DOI: 10.18129/B9.bioc.SparseArray  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SparseArray.

Efficient in-memory representation of multidimensional sparse arrays

Bioconductor version: 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>

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:



HTML R Script SparseArray objects
PDF   Reference Manual
Text   NEWS


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
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
macOS Binary (x86_64) SparseArray_1.0.12.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: