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
1 maintainer
Metadata
1 maintainer
Release files for hca-anndata-mcp 0.8.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| hca_anndata_mcp-0.8.1.tar.gz | 31.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| hca_anndata_mcp-0.8.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 49.3 kB
Release files / hca_anndata_mcp-0.8.1.tar.gz
| Download URL | hca_anndata_mcp-0.8.1.tar.gz |
|---|---|
| Size | 31.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Transparency logRelease files / hca_anndata_mcp-0.8.1-py3-none-any.whl
| Download URL | hca_anndata_mcp-0.8.1-py3-none-any.whl |
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| Size | 17.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
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