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Bioconductor - HDF5Array

HDF5Array

This is the released version of HDF5Array; for the devel version, see HDF5Array.

HDF5 datasets as array-like objects in R

Bioconductor version: Release (3.21)

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 [aut, cre] ORCID: 0009-0002-8272-4522

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

Citation (from within R, enter citation("HDF5Array")): Installation

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HDF5Array")
Details biocViews Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software Version 1.36.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License Artistic-2.0 Depends R (>= 3.4), methods, SparseArray(>= 1.7.5), DelayedArray(>= 0.33.5), h5mread(>= 0.99.4) Imports utils, stats, tools, Matrix, BiocGenerics(>= 0.51.2), S4Vectors, IRanges, S4Arrays(>= 1.1.1), rhdf5 System Requirements 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, SingleCellExperiment, DelayedMatrixStats, genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle Linking To 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, methodical, methrix, minfi, MOFA2, netSmooth, orthos, recountmethylation, scmeth, signatureSearch, SpliceWiz, TENxIO, transformGamPoi, vmrseq, xenLite, MafH5.gnomAD.v4.0.GRCh38, curatedTCGAData, HCAData, HCATonsilData, imcdatasets, MerfishData, MethylSeqData, orthosData, scMultiome, SingleCellMultiModal, TabulaMurisSenisData, TumourMethData, ebvcube, rliger Suggests Me beachmat, BiocGenerics, BiocSklearn, cellxgenedp, DeconvoBuddies, DelayedArray, DelayedMatrixStats, h5mread, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MuData, MultiAssayExperiment, PDATK, QFeatures, S4Arrays, 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.

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