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R Interface to HDF5

Bioconductor version: Release (3.19)

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.

Author: Bernd Fischer [aut], Mike Smith [aut, cre] , Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb]

Maintainer: Mike Smith <mike.smith at>

Citation (from within R, enter citation("rhdf5")):


To install this package, start R (version "4.4") and enter:

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


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


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

Reading HDF5 Files In The Cloud HTML R Script
rhdf5 - HDF5 interface for R HTML R Script
rhdf5 Practical Tips HTML R Script
Reference Manual PDF


biocViews DataImport, Infrastructure, Software
Version 2.48.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods
Imports Rhdf5lib(>= 1.13.4), rhdf5filters(>= 1.15.5)
System Requirements GNU make
Bug Reports
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Suggests bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel
Linking To Rhdf5lib
Depends On Me GSCA, HDF5Array, HiCBricks, LoomExperiment, MuData, octad
Imports Me alabaster.base, alabaster.bumpy, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.spatial, BayesSpace, biomformat, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, cTRAP, cytomapper, diffHic, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HicAggR, HiCcompare, HiCExperiment, IONiseR, mariner, methodical, MOFA2, MoleculeExperiment, phantasus, ptairMS, PureCN, recountmethylation, ribor, scCB2, scMitoMut, scone, scRNAseqApp, signatureSearch, SpliceWiz, SpotClean, SurfR, trackViewer, MafH5.gnomAD.v3.1.2.GRCh38, MafH5.gnomAD.v4.0.GRCh38, DmelSGI, MethylSeqData, ptairData, scMultiome, signatureSearchData, TumourMethData, ebvcube, file2meco, karyotapR, LOMAR, NEONiso, ondisc, rDataPipeline
Suggests Me beachmat.hdf5, edgeR, HiCDOC, pairedGSEA, phantasusLite, rhdf5filters, SCArray, scviR, slalom, SpatialFeatureExperiment, spatialHeatmap, Spectra, SummarizedExperiment, TENxIO, tximport, Voyager, zellkonverter, conos, CRMetrics, digitalDLSorteR, io, MplusAutomation, neonstore, neonUtilities, rbiom, SignacX, SpatialDDLS
Links To Me
Build Report Build Report

Package Archives

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

Source Package rhdf5_2.48.0.tar.gz
Windows Binary
macOS Binary (x86_64) rhdf5_2.48.0.tgz
macOS Binary (arm64) rhdf5_2.48.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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