HDF5Array

HDF5 datasets as array-like objects in R

Bioconductor version: Release (3.20)

The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements 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 "4.4") 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	1.34.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), methods, SparseArray(>= 1.5.42), DelayedArray(>= 0.31.8), rhdf5(>= 2.31.6)
Imports	utils, stats, tools, Matrix, rhdf5filters, BiocGenerics(>= 0.51.2), S4Vectors, IRanges, S4Arrays(>= 1.1.1)
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, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter
Linking To	S4Vectors(>= 0.27.13), Rhdf5lib
Enhances
Depends On Me	MAGAR, TENxBrainData, TENxPBMCData
Imports Me	alabaster.matrix, beachmat.hdf5, BgeeDB, biscuiteer, bsseq, Cepo, chihaya, clusterExperiment, CuratedAtlasQueryR, cytomapper, DelayedTensor, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, lemur, LoomExperiment, mariner, methrix, minfi, MOFA2, netSmooth, orthos, recountmethylation, scmeth, signatureSearch, SpliceWiz, TENxIO, transformGamPoi, xenLite, MafH5.gnomAD.v4.0.GRCh38, curatedTCGAData, HCAData, HCATonsilData, imcdatasets, MerfishData, MethylSeqData, orthosData, scMultiome, SingleCellMultiModal, TabulaMurisSenisData, TumourMethData, ebvcube
Suggests Me	beachmat, BiocGenerics, BiocSklearn, cellxgenedp, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MuData, MultiAssayExperiment, QFeatures, SCArray, scMerge, scran, scry, SparseArray, spatialHeatmap, SummarizedExperiment, zellkonverter, STexampleData, spicyWorkflow, SeuratObject, SpatialDDLS
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	HDF5Array_1.34.0.tar.gz
Windows Binary (x86_64)	HDF5Array_1.34.0.zip
macOS Binary (x86_64)	HDF5Array_1.34.0.tgz
macOS Binary (arm64)	HDF5Array_1.34.0.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