DOI: 10.18129/B9.bioc.HDF5Array  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HDF5Array.

HDF5 backend for DelayedArray objects

Bioconductor version: 3.16

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")):


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biocViews Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version 1.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7 years)
License Artistic-2.0
Depends R (>= 3.4), methods, DelayedArray(>= 0.15.16), rhdf5(>= 2.31.6)
Imports utils, stats, tools, Matrix, rhdf5filters, 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
URL https://bioconductor.org/packages/HDF5Array
BugReports https://github.com/Bioconductor/HDF5Array/issues
Depends On Me compartmap, MAGAR, restfulSEData, TENxBrainData, TENxPBMCData
Imports Me biscuiteer, bsseq, Cepo, clusterExperiment, curatedTCGAData, cytomapper, DelayedTensor, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, imcdatasets, LoomExperiment, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, methrix, MethylSeqData, minfi, MOFA2, netSmooth, NxtIRFcore, recountmethylation, scmeth, scry, signatureSearch, SingleCellMultiModal, SpliceWiz, TabulaMurisSenisData, transformGamPoi
Suggests Me beachmat, BiocSklearn, cellxgenedp, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MuData, MultiAssayExperiment, PDATK, QFeatures, SCArray, scMerge, scran, spatialHeatmap, SummarizedExperiment, TENxIO, zellkonverter
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Source Package HDF5Array_1.26.0.tar.gz
Windows Binary HDF5Array_1.26.0.zip
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Bioc Package Browser https://code.bioconductor.org/browse/HDF5Array/
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