How do I install the Glebis Genome Toolkit Genome Toolkit skill?

Run npx skillmds@latest add tomevault-io/glebis-genome-toolkit-genome-toolkit in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Glebis Genome Toolkit Genome Toolkit skill do?

Genome Analytics It is listed under Data & Analytics on SkillMD.

Is Glebis Genome Toolkit Genome Toolkit safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Glebis Genome Toolkit Genome Toolkit?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Glebis Genome Toolkit Genome Toolkit free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Glebis Genome Toolkit Genome Toolkit?

tomevault-io (@tomevault-io) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Glebis Genome Toolkit Genome Toolkit by tomevault-io

Name: Glebis Genome Toolkit Genome Toolkit
Author: tomevault-io

File contents

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

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

Source: glebis/genome-toolkit — distributed by TomeVault.

---name: glebis-genome-toolkit-genome-toolkitdescription: Genome Analytics---# Genome AnalyticsRun 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```bashpython3 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```bashpython3 scripts/analytics/snp_enrich.py --rsid rs4680python3 scripts/analytics/snp_enrich.py --gene CYP2D6```Queries SNPedia, ClinVar, MyVariant, gnomAD. Respects rate limits from config.### Vault Quality Audit```bashpython3 scripts/analytics/gap_audit.pypython3 scripts/analytics/consistency_checker.pypython3 scripts/analytics/vault_graph_analysis.pypython3 scripts/analytics/evidence_tier_analyzer.pypython3 scripts/analytics/claim_density.pypython3 scripts/analytics/intervention_matrix.py```Checks: schema compliance, link integrity, evidence quality, staleness, claim density.### Literature Monitoring```bashpython3 scripts/analytics/pubmed_monitor.py --months 6```Scans PubMed for new publications on genes in the vault.### Biomarker Analysis```bashpython3 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## Workflow1. 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 results5. 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).

Frequently asked questions

Glebis Genome Toolkit Genome Toolkit