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bioconductor-scarray.sat

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

Installation

To install this package, run one of the following:

Conda
$conda install bioconda::bioconductor-scarray.sat

Usage Tracking

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Description

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.

About

Summary

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

Last Updated

Mar 1, 2026 at 20:35

License

GPL-3

Total Downloads

3.3K

Version Downloads

26

Supported Platforms

noarch