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HDF5 backend for DelayedArray objects

Bioconductor version: Release (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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


Reference Manual PDF


biocViews Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version 1.30.1
In Bioconductor since BioC 3.3 (R-3.3) (8 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)
System Requirements GNU make
URL https://bioconductor.org/packages/HDF5Array
Bug Reports https://github.com/Bioconductor/HDF5Array/issues
See More
Suggests BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter
Linking To S4Vectors(>= 0.27.13), Rhdf5lib
Depends On Me compartmap, MAGAR, restfulSEData, TENxBrainData, TENxPBMCData
Imports Me alabaster.matrix, beachmat.hdf5, biscuiteer, bsseq, Cepo, chihaya, clusterExperiment, CuratedAtlasQueryR, curatedTCGAData, cytomapper, DelayedTensor, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, HCATonsilData, imcdatasets, lemur, LoomExperiment, MafH5.gnomAD.v3.1.2.GRCh38, mariner, methrix, MethylSeqData, minfi, MOFA2, netSmooth, orthos, orthosData, recountmethylation, scmeth, scMultiome, signatureSearch, SingleCellMultiModal, SpliceWiz, TabulaMurisSenisData, transformGamPoi, TumourMethData
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
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Package Archives

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

Source Package HDF5Array_1.30.1.tar.gz
Windows Binary HDF5Array_1.30.1.zip (64-bit only)
macOS Binary (x86_64) HDF5Array_1.30.0.tgz
macOS Binary (arm64) HDF5Array_1.30.1.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 3.18 Source Archive