BiocSingular

DOI: 10.18129/B9.bioc.BiocSingular  

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DimensionReduction, PrincipalComponent, Software
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	GPL-3
Depends
Imports	BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat
LinkingTo	Rcpp, beachmat
Suggests	testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
SystemRequirements	C++11
Enhances
URL	https://github.com/LTLA/BiocSingular
BugReports	https://github.com/LTLA/BiocSingular/issues
Depends On Me	compartmap
Imports Me	batchelor, BayesSpace, clusterExperiment, DelayedTensor, Dino, GSVA, miloR, mumosa, NanoMethViz, NewWave, PCAtools, scater, scDblFinder, scMerge, scran, scry, SingleR, velociraptor
Suggests Me	HCAData, ResidualMatrix, ScaledMatrix, spatialHeatmap, splatter, Voyager
Links To Me
Build Report

Package Archives

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

Source Package	BiocSingular_1.14.0.tar.gz
Windows Binary	BiocSingular_1.14.0.zip (64-bit only)
macOS Binary (x86_64)	BiocSingular_1.14.0.tgz
macOS Binary (arm64)	BiocSingular_1.14.0.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