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 Annoy library from Spotify.

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

You can install the package using pip:

pip install cell-neighbors

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)

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