DelayedArray

DOI: 10.18129/B9.bioc.DelayedArray    

A unified framework for working transparently with on-disk and in-memory array-like datasets

Bioconductor version: Release (3.15)

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.

Author: Hervé Pagès <hpages.on.github at gmail.com>, with contributions from Peter Hickey <peter.hickey at gmail.com> and Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Installation

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

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

BiocManager::install("DelayedArray")

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("DelayedArray")

 

PDF	R Script	DelayedArray / HDF5Array update
HTML		Implementing A DelayedArray Backend
PDF	R Script	Working with large arrays in R
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software
Version	0.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics(>= 0.37.0), MatrixGenerics(>= 1.1.3), S4Vectors(>= 0.27.2), IRanges(>= 2.17.3)
Imports	stats
LinkingTo	S4Vectors
Suggests	BiocParallel, HDF5Array(>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/DelayedArray
BugReports	https://github.com/Bioconductor/DelayedArray/issues
Depends On Me	DelayedDataFrame, DelayedMatrixStats, DelayedRandomArray, GDSArray, HDF5Array, restfulSE, restfulSEData, rhdf5client, SCArray, singleCellTK, TileDBArray, VCFArray
Imports Me	AUCell, batchelor, beachmat, bigPint, BiocSingular, bsseq, CAGEr, celaref, celda, celldex, Cepo, ChromSCape, clusterExperiment, compartmap, CRISPRseek, cytomapper, DelayedTensor, DEScan2, DropletUtils, ELMER, EWCE, flowWorkspace, FRASER, GenoGAM, GenomicScores, glmGamPoi, GSVA, hipathia, imcdatasets, LoomExperiment, Macarron, mbkmeans, MethReg, methrix, methylSig, mia, miaViz, minfi, MOFA2, MuData, mumosa, netSmooth, NewWave, NxtIRFcore, orthogene, PCAtools, ResidualMatrix, RTCGAToolbox, ScaledMatrix, scater, scDblFinder, scMerge, scmeth, scPCA, scran, scry, scuttle, signatureSearch, SingleCellExperiment, SingleR, SummarizedExperiment, transformGamPoi, TSCAN, VariantExperiment, velociraptor, weitrix, xcore, zellkonverter
Suggests Me	BiocGenerics, ChIPpeakAnno, CNVgears, gwascat, hermes, iSEE, MAST, ProteoDisco, S4Vectors, satuRn, SPOTlight, SQLDataFrame, TrajectoryUtils
Links To Me
Build Report

Package Archives

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

Source Package	DelayedArray_0.22.0.tar.gz
Windows Binary	DelayedArray_0.22.0.zip (64-bit only)
macOS Binary (x86_64)	DelayedArray_0.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DelayedArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DelayedArray
Package Short Url	https://bioconductor.org/packages/DelayedArray/
Package Downloads Report	Download Stats