SCArray.sat

This is the development version of SCArray.sat; for the stable release version, see SCArray.sat.

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


Bioconductor version: Development (3.20)

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 abbvie.com>

Citation (from within R, enter citation("SCArray.sat")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SCArray.sat")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SCArray.sat")
scRNA-seq data analysis with GDS files and Seurat HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, RNASeq, SingleCell, Software
Version 1.5.1
In Bioconductor since BioC 3.17 (R-4.3) (1.5 years)
License GPL-3
Depends methods, SCArray(>= 1.13.1), SeuratObject (>= 5.0), Seurat (>= 5.0)
Imports S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix
System Requirements
URL
Bug Reports https://github.com/AbbVie-ComputationalGenomics/SCArray/issues
See More
Suggests future, RUnit, knitr, markdown, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SCArray.sat_1.5.1.tar.gz
Windows Binary SCArray.sat_1.5.1.zip
macOS Binary (x86_64) SCArray.sat_1.5.1.tgz
macOS Binary (arm64) SCArray.sat_1.5.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/SCArray.sat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SCArray.sat
Bioc Package Browser https://code.bioconductor.org/browse/SCArray.sat/
Package Short Url https://bioconductor.org/packages/SCArray.sat/
Package Downloads Report Download Stats