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rhdf5

R Interface to HDF5

Bioconductor version: 3.23 · Package version: 2.56.0

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rhdf5")

Details

MaintainerHugo Gruson <hugo.gruson@embl.de>
AuthorBernd Fischer [aut], Mike Smith [aut] (ORCID: <https://orcid.org/0000-0002-7800-3848>, Maintainer from 2017 to 2025), Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb], Hugo Gruson [cre] (ORCID: <https://orcid.org/0000-0002-4094-1476>), German Network for Bioinformatics Infrastructure - de.NBI [fnd]
LicenseArtistic-2.0
URLhttps://huber-group-embl.github.io/rhdf5/, https://github.com/Huber-group-EMBL/rhdf5
Bug Reportshttps://github.com/Huber-group-EMBL/rhdf5/issues
System RequirementsGNU make
Downloads rank26269
Source branchRELEASE_3_23
biocViewsDataImport, Infrastructure, Software

Documentation

Download

Dependencies

Depends: methods, R (>= 4.0.0)

Imports: rhdf5filters (>= 1.15.5), Rhdf5lib (>= 1.33.3)

LinkingTo: Rhdf5lib

Suggests: bench, BiocParallel, BiocStyle, bit64, curl, dplyr, ggplot2, knitr, rmarkdown, testthat, withr

Reverse dependencies

Depends On Me (6): GSCA, h5mread, HiCBricks, LoomExperiment, MuData, octad

Imports Me (68): alabaster.base, alabaster.bumpy, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.spatial, BayesSpace, BgeeCall, bioRad, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DropletUtils, ebvcube, epigraHMM, EventPointer, file2meco, FRASER, GenomicScores, h5vc, HDF5Array, HicAggR, HiCcompare, HiCExperiment, HiCPotts, ImageArray, IONiseR, karyotapR, LOMAR, MafH5.gnomAD.v4.0.GRCh38, mariner, methodical, MethylSeqData, MOFA2, MoleculeExperiment, OmicFlow, phantasus, plotgardener, ptairData, ptairMS, PureCN, RBedMethyl, rDataPipeline, recountmethylation, ribor, scafari, scCB2, scMitoMut, scMultiome, scone, scRNAseqApp, signatureSearch, signatureSearchData, SpaceTrooper, SpliceWiz, SpotClean, SurfR, TENxIO, trackViewer, TumourMethData

Suggests Me (34): anndataR, beachmat.hdf5, biomformat, ClustAssess, conos, CRMetrics, edgeR, getRad, HiCDOC, HiCParser, imageFeatureTCGA, imageTCGAutils, io, mia, MicrobiotaProcess, MplusAutomation, neonstore, neonUtilities, pairedGSEA, phantasusLite, rhdf5filters, SCArray, scviR, SignacX, slalom, SpatialFeatureExperiment, spatialHeatmap, Spectra, strollur, SummarizedExperiment, tximport, Voyager, xcms, zellkonverter