This is the released version of SCArray.sat; for the devel version, see SCArray.sat.
Large-scale single-cell RNA-seq data analysis using GDS files and SeuratBioconductor version: Release (3.21)
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] ORCID: 0000-0002-1390-0708 , Seurat contributors [ctb] (for the classes and methods defined in Seurat)
Maintainer: Xiuwen Zheng <xiuwen.zheng at abbvie.com>
Citation (from within R, entercitation("SCArray.sat")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SCArray.sat")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SCArray.sat")Follow Installation instructions to use this package in your R session.
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