DOI: 10.18129/B9.bioc.rhdf5    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rhdf5.

R Interface to HDF5

Bioconductor version: 3.10

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], Gregoire Pau [aut], Mike Smith [aut, cre], 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 "3.6") and enter:

if (!requireNamespace("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 rhdf5
HTML R Script rhdf5 Practical Tips
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, Software
Version 2.30.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 15 years)
License Artistic-2.0
Depends R (>= 3.5.0), methods
Imports Rhdf5lib(>= 1.3.2)
LinkingTo Rhdf5lib
Suggests bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2
SystemRequirements GNU make
URL https://github.com/grimbough/rhdf5
BugReports https://github.com/grimbough/rhdf5/issues
Depends On Me GenoGAM, GSCA, HDF5Array, HiCBricks, LoomExperiment
Imports Me BgeeCall, biomformat, bsseq, CoGAPS, CopyNumberPlots, cTRAP, diffHic, DmelSGI, DropletUtils, EventPointer, gep2pep, h5vc, HiCcompare, IONiseR, KnowSeq, MOFA, phantasus, PureCN, scone, signatureSearch, signatureSearchData, slinky
Suggests Me edgeR, slalom, SummarizedExperiment, tximport
Links To Me
Build Report  

Package Archives

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

Source Package rhdf5_2.30.1.tar.gz
Windows Binary rhdf5_2.30.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) rhdf5_2.30.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/rhdf5
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rhdf5
Package Short Url https://bioconductor.org/packages/rhdf5/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: