BiocNeighbors
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BiocNeighbors.
Nearest Neighbor Detection for Bioconductor Packages
Bioconductor version: 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("BiocNeighbors")):
Installation
To install this package, start R (version "3.5") 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 | 1.0.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), BiocParallel |
| Imports | Rcpp, S4Vectors, stats, methods |
| System Requirements | C++11 |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy |
| Linking To | Rcpp, RcppAnnoy |
| Enhances | |
| Depends On Me | simpleSingleCell |
| Imports Me | cydar, scran |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiocNeighbors/ |
| Package Short Url | https://bioconductor.org/packages/BiocNeighbors/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |