DOI: 10.18129/B9.bioc.SCArray  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SCArray.

Large-scale single-cell RNA-seq data manipulation with GDS files

Bioconductor version: 3.16

Provides large-scale single-cell RNA-seq data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

Author: Xiuwen Zheng [aut, cre]

Maintainer: Xiuwen Zheng <xiuwen.zheng at>

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


To install this package, start R (version "4.2") 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 Overview
HTML R Script Single-cell RNA-seq data manipulation using GDS files
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.27.4), methods, DelayedArray(>= 0.16.0)
Imports BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment, SingleCellExperiment, DelayedMatrixStats
Suggests Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SCArray_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) SCArray_1.6.0.tgz
macOS Binary (arm64) SCArray_1.6.0.tgz
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: