Package: BiocSingular 1.27.1

Aaron Lun

BiocSingular: Singular Value Decomposition for Bioconductor Packages

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.

Authors:Aaron Lun [aut, cre, cph]

BiocSingular_1.27.1.tar.gz
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BiocSingular.pdf |BiocSingular.html✨
BiocSingular/json (API)
NEWS

# Install 'BiocSingular' in R:
install.packages('BiocSingular', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ltla/biocsingular/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:BiocSingular-1.27.1(bioc 3.23)BiocSingular-1.26.1(bioc 3.22)

softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decompositioncpp

12.25 score 8 stars 122 packages 1.1k scripts 23k downloads 2 mentions 22 exports 28 dependencies

Last updated from:9c87cf6785. Checks:3 ERROR, 11 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR170
linux-devel-arm64OK236
linux-devel-x86_64ERROR357
source / vignettesOK226
linux-release-arm64OK257
linux-release-x86_64ERROR276
macos-release-arm64OK162
macos-release-x86_64OK397
macos-oldrel-arm64OK140
macos-oldrel-x86_64OK291
windows-develOK315
windows-releaseOK203
windows-oldrelOK234
wasm-releaseOK159

Exports:bsdeferredbsfoldbsparamDeferredMatrixDeferredMatrixSeedDelayedArrayExactParamextract_arrayFastAutoParamIrlbaParamLowRankMatrixLowRankMatrixSeedRandomParamResidualMatrixResidualMatrixSeedrunExactSVDrunIrlbaSVDrunPCArunRandomSVDrunSVDshowt

Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayXVector

Singular value decomposition for Bioconductor packages

Aaron Lun

Rendered fromdecomposition.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2019-04-11
Started: 2019-02-09

Matrix representations to support decomposition

Aaron Lun

Rendered fromrepresentations.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2021-01-12
Started: 2019-02-09

Readme and manuals

Help Manual

Help pageTopics
Global SVD optionsBiocSingular-options
BiocSingularParam classesBiocSingularParam-class bsdeferred bsfold bsparam ExactParam ExactParam-class FastAutoParam FastAutoParam-class IrlbaParam IrlbaParam-class RandomParam RandomParam-class show,BiocSingularParam-method show,IrlbaParam-method show,RandomParam-method
The DeferredMatrix classDeferredMatrix DeferredMatrixSeed
The LowRankMatrix classDelayedArray,LowRankMatrixSeed-method dim,LowRankMatrixSeed-method dimnames,LowRankMatrixSeed-method dimnames<-,LowRankMatrix,ANY-method extract_array,LowRankMatrixSeed-method LowRankMatrix LowRankMatrix-class LowRankMatrixSeed LowRankMatrixSeed-class show,LowRankMatrixSeed-method t,LowRankMatrix-method [,LowRankMatrix,ANY,ANY,ANY-method
The ResidualMatrix classResidualMatrix ResidualMatrixSeed
Exact SVDrunExactSVD
Approximate SVD with 'irlba'runIrlbaSVD
Principal components analysisrunPCA runPCA,ANY-method
Approximate SVD with 'rsvd'runRandomSVD
Run SVDrunSVD runSVD,ExactParam-method runSVD,FastAutoParam-method runSVD,IrlbaParam-method runSVD,missing-method runSVD,RandomParam-method