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genome-analytics

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Aktualisiert29. März 2026 um 13:05

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".

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glebis

glebis/genome-toolkit

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Verwandte BerufeSOC

Basierend auf der SOC-Berufsklassifikation

SoftwareentwicklerInformatik- und Mathematikberufe·SOC 15-1252

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2 Dateien

SKILL.md

readonly

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

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

Mehr aus diesem Repository

gleiches Repository

genome-import

glebis/genome-toolkit

Universal genome data import supporting 23andMe v4/v5, AncestryDNA, MyHeritage, Nebula, and generic VCF. Also handles imputation prep and post-imputation import. Triggers on: /genome-import, "import my DNA data", "add raw file", "prepare for imputation", "import imputed data".

2026-04-1539

genome-onboard

glebis/genome-toolkit

Goal-driven onboarding for new genome vault users. Triggers on: /genome-onboard, "set up my vault", "I just imported my data", "help me get started with my genome". Two modes: --quick (4 questions, fast vault bootstrap) or --full (22-question interview with validated psychological instruments, generates Profile Card + Action Plan).

2026-04-1539

genome-log

glebis/genome-toolkit

Daily health tracking with genetic context: supplements, medications, symptoms, interventions, metrics. Use this skill whenever the user mentions taking supplements, logging symptoms, tracking health, reporting how they feel, or asks about their daily routine. Also triggers on: /genome-log, /log, "daily check-in", "track today", "I took my supplements", "feeling anxious", "my stomach hurts", "forgot my B12", "log symptoms", "how am I doing", "what did I take today". Even casual health mentions like "my nose is stuffed" or "had a rough night" should trigger this skill to offer logging.

2026-04-0239

genome-query

glebis/genome-toolkit

Query Obsidian vault frontmatter with SQL-like syntax. Filter, sort, group, and aggregate notes by any frontmatter field. Replaces Dataview for CLI use. Triggers on: /genome-query, "query vault", "find notes", "list genes", "show protocols", "vault stats", "vault schema", "filter by".

2026-04-0139

genome-validate

glebis/genome-toolkit

Multi-agent validation pipeline for fact-checking claims, verifying evidence tiers, and ensuring prescriber document accuracy. Uses Codex CLI, NotebookLM, PubMed subagents, and Tavily search. Supports: audit (full vault), gene SYMBOL (single gene fact-check), protocol NAME (protocol/report fact-check). Triggers on: /genome-validate, "validate this note", "fact-check", "cross-check claims", "verify evidence", "audit this report", "fact-check gene X", "check protocol X".

2026-04-0139

genome-create

glebis/genome-toolkit

Create gene, system, or phenotype notes from SQLite genotype data and templates. Triggers on: /new-gene SYMBOL, /new-system NAME, "add gene X", "create system note", "create phenotype note for X".

2026-03-2939

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

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