BiocSingular
This is the development version of BiocSingular; for the stable release version, see BiocSingular.
Singular Value Decomposition for Bioconductor Packages
Bioconductor version: Development (3.22)
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 "4.5") and enter:
if (!require("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")| 1. SVD and PCA | HTML | R Script |
| 2. Matrix classes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, PrincipalComponent, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat(>= 2.21.1) |
| 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, assorthead |
| Enhances | |
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows |
| Imports Me | batchelor, clusterExperiment, COTAN, DelayedTensor, Dino, GSVA, miloR, MPAC, mumosa, NanoMethViz, NewWave, ReactomeGSA, SCArray, SCArray.sat, scater, scDblFinder, scMerge, scran, scry, StabMap, velociraptor |
| Suggests Me | alabaster.matrix, chihaya, ResidualMatrix, ScaledMatrix, splatter, SuperCellCyto, Voyager, HCAData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocSingular_1.25.0.tar.gz |
| Windows Binary (x86_64) | BiocSingular_1.25.0.zip |
| macOS Binary (x86_64) | BiocSingular_1.25.0.tgz |
| macOS Binary (arm64) | BiocSingular_1.25.0.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 |