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Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: Release (3.19)

Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.

Author: Aaron Lun [aut, cre, cph]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at>

Citation (from within R, enter citation("BiocNeighbors")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Detecting exact nearest neighbors HTML R Script
2. Detecting approximate nearest neighbors HTML R Script
3. Detecting neighbors within range HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, Software
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Imports Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
System Requirements C++11
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW
Linking To Rcpp, RcppHNSW
Depends On Me OSCA.advanced, OSCA.workflows, SingleRBook
Imports Me batchelor, bluster, CellMixS, cydar, GeDi, imcRtools, lemur, miloR, mumosa, scater, scDblFinder, scMerge, SpatialFeatureExperiment, SpotSweeper, UCell
Suggests Me concordexR, TrajectoryUtils, TSCAN
Links To Me SingleR
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BiocNeighbors_1.22.0.tar.gz
Windows Binary
macOS Binary (x86_64) BiocNeighbors_1.22.0.tgz
macOS Binary (arm64) BiocNeighbors_1.22.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Package Short Url
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