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 0.8.2
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-0.8.2.tar.gz | 32.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| hca_anndata_mcp-0.8.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 49.5 kB
Release files / hca_anndata_mcp-0.8.2.tar.gz
| Download URL | hca_anndata_mcp-0.8.2.tar.gz |
|---|---|
| Size | 32.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
109a61663ece4721105d7dbfc2387b490b81c64cd0dd7cc546e4f4f227404447
|
|
BLAKE2b-256 checksum How to use checksums |
bd2da7dd5f16fa67936f00bbefdca64ac48ba994d4f3641c78d34ed8007a1eb8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 30, 2026.
Transparency logRelease files / hca_anndata_mcp-0.8.2-py3-none-any.whl
| Download URL | hca_anndata_mcp-0.8.2-py3-none-any.whl |
|---|---|
| Size | 17.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
c87cfa67a2daab40977bf4ebba6a81f4cba20a76275c3fc51dfe451960bafb2a
|
|
BLAKE2b-256 checksum How to use checksums |
40797b9b052451f6ebb3ff1e18802d70410f2bd46162a537ed3443549090256c
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 30, 2026.
Transparency log
