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SCArray

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

Large-scale single-cell RNA-seq data manipulation with GDS files


Bioconductor version: Development (3.19)

Provides large-scale single-cell RNA-seq data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

Author: Xiuwen Zheng [aut, cre]

Maintainer: Xiuwen Zheng <xiuwen.zheng at abbvie.com>

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

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")

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")
Overview HTML
Single-cell RNA-seq data manipulation using GDS files HTML R Script
Reference Manual PDF

Details

biocViews DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software
Version 1.11.1
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 3.5.0), gdsfmt(>= 1.36.0), methods, DelayedArray(>= 0.28.0)
Imports S4Vectors, utils, Matrix, BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular
System Requirements
URL https://github.com/AbbVie-ComputationalGenomics/SCArray
See More
Suggests BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array
Linking To
Enhances
Depends On Me SCArray.sat
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_1.11.1.tar.gz
Windows Binary
macOS Binary (x86_64) SCArray_1.11.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SCArray
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SCArray
Bioc Package Browser https://code.bioconductor.org/browse/SCArray/
Package Short Url https://bioconductor.org/packages/SCArray/
Package Downloads Report Download Stats