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Bioconductor - DelayedArray (development version)

DelayedArray

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

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

Bioconductor version: Development (3.22)

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], Aaron Lun [ctb], Peter Hickey [ctb]

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

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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 2. Implementing A DelayedArray Backend HTML 3. A DelayedArray / HDF5Array update (slides from April 2021) PDF R Script Reference Manual PDF NEWS Text Details biocViews Annotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software Version 0.35.2 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics(>= 0.53.3), MatrixGenerics(>= 1.1.3), S4Vectors(>= 0.27.2), IRanges(>= 2.17.3), S4Arrays(>= 1.5.4), SparseArray(>= 1.7.5) Imports stats System Requirements URL https://bioconductor.org/packages/DelayedArray Bug Reports https://github.com/Bioconductor/DelayedArray/issues See More Suggests BiocParallel, HDF5Array(>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit Linking To S4Vectors Enhances Depends On Me chihaya, DelayedDataFrame, DelayedMatrixStats, DelayedRandomArray, GDSArray, HDF5Array, Rarr, rhdf5client, SCArray, SQLDataFrame, TileDBArray, VCFArray Imports Me adverSCarial, alabaster.matrix, AUCell, batchelor, beachmat, beachmat.hdf5, beachmat.tiledb, BiocSingular, bsseq, celda, Cepo, clusterExperiment, concordexR, CRISPRseek, cytomapper, decontX, DelayedTensor, DEScan2, dreamlet, DropletUtils, ELMER, EWCE, flowWorkspace, FRASER, GenomicScores, glmGamPoi, GSVA, hipathia, LoomExperiment, Macarron, mariner, mbkmeans, methodical, MethReg, methrix, methylSig, mia, miaViz, minfi, MOFA2, MuData, MultiAssayExperiment, mumosa, NetActivity, netSmooth, NewWave, orthogene, orthos, PCAtools, ResidualMatrix, RTCGAToolbox, ScaledMatrix, SCArray.sat, scater, scDblFinder, scFeatures, scMerge, scmeth, scPCA, scran, scrapper, scry, scuttle, signatureSearch, SingleCellAlleleExperiment, SingleCellExperiment, SingleR, sketchR, SpliceWiz, SummarizedExperiment, transformGamPoi, TSCAN, VariantExperiment, velociraptor, vmrseq, Voyager, weitrix, xcore, zellkonverter, ZygosityPredictor, celldex, imcdatasets, scRNAseq, ebvcube, rliger, scDiffCom, spatialGE Suggests Me BiocGenerics, ChIPpeakAnno, gwascat, hermes, iSEE, lute, MatrixGenerics, ProteoDisco, S4Arrays, S4Vectors, satuRn, scone, SPOTlight, TrajectoryUtils, Seurat, SeuratObject, SpatialDDLS Links To Me Build Report Build Report Package Archives

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

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