HDF5Array

DOI: 10.18129/B9.bioc.HDF5Array    

This is the development version of HDF5Array; for the stable release version, see HDF5Array.

HDF5 backend for DelayedArray objects

Bioconductor version: Development (3.13)

Implement the HDF5Array, TENxMatrix, and H5ADMatrix classes, 3 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) a 10x Genomics sparse matrix, or (3) the matrix stored in an .h5ad file. These containers are DelayedArray extensions and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.

Author: Hervé Pagès

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.19.9
In Bioconductor since	BioC 3.3 (R-3.3) (5 years)
License	Artistic-2.0 + file src/lzf/LICENSE.txt
Depends	R (>= 3.4), methods, DelayedArray(>= 0.15.16), rhdf5(>= 2.31.6)
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.31.5), S4Vectors, IRanges
LinkingTo	S4Vectors(>= 0.27.13), Rhdf5lib
Suggests	BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment
SystemRequirements	GNU make
Enhances
URL	https://bioconductor.org/packages/HDF5Array
BugReports	https://github.com/Bioconductor/HDF5Array/issues
Depends On Me	GenoGAM, TENxBrainData, TENxPBMCData
Imports Me	biscuiteer, bsseq, clusterExperiment, curatedTCGAData, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, LoomExperiment, MafH5.gnomAD.r3.0.GRCh38, methrix, MethylSeqData, minfi, MOFA2, netSmooth, recountmethylation, scmeth, scry, sesame, signatureSearch, SingleCellMultiModal, spatialHeatmap
Suggests Me	BiocSklearn, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MultiAssayExperiment, scMerge, scran, SummarizedExperiment, zellkonverter
Links To Me
Build Report

Package Archives

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

Source Package	HDF5Array_1.19.9.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	HDF5Array_1.19.5.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