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Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution
Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.
Bioconductor method adapters for the md-lab substrate. Each adapter wraps one method (limma, fgsea, DESeq2, …) as an MCP tool backed by a small FastAPI-in-Docker container that runs R via rpy2.
Replaces the originally planned playbase-mcp. OmicsPlayground is CC BY-NC-ND (commercial-unsafe); we wrap Bioconductor directly. See md-lab/NOTES.md §3.
v0.1.0 skeleton. Only limma is scaffolded, and its container doesn't exist yet — tool calls return status: "container_unavailable" until the container ships. This repo exists to prove the adapter pattern end-to-end.
Cowork / Codex / Jupyter
↓ MCP tool call: limma(intensity_parquet=..., contrast=..., ...)
methods-mcp (FastMCP, this repo)
↓ HTTP POST /run
method-limma container (FastAPI + rpy2, separate repo)
↓ rpy2
R: limma::eBayes(limma::lmFit(...))
↑ result parquet
methods-mcp
↑ {results_parquet, summary, methods_sentence, provenance}
Caller
Each adapter has four files: manifest.yaml, adapter.py, Dockerfile, README.md. See src/methods_mcp/adapters/limma/ for the reference shape.
| Method | Status | Container |
|---|---|---|
| limma | skeleton | not built |
| fgsea | — | — |
| fisher_ora | — | — |
| DESeq2 | — | — |
| WGCNA | — | — |
| glmnet + RF | — | — |
| survival (coxph) | — | — |
| sva + ComBat | — | — |
Single-cell (Seurat, monocle3, Azimuth) is also in v0.1 scope per interview answers §Q4.
pip install -e ".[dev]"
pytest
# run server
python mcp_server.py # stdio transport
python mcp_server_http.py # HTTP transport, port 7102
Once the pattern holds, any contributor can ship an adapter package: manifest.yaml + adapter.py + Dockerfile + README.md. md-lab methods install <name> fetches from the central YAML index in webwebb56/md-methods-registry. Homebrew-style install-by-fetch, not npm-style auto-resolution.
Добавь это в claude_desktop_config.json и перезапусти Claude Desktop.
{
"mcpServers": {
"methods-mcp": {
"command": "npx",
"args": []
}
}
}