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("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 | ||
NEWS | Text |
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 |
See More
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 |