DOI: 10.18129/B9.bioc.SCArray.sat  

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

Large-scale single-cell RNA-seq data analysis using GDS files and Seurat

Bioconductor version: 3.17

Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.

Author: Xiuwen Zheng [aut, cre] , Seurat contributors [ctb] (for the classes and methods defined in Seurat)

Maintainer: Xiuwen Zheng <xiuwen.zheng at>

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biocViews DataImport, DataRepresentation, RNASeq, SingleCell, Software
Version 1.0.3
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License GPL-3
Depends methods, SCArray(>= 1.7.13), SeuratObject (>= 4.0), Seurat (>= 4.0)
Imports S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment
Suggests RUnit, knitr, markdown, rmarkdown, BiocStyle
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