jvecfor: Fast K-Nearest Neighbor Search for Single-Cell Analysis

Drop-in replacement for BiocNeighbors::findKNN using the jvecfor Java library (HNSW-DiskANN approximate and VP-tree exact methods). Achieves approximately 2x speedup over Annoy-based search at n >= 50K cells. Convenience wrappers delegate SNN/KNN graph construction to the bluster package.

Main functions

fastFindKNN

KNN search – returns index + distance matrices.

fastMakeSNNGraph

KNN -> SNN graph via bluster.

fastMakeKNNGraph

KNN -> KNN graph via bluster.

JvecforParam

BiocNeighbors parameter class for drop-in integration with scran, scater, etc.

jvecfor_setup

Install a custom jvecfor JAR.

Options

jvecfor.verbose

Logical. Enable Java/jvecfor progress logging globally. Default FALSE.

jvecfor.jar

Character. Path to a custom jvecfor JAR file. Overrides the bundled JAR in inst/java/.

See also

Useful links:

• https://github.com/gkanogiannis/jvecfor

• Report bugs at https://github.com/gkanogiannis/jvecfor/issues

Author

Maintainer: Anestis Gkanogiannis anestis@gkanogiannis.com (ORCID)