SCArray

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SCArray.

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

Bioconductor version: 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>

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

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")

Overview HTML

Single-cell RNA-seq data manipulation using GDS files HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software

Version 1.6.0

In Bioconductor since BioC 3.13 (R-4.1) (3 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

System Requirements

URL https://github.com/AbbVie-ComputationalGenomics/SCArray

Suggests Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array

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Build Report 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

Old Source Packages for BioC 3.16 Source Archive