locus-to-gene-mapper-skill — Codex skill: setup and features
Maps GWAS loci to ranked candidate genes through linked genomics databases. Helpful for variant prioritization starting from phenotype queries or seed rsIDs.
npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a codexWhat locus-to-gene-mapper-skill does
The skill evaluates genetic loci against candidate genes by querying ontologies and functional genomics sources in sequence. It handles trait terms, EFO identifiers, and rsID lists, querying databases like GWAS Catalog, Open Targets, GTEx, and ClinVar. The runner generates structured outputs. Results are saved directly into locus_to_gene_mapping.json and a Markdown summary report.
Processing is handled by scripts/map_locus_to_gene.py. You need an environment with Python 3.11 or higher and the requests package. Optional figure rendering needs pandas, matplotlib, and seaborn. Without Python 3.11 and requests, execution halts immediately.
What it helps with
- prioritize candidate genes from GWAS summary statistics
- aggregate evidence across GTEx, ClinVar, and Open Targets
- normalize variant rsIDs to GRCh37 and GRCh38 placements
- export structured mapping JSON and Markdown summaries
Example prompts for the agent
- Map candidate genes for trait
type 2 diabetes - Prioritize loci for EFO identifier
EFO_0000341 - Run mapping for seed variants
rs1873625andrs7903146
How to install locus-to-gene-mapper-skill
1Skills CLI (Vercel)
npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a codex2Manually: put the files in place
.agents/skills/locus-to-gene-mapper-skill/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a claude-code2Manually: put the files in place
~/.claude/skills/locus-to-gene-mapper-skill/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/locus-to-gene-mapper-skill/
Manually: put the files in place
.cursor/skills/locus-to-gene-mapper-skill/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install openai/plugins locus-to-gene-mapper-skill2Manually: put the files in place
.github/skills/locus-to-gene-mapper-skill/SKILL.mdPlatform CLI
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/locus-to-gene-mapper-skillManually: put the files in place
.devin/skills/locus-to-gene-mapper-skill/SKILL.mdThe legacy .windsurf/skills/ path still works
Claude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: Codex skills: how to install, where they live, how to call them
Questions about locus-to-gene-mapper-skill
How do I install locus-to-gene-mapper-skill in Codex?
Run npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a codex in your terminal.
What does locus-to-gene-mapper-skill do?
It maps genetic association signals to potential causal genes by aggregating evidence from multiple genomics databases.
What packages are needed for figure rendering?
Generating plots requires pandas, matplotlib, and seaborn installed in your Python environment.
