HDF5Array

DOI: 10.18129/B9.bioc.HDF5Array    

HDF5 backend for DelayedArray objects

Bioconductor version: Release (3.11)

Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed.

Author: Hervé Pagès

Maintainer: Hervé Pagès <hpages at fredhutch.org>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("HDF5Array")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version	1.16.1
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), methods, DelayedArray(>= 0.13.9), rhdf5(>= 2.31.6)
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.31.5), S4Vectors, IRanges
LinkingTo	S4Vectors(>= 0.21.6), Rhdf5lib
Suggests	BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, GenomicFeatures, BiocStyle
SystemRequirements	GNU make
Enhances
URL
Depends On Me	GenoGAM, TENxBrainData, TENxPBMCData
Imports Me	biscuiteer, bsseq, clusterExperiment, curatedTCGAData, DelayedMatrixStats, DropletUtils, FRASER, GenomicScores, glmGamPoi, HCAData, LoomExperiment, MafH5.gnomAD.r3.0.GRCh38, methrix, minfi, netSmooth, scmeth, sesame, signatureSearch
Suggests Me	BiocSklearn, DelayedArray, MAST, mbkmeans, MultiAssayExperiment, scMerge, scran, SummarizedExperiment
Links To Me
Build Report

Package Archives

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

Source Package	HDF5Array_1.16.1.tar.gz
Windows Binary	HDF5Array_1.16.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	HDF5Array_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HDF5Array
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HDF5Array
Package Short Url	https://bioconductor.org/packages/HDF5Array/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive