BiocSingular

DOI: 10.18129/B9.bioc.BiocSingular    

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: Release (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>

Citation (from within R, enter citation("BiocSingular")):

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

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