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].

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