BiocSingular

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: 3.24 · Package version: 1.29.1

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocSingular")

Details

Maintainer	Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Author	Aaron Lun [aut, cre, cph]
License	GPL-3
URL	https://github.com/LTLA/BiocSingular
Bug Reports	https://github.com/LTLA/BiocSingular/issues
System Requirements	C++17
Downloads rank	17343
Source branch	devel
biocViews	DimensionReduction, PrincipalComponent, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source package	BiocSingular_1.29.1.tar.gz
Windows binary (x86_64)	BiocSingular_1.29.1.zip
macOS binary (arm64)	BiocSingular_1.29.1.tgz
macOS binary (x86_64)	BiocSingular_1.29.1.tgz

Dependencies

Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>= 2.25.1)

LinkingTo: Rcpp, beachmat, assorthead

Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix

Reverse dependencies

Imports Me (27): batchelor, BayesSpace, BiocDuckDB, clusterExperiment, clustSIGNAL, COTAN, DelayedTensor, Dino, miloR, MPAC, mumosa, NanoMethViz, NewWave, omicsGMF, PCAtools, ReactomeGSA, SCArray, SCArray.sat, scater, scDblFinder, scMerge, scran, scry, Seqtometry, SpaNorm, StabMap, velociraptor

Suggests Me (11): alabaster.matrix, chihaya, HCAData, ResidualMatrix, S4Cartographer, ScaledMatrix, scDiagnostics, spatialHeatmap, splatter, SuperCellCyto, Voyager