BiocNeighbors

DOI: 10.18129/B9.bioc.BiocNeighbors    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BiocNeighbors.

Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: 3.8

Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm, as described by Wang (2012). This is faster than conventional kd-trees for neighbor searching in higher (> 20) dimensional data. The approximate method uses the Annoy algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.

Author: Aaron Lun [aut, cre, cph]

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

Installation

To install this package, start R (version "3.5") 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	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
License	GPL-3
Depends	R (>= 3.5), BiocParallel
Imports	Rcpp, S4Vectors, stats, methods
LinkingTo	Rcpp, RcppAnnoy
Suggests	testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy
SystemRequirements	C++11
Enhances
URL
Depends On Me	simpleSingleCell
Imports Me	cydar, scran
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BiocNeighbors_1.0.0.tar.gz
Windows Binary	BiocNeighbors_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	BiocNeighbors_1.0.0.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	http://bioconductor.org/packages/BiocNeighbors/
Package Downloads Report	Download Stats