BiocSingular

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BiocSingular.

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: 3.17

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocSingular")

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("BiocSingular")

1. SVD and PCA	HTML	R Script
2. Matrix classes	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, PrincipalComponent, Software
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (5 years)
License	GPL-3
Depends
Imports	BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat
System Requirements	C++11
URL	https://github.com/LTLA/BiocSingular
Bug Reports	https://github.com/LTLA/BiocSingular/issues

Suggests	testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
Linking To	Rcpp, beachmat
Enhances
Depends On Me	compartmap
Imports Me	batchelor, BayesSpace, clusterExperiment, DelayedTensor, Dino, GSVA, miloR, mumosa, NanoMethViz, NewWave, PCAtools, SCArray, SCArray.sat, scater, scDblFinder, scMerge, scran, scry, SingleR, velociraptor
Suggests Me	chihaya, HCAData, ResidualMatrix, ScaledMatrix, spatialHeatmap, splatter, Voyager
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BiocSingular_1.16.0.tar.gz
Windows Binary	BiocSingular_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	BiocSingular_1.16.0.tgz
macOS Binary (arm64)	BiocSingular_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocSingular
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocSingular
Bioc Package Browser	https://code.bioconductor.org/browse/BiocSingular/
Package Short Url	https://bioconductor.org/packages/BiocSingular/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive