# Glebis Genome Toolkit Genome Toolkit

> Genome Analytics

- Skill: `tomevault-io/glebis-genome-toolkit-genome-toolkit` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/glebis-genome-toolkit-genome-toolkit`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/glebis-genome-toolkit-genome-toolkit/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Data & Analytics
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/glebis-genome-toolkit-genome-toolkit

---


# 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
```bash
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
```bash
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
```bash
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
```bash
python3 scripts/analytics/pubmed_monitor.py --months 6
```
Scans PubMed for new publications on genes in the vault.

### Biomarker Analysis
```bash
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

---
> Source: [glebis/genome-toolkit](https://github.com/glebis/genome-toolkit) — distributed by [TomeVault](https://tomevault.io).
<!-- tomevault:4.0:skill_md:2026-06-18 -->