hca-anndata-mcp

MCP server for interactive exploration of AnnData h5ad files.

Usage

# Run the MCP server
hca-anndata-mcp

Point an MCP client at the venv binary directly, not at a wrapper command:

{
  "mcpServers": {
    "hca-anndata-mcp": {
      "command": "/abs/path/to/packages/hca-anndata-mcp/.venv/bin/hca-anndata-mcp"
    }
  }
}

uv run hca-anndata-mcp (like poetry run before it) does not work here. An MCP client needs a stable executable to spawn, and a wrapper command that resolves and syncs an environment first is not one.

Tools

locate_files — Find all .h5ad files in a directory
get_summary — Structural overview: cell/gene counts, columns, embeddings, layers
get_storage_info — HDF5 compression, chunking, sparse format details
get_descriptive_stats — Descriptive statistics and value counts for obs/var columns
view_data — View slices of any attribute (obs, var, X, obsm, uns, etc.)
plot_embedding — UMAP/PCA scatter plots colored by obs column or gene
get_cap_annotations — Inspect CAP cell annotation metadata, marker genes, rationale

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Source Distribution

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