genome-analytics

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 variants
• pathway_enrichment.py — KEGG/Reactome pathway analysis
• effect_size_aggregator.py — Audit effect sizes vs published data
• prediction_tracker.py — Track genetic prediction accuracy

Workflow

1. Ask user what analysis they need (or detect from context)
2. Check prerequisites (database populated, relevant notes exist)
3. Run appropriate script(s)
4. Summarize results
5. 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