BiocNeighbors

DOI: 10.18129/B9.bioc.BiocNeighbors    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BiocNeighbors.

Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: 3.13

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 gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocNeighbors")

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

Documentation

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

browseVignettes("BiocNeighbors")

 

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

Details

biocViews	Classification, Clustering, Software
Version	1.10.0
In Bioconductor since	BioC 3.8 (R-3.5) (3 years)
License	GPL-3
Depends
Imports	Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
LinkingTo	Rcpp, RcppHNSW
Suggests	testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW
SystemRequirements	C++11
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.workflows
Imports Me	batchelor, bluster, CellMixS, cydar, CytoTree, miloR, mumosa, scater, scDblFinder, SingleR
Suggests Me	TrajectoryUtils, TSCAN
Links To Me
Build Report

Package Archives

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

Source Package	BiocNeighbors_1.10.0.tar.gz
Windows Binary	BiocNeighbors_1.10.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	BiocNeighbors_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocNeighbors
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocNeighbors
Package Short Url	https://bioconductor.org/packages/BiocNeighbors/
Package Downloads Report	Download Stats