Package: SCArray.sat
Type: Package
Title: Large-scale single-cell RNA-seq data analysis using GDS files
        and Seurat
Version: 1.11.2
Date: 2026-02-24
Depends: methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat
        (>= 5.0)
Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt,
        DelayedArray, BiocSingular, SummarizedExperiment, Matrix
Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre"), email=
        "xiuwen.zheng@abbvie.com", comment=c(ORCID="0000-0002-1390-0708")),
        person("Seurat contributors", role="ctb",
        comment="for the classes and methods defined in Seurat"))
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.
License: GPL-3
VignetteBuilder: knitr
BugReports: https://github.com/AbbVie-ComputationalGenomics/SCArray/issues
biocViews: DataRepresentation, DataImport, SingleCell, RNASeq
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-02-25 04:21:12 UTC
RemoteUrl: https://github.com/bioc/SCArray.sat
RemoteRef: HEAD
RemoteSha: c6a8d42ade6469a7a88a09acb1a0bd25d5c3250f
NeedsCompilation: no
Packaged: 2026-02-26 06:04:05 UTC; root
Author: Xiuwen Zheng [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1390-0708>),
  Seurat contributors [ctb] (for the classes and methods defined in
    Seurat)
Maintainer: Xiuwen Zheng <xiuwen.zheng@abbvie.com>
Built: R 4.6.0; ; 2026-02-26 06:06:28 UTC; windows
