cell-neighbors

Neighbor graphs for single-cell data (AnnData)

This repository provides a Python package for building k-nearest neighbor (kNN) graphs from AnnData objects.

The package is built on the Voyager library from Spotify.

Features

• Efficient kNN Graph Construction from Voyager.
• Direct AnnData integration
• Flexible querying of neighbors in the constructed kNN graph index.

Installation

Install the latest release from PyPI:

pip install cell-neighbors

or, if you use uv:

uv pip install cell-neighbors
# or, to add it to your pyproject.toml
uv add cell-neighbors

Example

import cell_neighbors

# Initialize kNN graph builder
knn_graph = cell_neighbors.kNN(adata), use_key="X_pca")

# Query neighbors
X_query = [...]  # Your query points as numpy array
neighbors = knn_graph.query(X_query)

Documentation

For real examples, detailed usage instructions, and API reference, please refer to the documentation [coming soon].