Run any Skill in Manus with one click

genome-analytics

Stars39

Forks2

UpdatedMarch 29, 2026 at 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".

Installation

Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.

Run Skill in Manus

Source

glebis

glebis/genome-toolkit

View GitHub Repository View Creator Repositories

Download

Run Skill in Manus

Related occupationsSOC

Based on SOC occupation classification

Software DevelopersComputer and Mathematical Occupations·SOC 15-1252

File Explorer

2 files

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

More from this repository

same 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