DOI: 10.18129/B9.bioc.SCArray.sat

Bioconductor version: Release (3.22)

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>