BiocSingular
This is the development version of BiocSingular; for the stable release version, see BiocSingular.
All Bioconductor versions of BiocSingular
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9
Singular Value Decomposition for Bioconductor Packages
Bioconductor version: 3.24 · Package version: 1.29.1
Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.
Author: Aaron Lun [aut, cre, cph]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Citation
From within R, enter citation("BiocSingular"):
Aaron Lun. BiocSingular: Singular Value Decomposition for Bioconductor Packages. doi:10.18129/B9.bioc.BiocSingular, R package version 1.29.1, https://bioconductor.org/packages/BiocSingular.
Generated from the package metadata; it may differ from the package's own citation.
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("BiocSingular")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.29.1 |
| License | GPL-3 |
| URL | https://github.com/LTLA/BiocSingular |
| Bug Reports | https://github.com/LTLA/BiocSingular/issues |
| System Requirements | C++17 |
| Last updated | 2026-08-27 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 years) |
| Downloads rank | 52 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, PrincipalComponent, Software |
| Package Short Url | https://bioconductor.org/packages/BiocSingular/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BiocSingular")| Singular value decomposition for Bioconductor packages | HTML | R Script |
| Matrix representations to support decomposition | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | BiocSingular_1.29.1.tar.gz |
| Windows binary (x86_64) | BiocSingular_1.29.1.zip |
| macOS binary (arm64) | BiocSingular_1.29.1.tgz |
| macOS binary (x86_64) | BiocSingular_1.29.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocSingular |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocSingular |
| Package Downloads Report | Download Stats |
Dependencies
Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>= 2.25.1)
LinkingTo: Rcpp, beachmat, assorthead
Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
Reverse dependencies
Imports Me (27): batchelor, BayesSpace, BiocDuckDB, clusterExperiment, clustSIGNAL, COTAN, DelayedTensor, Dino, miloR, MPAC, mumosa, NanoMethViz, NewWave, omicsGMF, PCAtools, ReactomeGSA, SCArray, SCArray.sat, scater, scDblFinder, scMerge, scran, scry, Seqtometry, SpaNorm, StabMap, velociraptor
Suggests Me (11): alabaster.matrix, chihaya, HCAData, ResidualMatrix, S4Cartographer, ScaledMatrix, scDiagnostics, spatialHeatmap, splatter, SuperCellCyto, Voyager