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Efficient in-memory representation of multidimensional sparse arrays

Bioconductor version: Release (3.18)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

SparseArray objects HTML R Script
Reference Manual PDF


biocViews DataRepresentation, Infrastructure, Software
Version 1.2.4
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.3.0), methods, Matrix, BiocGenerics(>= 0.43.1), MatrixGenerics(>= 1.11.1), S4Vectors, S4Arrays(>= 1.1.6)
Imports stats, matrixStats, IRanges, XVector
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Suggests DelayedArray, testthat, knitr, rmarkdown, BiocStyle
Linking To S4Vectors, IRanges, XVector
Depends On Me DelayedArray
Imports Me alabaster.matrix, beachmat
Suggests Me MatrixGenerics, S4Arrays
Links To Me
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Source Package SparseArray_1.2.4.tar.gz
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macOS Binary (arm64) SparseArray_1.2.4.tgz
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