BiocSingular
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BiocSingular.
Singular Value Decomposition for Bioconductor Packages
Bioconductor version: 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("BiocSingular")):
Installation
To install this package, start R (version "3.6") 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 |
Details
| biocViews | DimensionReduction, PrincipalComponent, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL-3 |
| Depends | |
| Imports | BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp |
| 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, beachmat |
| Linking To | Rcpp, beachmat |
| Enhances | |
| Depends On Me | |
| Imports Me | batchelor, scater, scran |
| Suggests Me | simpleSingleCell |
| Links To Me | |
| Build Report | 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 |
| 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 3.9 | Source Archive |