BiocNeighbors

DOI: 10.18129/B9.bioc.BiocNeighbors    

Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BiocNeighbors", version = "3.8")

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
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

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