BiocNeighbors
This is the development version of BiocNeighbors; for the stable release version, see BiocNeighbors.
Nearest Neighbor Detection for Bioconductor Packages
Bioconductor version: Development (3.24)
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, vantage point trees, or an exhaustive search. Approximate searches can be performed using the Annoy or HNSW libraries. Each search can be performed with a variety of different distance metrics, parallelization, and variable numbers of neighbors. Range-based searches (to find all neighbors within a certain distance) are also supported.
Author: Aaron Lun [aut, cre, cph]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("BiocNeighbors")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, Software |
| Version | 2.7.2 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 |
| Depends | |
| Imports | Rcpp, methods |
| System Requirements | C++17 |
| URL | https://github.com/knncolle/BiocNeighbors |
| Bug Reports | https://github.com/knncolle/BiocNeighbors/issues |
See More
| Suggests | Matrix, DelayedArray, beachmat, BiocParallel, testthat, BiocStyle, S4Vectors, knitr, rmarkdown |
| Linking To | Rcpp, assorthead, beachmat |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.workflows, SingleRBook |
| Imports Me | batchelor, bluster, CellMixS, clustSIGNAL, concordexR, cydar, GeDi, imcRtools, jvecfor, lemur, miloR, mumosa, poem, scater, scDblFinder, scider, scMerge, scrapper, smoothclust, SpatialFeatureExperiment, SpotSweeper, StabMap, SVP, UCell |
| Suggests Me | ClassifyR, scLANE, TrajectoryUtils, TSCAN, thisutils |
| Links To Me | scrapper |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocNeighbors_2.7.2.tar.gz |
| Windows Binary (x86_64) | BiocNeighbors_2.7.2.zip |
| macOS Binary (big-sur-x86_64) | BiocNeighbors_2.7.2.tgz |
| macOS Binary (sonoma-arm64) | BiocNeighbors_2.7.2.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 |