Package: BiocSingular 1.23.0
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:
BiocSingular_1.23.0.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
On BioConductor:BiocSingular-1.23.0(bioc 3.21)BiocSingular-1.22.0(bioc 3.20)
softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decompositioncpp
Last updated 2 months agofrom:bd97d96ca7. Checks:OK: 1 ERROR: 1 WARNING: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.5-linux-x86_64 | ERROR | Dec 19 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 19 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 19 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 19 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 19 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 19 2024 |
Exports:bsdeferredbsfoldbsparamDeferredMatrixDeferredMatrixSeedDelayedArrayExactParamextract_arrayFastAutoParamIrlbaParamLowRankMatrixLowRankMatrixSeedRandomParamResidualMatrixResidualMatrixSeedrunExactSVDrunIrlbaSVDrunPCArunRandomSVDrunSVDshowt
Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelcodetoolscpp11crayonDelayedArrayformatRfutile.loggerfutile.optionsgenericsIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayXVectorzlibbioc
Singular value decomposition for Bioconductor packages
Rendered fromdecomposition.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2019-04-11
Started: 2019-02-09
Matrix representations to support decomposition
Rendered fromrepresentations.Rmdusingknitr::rmarkdownon Dec 19 2024.Last update: 2021-01-12
Started: 2019-02-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Global SVD options | BiocSingular-options |
| BiocSingularParam classes | BiocSingularParam-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 class | DeferredMatrix DeferredMatrixSeed |
| The LowRankMatrix class | DelayedArray,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 class | ResidualMatrix ResidualMatrixSeed |
| Exact SVD | runExactSVD |
| Approximate SVD with 'irlba' | runIrlbaSVD |
| Principal components analysis | runPCA runPCA,ANY-method |
| Approximate SVD with 'rsvd' | runRandomSVD |
| Run SVD | runSVD runSVD,ExactParam-method runSVD,FastAutoParam-method runSVD,IrlbaParam-method runSVD,missing-method runSVD,RandomParam-method |
