Package: BiocSingular 1.21.4

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]

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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'))

Peer review:

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

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

On BioConductor:BiocSingular-1.21.4(bioc 3.20)BiocSingular-1.20.0(bioc 3.19)

softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decomposition

22 exports 7 stars 11.94 score 29 dependencies 98 dependents 2 mentions 884 scripts 20.1k downloads

Last updated 23 days agofrom:1bbcc83e39. Checks:OK: 7 ERROR: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 24 2024
R-4.5-win-x86_64NOTESep 24 2024
R-4.5-linux-x86_64ERRORSep 24 2024
R-4.4-win-x86_64OKSep 24 2024
R-4.4-mac-x86_64OKSep 24 2024
R-4.4-mac-aarch64OKSep 24 2024
R-4.3-win-x86_64OKSep 24 2024
R-4.3-mac-x86_64OKSep 24 2024
R-4.3-mac-aarch64OKSep 24 2024

Exports:bsdeferredbsfoldbsparamDeferredMatrixDeferredMatrixSeedDelayedArrayExactParamextract_arrayFastAutoParamIrlbaParamLowRankMatrixLowRankMatrixSeedRandomParamResidualMatrixResidualMatrixSeedrunExactSVDrunIrlbaSVDrunPCArunRandomSVDrunSVDshowt

Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelcodetoolscpp11crayonDelayedArrayformatRfutile.loggerfutile.optionsIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayXVectorzlibbioc

Singular value decomposition for Bioconductor packages

Rendered fromdecomposition.Rmdusingknitr::rmarkdownon Sep 24 2024.

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

Matrix representations to support decomposition

Rendered fromrepresentations.Rmdusingknitr::rmarkdownon Sep 24 2024.

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