jvecfor
This is the development version of jvecfor; to use it, please install the devel version of Bioconductor.
Fast K-Nearest Neighbor Search for Single-Cell Analysis
Bioconductor version: Development (3.23)
Drop-in replacement for BiocNeighbors::findKNN using the jvecfor Java library, which builds on the jvector library to leverage the Java Vector API for portable SIMD acceleration across AVX2, AVX-512, and ARM NEON hardware. jvecfor/jvector implements HNSW-DiskANN approximate search and VP-tree exact search. The package achieves approximately 2x speedup over Annoy-based search at n >= 50K cells while returning output structurally identical to BiocNeighbors, making it suitable for seamless integration into existing Bioconductor single-cell workflows. Convenience wrappers delegate shared nearest-neighbor (SNN) and k-nearest-neighbor (KNN) graph construction to the bluster package.
Author: Anestis Gkanogiannis [aut, cre]
Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>
citation("jvecfor")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("jvecfor")
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("jvecfor")| jvecfor | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, Clustering, GraphAndNetwork, SingleCell, Software |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.6.0) |
| Imports | BiocNeighbors, BiocParallel, Matrix, bluster, data.table, methods, processx |
| System Requirements | Java (>= 20) |
| URL | https://github.com/gkanogiannis/jvecfor |
| Bug Reports | https://github.com/gkanogiannis/jvecfor/issues |
See More
| Suggests | BiocStyle, igraph, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | jvecfor_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/jvecfor |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/jvecfor |
| Bioc Package Browser | https://code.bioconductor.org/browse/jvecfor/ |
| Package Short Url | https://bioconductor.org/packages/jvecfor/ |
| Package Downloads Report | Download Stats |