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BiocSingular

Singular Value Decomposition for Bioconductor Packages


Bioconductor version: Release (3.18)

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

Details

biocViews DimensionReduction, PrincipalComponent, Software
Version 1.18.0
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++17
URL https://github.com/LTLA/BiocSingular
Bug Reports https://github.com/LTLA/BiocSingular/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
Linking To Rcpp, beachmat
Enhances
Depends On Me compartmap
Imports Me batchelor, BayesSpace, clusterExperiment, COTAN, 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_1.18.0.tar.gz
Windows Binary BiocSingular_1.18.0.zip
macOS Binary (x86_64) BiocSingular_1.18.0.tgz
macOS Binary (arm64) BiocSingular_1.18.0.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