BiocSingular

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BiocSingular.

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: 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>

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

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")

1. SVD and PCA HTML R Script

2. Matrix classes HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, PrincipalComponent, Software

Version 1.14.0

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++11

URL https://github.com/LTLA/BiocSingular

Bug Reports https://github.com/LTLA/BiocSingular/issues

Suggests testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix

Linking To Rcpp, beachmat

Enhances

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 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

Old Source Packages for BioC 3.16 Source Archive