SCArray

DOI: 10.18129/B9.bioc.SCArray  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	GPL-3
Depends	R (>= 3.5.0), gdsfmt(>= 1.27.4), methods, DelayedArray(>= 0.16.0)
Imports	BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment, SingleCellExperiment, DelayedMatrixStats
LinkingTo
Suggests	Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array
SystemRequirements
Enhances
URL	https://github.com/AbbVie-ComputationalGenomics/SCArray
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SCArray_1.6.0.tar.gz
Windows Binary	SCArray_1.6.0.zip
macOS Binary (x86_64)	SCArray_1.6.0.tgz
macOS Binary (arm64)	SCArray_1.6.0.tgz
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