HDF5Array

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

HDF5 backend for DelayedArray objects

Bioconductor version: Development (3.18)

Implement the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.

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 "4.3") and enter:

if (!require("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


Reference Manual	PDF
NEWS	Text

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version	1.29.3
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), methods, DelayedArray(>= 0.27.2), rhdf5(>= 2.31.6)
Imports	utils, stats, tools, Matrix, rhdf5filters, BiocGenerics(>= 0.31.5), S4Vectors, IRanges, S4Arrays(>= 1.1.1)
Linking To	S4Vectors(>= 0.27.13), Rhdf5lib
Suggests	BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment
System Requirements	GNU make
Enhances
URL	https://bioconductor.org/packages/HDF5Array
Bug Reports	https://github.com/Bioconductor/HDF5Array/issues

Depends On Me	compartmap, MAGAR, restfulSEData, TENxBrainData, TENxPBMCData
Imports Me	alabaster.matrix, biscuiteer, bsseq, Cepo, chihaya, clusterExperiment, CuratedAtlasQueryR, curatedTCGAData, cytomapper, DelayedTensor, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, imcdatasets, LoomExperiment, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, mariner, methrix, MethylSeqData, minfi, MOFA2, netSmooth, orthos, orthosData, recountmethylation, scmeth, scMultiome, signatureSearch, SingleCellMultiModal, SpliceWiz, TabulaMurisSenisData, transformGamPoi
Suggests Me	beachmat, BiocSklearn, cellxgenedp, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MuData, MultiAssayExperiment, PDATK, QFeatures, SCArray, scMerge, scran, scry, spatialHeatmap, spicyWorkflow, SummarizedExperiment, TENxIO, zellkonverter
Links To Me
Build Report

Package Archives

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

Source Package	HDF5Array_1.29.3.tar.gz
Windows Binary	HDF5Array_1.29.3.zip (64-bit only)
macOS Binary (x86_64)	HDF5Array_1.29.3.tgz
macOS Binary (arm64)
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