BiocSingular

DOI: 10.18129/B9.bioc.BiocSingular    

This is the development version of BiocSingular; for the stable release version, see BiocSingular.

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: Development (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.2
In Bioconductor since BioC 3.9 (R-3.6) (1 year)
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, PCAtools, scater, scMerge, scran, SingleR
Suggests Me HCAData
Links To Me
Build Report  

Package Archives

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

Source Package BiocSingular_1.3.2.tar.gz
Windows Binary BiocSingular_1.3.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BiocSingular_1.3.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocSingular
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocSingular
Package Short Url https://bioconductor.org/packages/BiocSingular/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: