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 (3.21)

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: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, RNASeq, SingleCell, Software
Version	1.7.0
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

Suggests	future, RUnit, knitr, markdown, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SCArray.sat_1.7.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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