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This is the development version of SCArray; for the stable release version, see SCArray.

Large-scale single-cell omics data manipulation with GDS files

Bioconductor version: Development (3.20)

Provides large-scale single-cell omics 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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

Overview HTML
Single-cell RNA-seq data manipulation using GDS files HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.36.0), methods, DelayedArray(>= 0.28.0)
Imports S4Vectors, utils, Matrix, BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular
System Requirements
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Suggests BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array
Linking To
Depends On Me SCArray.sat
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package SCArray_1.13.0.tar.gz
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macOS Binary (x86_64) SCArray_1.13.0.tgz
macOS Binary (arm64) SCArray_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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