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DelayedArray

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

Bioconductor version: 3.23 · Package version: 0.38.2

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.

Installation

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

BiocManager::install("DelayedArray")

Details

MaintainerHervé Pagès <hpages.on.github@gmail.com>
AuthorHervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>), Aaron Lun [ctb], Peter Hickey [ctb]
LicenseArtistic-2.0
URLhttps://bioconductor.org/packages/DelayedArray
Bug Reportshttps://github.com/Bioconductor/DelayedArray/issues
Downloads rank53651
Source branchRELEASE_3_23
biocViewsAnnotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software

Documentation

Download

Dependencies

Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6), IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>= 1.7.5)

Imports: stats

Suggests: BiocParallel, HDF5Array (>= 1.17.12), ZarrArray, genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit

Reverse dependencies

Depends On Me (14): chihaya, DelayedDataFrame, DelayedMatrixStats, DelayedRandomArray, GDSArray, HDF5Array, PlinkMatrix, rhdf5client, SCArray, singleCellTK, SQLDataFrame, TileDBArray, VCFArray, ZarrArray

Imports Me (94): adverSCarial, alabaster.matrix, AUCell, batchelor, beachmat, beachmat.hdf5, beachmat.tiledb, BiocSingular, bsseq, celaref, celda, celldex, cellGeometry, Cepo, ChromSCape, clusterExperiment, concordexR, CRISPRseek, cytomapper, decontX, DelayedTensor, DEScan2, dreamlet, DropletUtils, ebvcube, ELMER, EWCE, flowWorkspace, FRASER, GenomicScores, glmGamPoi, GSVA, hipathia, ImageArray, imcdatasets, LoomExperiment, Macarron, mariner, mbkmeans, methodical, MethReg, 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, spatialGE, SpliceWiz, SummarizedExperiment, transformGamPoi, TSCAN, VariantExperiment, velociraptor, vmrseq, Voyager, weitrix, xcore, zellkonverter, ZygosityPredictor

Suggests Me (19): BiocGenerics, BiocNeighbors, ChIPpeakAnno, gwascat, hermes, iSEE, MAST, MatrixGenerics, methFuse, ProteoDisco, S4Arrays, S4Vectors, satuRn, scone, Seurat, SeuratObject, spatialHeatmap, SPOTlight, TrajectoryUtils