MCP server for interactive exploration of AnnData h5ad files

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  • License: MIT License (MIT)
  • Author: Clever Canary
  • Requires: Python <4.0, >=3.10
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Project description

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

Project details

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  • License: MIT License (MIT)
  • Author: Clever Canary
  • Requires: Python <4.0, >=3.10
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0.5.0

0.4.1

0.3.0

0.2.0

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