BiocSingular

DOI: 10.18129/B9.bioc.BiocSingular    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BiocSingular.

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: 3.9

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 "3.6") and enter:

if (!requireNamespace("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

Details

biocViews	DimensionReduction, PrincipalComponent, Software
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends
Imports	BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp
LinkingTo	Rcpp, beachmat
Suggests	testthat, BiocStyle, knitr, rmarkdown, beachmat
SystemRequirements	C++11
Enhances
URL	https://github.com/LTLA/BiocSingular
BugReports	https://github.com/LTLA/BiocSingular/issues
Depends On Me
Imports Me	batchelor, scater, scran
Suggests Me	simpleSingleCell
Links To Me
Build Report

Package Archives

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

Source Package	BiocSingular_1.0.0.tar.gz
Windows Binary	BiocSingular_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	BiocSingular_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocSingular
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocSingular
Package Short Url	https://bioconductor.org/packages/BiocSingular/
Package Downloads Report	Download Stats