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Bioconductor - BiocSingular (development version)

BiocSingular

This is the development version of BiocSingular; for the stable release version, see BiocSingular.

Singular Value Decomposition for Bioconductor Packages

Bioconductor version: Development (3.22)

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.

Author: Aaron Lun [aut, cre, cph]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("BiocSingular")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BiocSingular")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiocSingular")

Details biocViews DimensionReduction, PrincipalComponent, Software Version 1.25.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License GPL-3 Depends Imports BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat(>= 2.21.1) System Requirements C++17 URL https://github.com/LTLA/BiocSingular Bug Reports https://github.com/LTLA/BiocSingular/issues See More Suggests testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix Linking To Rcpp, beachmat, assorthead Enhances Depends On Me OSCA.advanced, OSCA.basic, OSCA.multisample, OSCA.workflows Imports Me batchelor, BayesSpace, clusterExperiment, COTAN, DelayedTensor, Dino, GSVA, miloR, MPAC, mumosa, NanoMethViz, NewWave, PCAtools, ReactomeGSA, SCArray, SCArray.sat, scater, scDblFinder, scMerge, scran, scry, StabMap, velociraptor Suggests Me alabaster.matrix, chihaya, ResidualMatrix, ScaledMatrix, spatialHeatmap, splatter, Voyager, HCAData Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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