BiocNeighbors

DOI: 10.18129/B9.bioc.BiocNeighbors    

Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: Release (3.9)

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>

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

Installation

To install this package, start R (version "3.6") 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 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (0.5 years)
License GPL-3
Depends
Imports Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods
LinkingTo Rcpp, RcppAnnoy, RcppHNSW
Suggests testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me batchelor, CellMixS, cydar, scater, scran
Suggests Me simpleSingleCell
Links To Me
Build Report  

Package Archives

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

Source Package BiocNeighbors_1.2.0.tar.gz
Windows Binary BiocNeighbors_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BiocNeighbors_1.2.0.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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