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
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| Author | Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>), Aaron Lun [ctb], Peter Hickey [ctb] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/DelayedArray |
| Bug Reports | https://github.com/Bioconductor/DelayedArray/issues |
| Downloads rank | 53651 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software |
Documentation
- Working with large arrays in R (slides from July 2017)
- Implementing A DelayedArray Backend
- A DelayedArray / HDF5Array update (slides from April 2021)
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