hca-anndata-mcp
MCP server for interactive exploration of AnnData h5ad files.
Usage
# Run the MCP server
hca-anndata-mcp
# Or via poetry
poetry run hca-anndata-mcp
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
1 maintainer
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