HDF5Array

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HDF5Array.

HDF5 backend for DelayedArray objects

Bioconductor version: 3.12

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.on.github at gmail.com>

Citation (from within R, enter citation("HDF5Array")):

Installation

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


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

BiocManager::install("HDF5Array")

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

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version	1.18.1
In Bioconductor since	BioC 3.3 (R-3.3) (8 years)
License	Artistic-2.0
Depends	R (>= 3.4), methods, DelayedArray(>= 0.15.16), rhdf5(>= 2.31.6)
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.31.5), S4Vectors, IRanges
System Requirements	GNU make
URL	https://bioconductor.org/packages/HDF5Array
Bug Reports	https://github.com/Bioconductor/HDF5Array/issues

Suggests	BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, GenomicFeatures, BiocStyle
Linking To	S4Vectors(>= 0.27.13), Rhdf5lib
Enhances
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, MethylSeqData, minfi, MOFA2, netSmooth, recountmethylation, scmeth, scry, signatureSearch, SingleCellMultiModal
Suggests Me	BiocSklearn, DelayedArray, iSEE, MAST, mbkmeans, MultiAssayExperiment, scMerge, scran, sesame, SummarizedExperiment, zellkonverter
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	HDF5Array_1.18.1.tar.gz
Windows Binary	HDF5Array_1.18.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	HDF5Array_1.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HDF5Array
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HDF5Array
Bioc Package Browser	https://code.bioconductor.org/browse/HDF5Array/
Package Short Url	https://bioconductor.org/packages/HDF5Array/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.12	Source Archive