BiocNeighbors

This is the development version of BiocNeighbors; for the stable release version, see BiocNeighbors.

Nearest Neighbor Detection for Bioconductor Packages


Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Finding neighbors in high-dimensional space HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, Software
Version 2.1.1
In Bioconductor since BioC 3.8 (R-3.5) (6 years)
License GPL-3
Depends
Imports Rcpp, methods
System Requirements C++17
URL
See More
Suggests BiocParallel, testthat, BiocStyle, knitr, rmarkdown
Linking To Rcpp, assorthead
Enhances
Depends On Me OSCA.workflows, SingleRBook
Imports Me batchelor, bluster, CellMixS, concordexR, cydar, GeDi, imcRtools, lemur, miloR, mumosa, scater, scDblFinder, scMerge, scrapper, SingleR, SpatialFeatureExperiment, SpotSweeper, StabMap, UCell
Suggests Me TrajectoryUtils, TSCAN
Links To Me scrapper, SingleR
Build Report Build Report

Package Archives

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

Source Package BiocNeighbors_2.1.1.tar.gz
Windows Binary (x86_64) BiocNeighbors_2.1.1.zip
macOS Binary (x86_64) BiocNeighbors_2.1.1.tgz
macOS Binary (arm64) BiocNeighbors_2.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocNeighbors
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocNeighbors
Bioc Package Browser https://code.bioconductor.org/browse/BiocNeighbors/
Package Short Url https://bioconductor.org/packages/BiocNeighbors/
Package Downloads Report Download Stats