SparseArray

DOI: 10.18129/B9.bioc.SparseArray  

Efficient in-memory representation of multidimensional sparse arrays

Bioconductor version: Release (3.17)

The SparseArray package is an infrastructure package that provides an array-like container for efficient in-memory representation of multidimensional sparse data in R. The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data, the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.

Author: Hervé Pagès [aut, cre], Vince Carey [fnd], Rafael A. Irizarry [fnd]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("SparseArray")):

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("SparseArray")

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("SparseArray")

 

HTML R Script SparseArray objects
PDF   Reference Manual
Text   NEWS

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.0.12
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3.0), methods, Matrix, BiocGenerics(>= 0.43.1), MatrixGenerics(>= 1.11.1), S4Vectors, S4Arrays(>= 1.0.6)
Imports stats, matrixStats, IRanges, XVector
LinkingTo S4Vectors, IRanges, XVector
Suggests DelayedArray, testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL https://bioconductor.org/packages/SparseArray
BugReports https://github.com/Bioconductor/SparseArray/issues
Depends On Me
Imports Me
Suggests Me MatrixGenerics, S4Arrays
Links To Me
Build Report  

Package Archives

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

Source Package SparseArray_1.0.12.tar.gz
Windows Binary SparseArray_1.0.12.zip
macOS Binary (x86_64) SparseArray_1.0.12.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SparseArray
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SparseArray
Bioc Package Browser https://code.bioconductor.org/browse/SparseArray/
Package Short Url https://bioconductor.org/packages/SparseArray/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

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