| name | genome-analytics |
| description | Run analysis scripts: PRS, enrichment, vault audit, PubMed monitoring, consistency checks.
Triggers on: /genome-analytics, "run PRS", "audit vault", "check PubMed",
"run enrichment", "check consistency", "analyze pathway".
|
Genome Analytics
Run analysis and quality assurance scripts on the genome vault.
Vault Configuration
- Database:
data/genome.db
- Scripts:
scripts/analytics/
- Output:
data/output/
Available Analyses
Risk Scores
python3 scripts/analytics/prs_calculator.py --details
Calculates Polygenic Risk Scores for: GAD/Anxiety, Depression, BMI, CAD, T2D, Ankylosing Spondylitis.
Uses scripts/data/prs_snp_weights.json for effect sizes.
Enrichment
python3 scripts/analytics/snp_enrich.py --rsid rs4680
python3 scripts/analytics/snp_enrich.py --gene CYP2D6
Queries SNPedia, ClinVar, MyVariant, gnomAD. Respects rate limits from config.
Vault Quality Audit
python3 scripts/analytics/gap_audit.py
python3 scripts/analytics/consistency_checker.py
python3 scripts/analytics/vault_graph_analysis.py
python3 scripts/analytics/evidence_tier_analyzer.py
python3 scripts/analytics/claim_density.py
python3 scripts/analytics/intervention_matrix.py
Checks: schema compliance, link integrity, evidence quality, staleness, claim density.
Literature Monitoring
python3 scripts/analytics/pubmed_monitor.py --months 6
Scans PubMed for new publications on genes in the vault.
Biomarker Analysis
python3 scripts/analytics/biomarker_analyzer.py
Trend analysis across lab results, comparison against genetic predictions.
Specialized
ld_analysis.py — Linkage disequilibrium between vault variantspathway_enrichment.py — KEGG/Reactome pathway analysiseffect_size_aggregator.py — Audit effect sizes vs published dataprediction_tracker.py — Track genetic prediction accuracy
Workflow
- Ask user what analysis they need (or detect from context)
- Check prerequisites (database populated, relevant notes exist)
- Run appropriate script(s)
- Summarize results
- Suggest follow-up actions (create notes, update reports, research)
Output
- Analysis results (console + text/markdown reports in
data/output/)
- Recommendations for vault updates
- Flags for human review
