construction, Calibration, Reporting **'Compute a PRS for my cohort using

gctb \
plink2 --bfile target \
Calculate multiple PGS for cohort
nextflow run pgscatalog/pgsc_calc \
python PRScsx.py \
Score each ancestry-specific posterior, then combine on tuning set
for pop in EUR AFR EAS; do
done
bivariate LDSC for sample overlap
ldsc.py \