lynnlangit/precision-medicine-mcp
Skill Claude CodeCodex
Audits all Markdown files in the precision-medicine-mcp repo against six canonical principles: (A) server Python code is the authoritative tool count, (B) server-registry.md is the authoritative server/tool summary, (C) all three patient outcomes (PAT001/PAT002/PAT003) must be represented consistently, (D) no content…
lynnlangit/precision-medicine-mcp
Instructions file
Instructions for lynnlangit/precision-medicine-mcp, covering claude.md — project context for claude code, git workflow, session management, what this project is and repository structure.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "deidentify" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-deidentify Python package. Needs 2 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "fgbio" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-fgbio Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "spatialtools" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-spatialtools Python package. Needs 4 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "openimagedata" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-openimagedata Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "genomic-results" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-genomic-results Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "mockepic" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-mockepic Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "mocktcga" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-mocktcga Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "multiomics" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-multiomics Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "patient-report" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-patient-report Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "deepcell" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-deepcell Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "cell-classify" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-cell-classify Python package. Needs 2 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "epic" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-epic Python package. Needs 4 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "perturbation" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-perturbation Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "quantum-celltype-fidelity" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-quantum-celltype-fidelity Python package. Needs 3 environment variables to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "geodownload" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-geodownload Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "opentargets" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-opentargets Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "cibersortx" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-cibersortx Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "neoantigen" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-neoantigen Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
MCP server Claude CodeCodexCursor +2
MCP server "cardiometabolic" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-cardiometabolic Python package. Needs 1 environment variable to run.
lynnlangit/precision-medicine-mcp
Skill Claude CodeCodex
Ensures all development meets clinical compliance and security standards. Focuses on HIPAA-friendly logging, audit trails, risk assessment, and scientific nomenclature.
lynnlangit/precision-medicine-mcp
Skill Claude CodeCodex
Guide for managing patient data and bioinformatics datasets (h5ad, CSV). Standardizes data loading, preprocessing, and path management.
lynnlangit/precision-medicine-mcp
Skill Claude CodeCodex
Expert guide for project-specific documentation and clinical reporting. Maintains consistency across persona-based guides and automated reports.