BiocNeighbors
Nearest Neighbor Detection for Bioconductor Packages
Bioconductor version: Release (3.17)
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("BiocNeighbors")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| 1. Detecting exact nearest neighbors | HTML | R Script |
| 2. Detecting approximate nearest neighbors | HTML | R Script |
| 3. Detecting neighbors within range | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5 years) |
| License | GPL-3 |
| Depends | |
| Imports | Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix |
| Linking To | Rcpp, RcppHNSW |
| Suggests | testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW |
| System Requirements | C++11 |
| Enhances | |
| URL |
See More
| Depends On Me | OSCA.advanced, OSCA.workflows, SingleRBook |
| Imports Me | batchelor, bluster, CellMixS, cydar, imcRtools, miloR, mumosa, scater, scDblFinder, scMerge, SpatialFeatureExperiment, UCell |
| Suggests Me | concordexR, TrajectoryUtils, TSCAN |
| Links To Me | SingleR |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocNeighbors_1.18.0.tar.gz |
| Windows Binary | BiocNeighbors_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | BiocNeighbors_1.18.0.tgz |
| macOS Binary (arm64) | BiocNeighbors_1.18.0.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 |