DelayedArray

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

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

Bioconductor version: Development (3.24)

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 [aut, cre] ORCID: 0009-0002-8272-4522 , Aaron Lun [ctb], Peter Hickey [ctb]

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

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

Hervé Pagès. DelayedArray: A unified framework for working transparently with on-disk and in-memory array-like datasets. doi:10.18129/B9.bioc.DelayedArray, R package version 0.39.8, https://bioconductor.org/packages/DelayedArray.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

1. Working with large arrays in R (slides from July 2017)	PDF	R Script
3. A DelayedArray / HDF5Array update (slides from April 2021)	PDF	R Script
2. Implementing A DelayedArray Backend	HTML
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software
Version	0.39.8
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.59.12), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.51.2), IRanges (>= 2.47.1), S4Arrays (>= 1.13.2), SparseArray (>= 1.7.5)
Imports	stats
System Requirements
URL	https://bioconductor.org/packages/DelayedArray
Bug Reports	https://github.com/Bioconductor/DelayedArray/issues

Suggests	BiocParallel, HDF5Array (>= 1.17.12), ZarrArray, genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit
Linking To
Enhances
Depends On Me	chihaya, DelayedDataFrame, DelayedMatrixStats, DelayedRandomArray, DuckDBArray, GDSArray, HDF5Array, PlinkMatrix, rhdf5client, SCArray, singleCellTK, TileDBArray, VCFArray, ZarrArray
Imports Me	adverSCarial, alabaster.matrix, AUCell, batchelor, beachmat, beachmat.hdf5, beachmat.tiledb, BiocDuckDB, BiocSingular, bsseq, celaref, celldex, cellGeometry, Cepo, ChromSCape, clusterExperiment, concordexR, CRISPRseek, cytomapper, decontX, DelayedTensor, DEScan2, dreamlet, DropletUtils, DuckDBDataFrame, DuckDBGRanges, ebvcube, ELMER, EWCE, flowWorkspace, FRASER, GenomicScores, glmGamPoi, GSVA, hipathia, ImageArray, imcdatasets, LoomExperiment, Macarron, mariner, mbkmeans, methodical, methrix, methylSig, mia, miaViz, minfi, MOFA2, MuData, MultiAssayExperiment, mumosa, mutscan, NetActivity, netSmooth, NewWave, omicsGMF, orthogene, orthos, PCAtools, RBedMethyl, ResidualMatrix, rliger, RTCGAToolbox, ScaledMatrix, SCArray.sat, scater, scDblFinder, scDiffCom, scFeatures, scMerge, scmeth, scPCA, scran, scrapper, scRNAseq, scry, scuttle, signatureSearch, SingleCellAlleleExperiment, SingleCellExperiment, SingleR, sketchR, SpaNorm, spatialdataR, spatialGE, SpliceWiz, SummarizedExperiment, transformGamPoi, TSCAN, VariantExperiment, velociraptor, vmrseq, Voyager, weitrix, xcore, zellkonverter, ZygosityPredictor
Suggests Me	anndataR, BiocGenerics, BiocNeighbors, cellNexus, ChIPpeakAnno, gwascat, hermes, iSEE, MAST, MatrixGenerics, methFuse, presto, ProteoDisco, S4Arrays, S4Cartographer, S4Vectors, satuRn, scone, Seurat, SeuratObject, SigBridgeRUtils, spatialHeatmap, SPOTlight, TrajectoryUtils, UCell
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DelayedArray_0.39.8.tar.gz
Windows Binary (x86_64)	DelayedArray_0.39.8.zip (64-bit only)
macOS Binary (big-sur-x86_64)	DelayedArray_0.39.8.tgz
macOS Binary (sonoma-arm64)	DelayedArray_0.39.8.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