DelayedArray

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DelayedArray.

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


Bioconductor version: 3.10

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, and ordinary arrays and data frames.

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

Maintainer: Hervé Pagès <hpages at fredhutch.org>

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

Installation

To install this package, start R (version "3.6") 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")
Implementing A DelayedArray Backend HTML
Working with large arrays in R PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, DataRepresentation, GenomeAnnotation, Infrastructure, Software
Version 0.12.3
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.4), methods, stats4, matrixStats, BiocGenerics(>= 0.31.5), S4Vectors(>= 0.24.4), IRanges(>= 2.17.3), BiocParallel
Imports stats, Matrix
System Requirements
URL
See More
Suggests HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit
Linking To S4Vectors
Enhances
Depends On Me DelayedDataFrame, DelayedMatrixStats, GDSArray, HDF5Array, restfulSE, rhdf5client, singleCellTK, SummarizedExperiment, VCFArray
Imports Me batchelor, beachmat, BiocSingular, bsseq, CAGEr, celaref, ChIPpeakAnno, clusterExperiment, DEScan2, DSS, ELMER, GenoGAM, gramm4R, hipathia, LoomExperiment, mbkmeans, methrix, minfi, netSmooth, PCAtools, RTCGAToolbox, scater, scDblFinder, scMerge, scmeth, scran, signatureSearch, SingleR, VariantExperiment
Suggests Me BiocGenerics, gwascat, iSEE, MAST, S4Vectors, SQLDataFrame
Links To Me
Build Report Build Report

Package Archives

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

Source Package DelayedArray_0.12.3.tar.gz
Windows Binary DelayedArray_0.12.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DelayedArray_0.12.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/DelayedArray
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DelayedArray
Bioc Package Browser https://code.bioconductor.org/browse/DelayedArray/
Package Short Url https://bioconductor.org/packages/DelayedArray/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive