DOI: 10.18129/B9.bioc.rhdf5  

R Interface to HDF5

Bioconductor version: Release (3.17)

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 embl.de>

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


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.


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



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


biocViews DataImport, Infrastructure, Software
Version 2.44.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods
Imports Rhdf5lib(>= 1.13.4), rhdf5filters
LinkingTo Rhdf5lib
Suggests bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel
SystemRequirements GNU make
URL https://github.com/grimbough/rhdf5
BugReports https://github.com/grimbough/rhdf5/issues
Depends On Me GSCA, HDF5Array, HiCBricks, LoomExperiment, MuData, octad
Imports Me alabaster.base, alabaster.matrix, BayesSpace, BgeeCall, biomformat, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DmelSGI, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HiCcompare, HiCDOC, HiCExperiment, IONiseR, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, mariner, MethylSeqData, MOFA2, MoleculeExperiment, NxtIRFcore, phantasus, ptairData, ptairMS, PureCN, recountmethylation, ribor, scCB2, scMultiome, scone, signatureSearch, signatureSearchData, SpliceWiz, SpotClean, trackViewer
Suggests Me edgeR, pairedGSEA, rhdf5filters, SCArray, scviR, slalom, SpatialFeatureExperiment, Spectra, SummarizedExperiment, TENxIO, tximport, Voyager, zellkonverter
Links To Me
Build Report  

Package Archives

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

Source Package rhdf5_2.44.0.tar.gz
Windows Binary rhdf5_2.44.0.zip (64-bit only)
macOS Binary (x86_64) rhdf5_2.44.0.tgz
macOS Binary (arm64) rhdf5_2.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rhdf5
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rhdf5
Bioc Package Browser https://code.bioconductor.org/browse/rhdf5/
Package Short Url https://bioconductor.org/packages/rhdf5/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

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