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Bioconductor - BiocNeighbors (development version)

BiocNeighbors

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

Nearest Neighbor Detection for Bioconductor Packages

Bioconductor version: Development (3.22)

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")
Details biocViews Classification, Clustering, Software Version 2.3.1 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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.advanced, OSCA.workflows, SingleRBook Imports Me batchelor, bluster, CellMixS, clustSIGNAL, concordexR, cydar, GeDi, imcRtools, lemur, miloR, mumosa, poem, scater, scDblFinder, scMerge, scrapper, SingleR, SpatialFeatureExperiment, SpotSweeper, StabMap, SVP, UCell Suggests Me ClassifyR, TrajectoryUtils, TSCAN Links To Me scrapper, SingleR Build Report Build Report Package Archives

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


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