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High-performance sparse data representation and manipulation in R

Bioconductor version: Release (3.19)

The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). 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], Jacques Serizay [ctb]

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

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


To install this package, start R (version "4.4") 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 1.4.8
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(>= 1.4.1)
Imports utils, stats, matrixStats, IRanges, XVector
System Requirements
Bug Reports
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Suggests DelayedArray, testthat, knitr, rmarkdown, BiocStyle
Linking To S4Vectors, IRanges, XVector
Depends On Me DelayedArray
Imports Me alabaster.matrix, beachmat, scRNAseq
Suggests Me MatrixGenerics, S4Arrays
Links To Me
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Package Archives

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

Source Package SparseArray_1.4.8.tar.gz
Windows Binary
macOS Binary (x86_64) SparseArray_1.4.8.tgz
macOS Binary (arm64) SparseArray_1.4.8.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive