Package: BiocSingular 1.29.2

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_1.29.2.tar.gz
BiocSingular_1.29.2.zip(r-4.7-x86_64)BiocSingular_1.29.2.zip(r-4.7-arm64)BiocSingular_1.29.2.zip(r-4.6-x86_64)BiocSingular_1.29.2.zip(r-4.6-arm64)BiocSingular_1.29.2.zip(r-4.5-x86_64)
BiocSingular_1.29.2.tgz(r-4.6-x86_64)BiocSingular_1.29.2.tgz(r-4.6-arm64)BiocSingular_1.29.2.tgz(r-4.5-x86_64)BiocSingular_1.29.2.tgz(r-4.5-arm64)
BiocSingular_1.29.2.tar.gz(r-4.7-arm64)BiocSingular_1.29.2.tar.gz(r-4.7-x86_64)BiocSingular_1.29.2.tar.gz(r-4.6-arm64)BiocSingular_1.29.2.tar.gz(r-4.6-x86_64)
BiocSingular_1.29.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiocSingular/json (API)

# 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-1.29.1(bioc 3.24)BiocSingular-1.28.0(bioc 3.23)

softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decompositioncpp

12.64 score 8 stars 121 packages 1.2k scripts 35k downloads 2 mentions 22 exports 28 dependencies

Last updated from:e9c9f7b8ac. Checks:5 ERROR, 2 OK, 9 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR168
linux-devel-arm64ERROR215
linux-devel-x86_64ERROR364
source / vignettesOK262
linux-release-arm64ERROR209
linux-release-x86_64ERROR297
macos-release-arm64NOTE202
macos-release-x86_64NOTE320
macos-oldrel-arm64NOTE188
macos-oldrel-x86_64NOTE417
windows-devel-arm64NOTE298
windows-devel-x86_64NOTE280
windows-release-arm64NOTE337
windows-release-x86_64NOTE204
windows-oldrel-x86_64NOTE261
wasm-releaseOK136

Exports:bsdeferredbsfoldbsparamDeferredMatrixDeferredMatrixSeedDelayedArrayExactParamextract_arrayFastAutoParamIrlbaParamLowRankMatrixLowRankMatrixSeedRandomParamResidualMatrixResidualMatrixSeedrunExactSVDrunIrlbaSVDrunPCArunRandomSVDrunSVDshowt

Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayXVector

Matrix representations to support decomposition
Overview | The DeferredMatrix class | The LowRankMatrix class | The ResidualMatrix class | Session information
Rendered fromrepresentations.Rmdusingknitr::rmarkdown

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

Singular value decomposition for Bioconductor packages
Overview | Taking the cross-product | Centering and/or scaling | Other SVD-related options | Running the PCA | Session information
Rendered fromdecomposition.Rmdusingknitr::rmarkdown

Last update: 2019-04-11
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