rhdf5

This is the development version of rhdf5; for the stable release version, see rhdf5.

R Interface to HDF5

Bioconductor version: Development (3.22)

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] (ORCID: ORCID: 0000-0002-7800-3848 , Maintainer from 2017 to 2025), Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb], Hugo Gruson [cre] ORCID: 0000-0002-4094-1476

Maintainer: Hugo Gruson <hugo.gruson at embl.de>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rhdf5")

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("rhdf5")

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
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, Software
Version	2.53.6
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 20.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods
Imports	Rhdf5lib(>= 1.13.4), rhdf5filters(>= 1.15.5)
System Requirements	GNU make
URL	https://github.com/Huber-group-EMBL/rhdf5
Bug Reports	https://github.com/Huber-group-EMBL/rhdf5/issues

Suggests	bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel
Linking To	Rhdf5lib
Enhances
Depends On Me	GSCA, h5mread, HiCBricks, LoomExperiment, MuData, octad
Imports Me	alabaster.base, alabaster.bumpy, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.spatial, BayesSpace, BgeeCall, biomformat, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, cTRAP, cytomapper, diffHic, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HDF5Array, HicAggR, HiCcompare, HiCExperiment, HiCPotts, IONiseR, mariner, MOFA2, MoleculeExperiment, phantasus, plotgardener, ptairMS, PureCN, recountmethylation, ribor, scafari, scCB2, scMitoMut, scone, scRNAseqApp, signatureSearch, SpaceTrooper, SpliceWiz, SpotClean, SurfR, TENxIO, trackViewer, MafH5.gnomAD.v4.0.GRCh38, MethylSeqData, ptairData, scMultiome, signatureSearchData, TumourMethData, bioRad, ebvcube, file2meco, karyotapR, LOMAR, NEONiso, OmicFlow, rDataPipeline
Suggests Me	beachmat.hdf5, edgeR, HiCDOC, HiCParser, mia, pairedGSEA, phantasusLite, rhdf5filters, SCArray, scviR, slalom, SpatialFeatureExperiment, Spectra, SummarizedExperiment, tximport, Voyager, xcms, zellkonverter, ClustAssess, conos, CRMetrics, getRad, io, MplusAutomation, neonstore, neonUtilities, 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_2.53.6.tar.gz
Windows Binary (x86_64)	rhdf5_2.53.4.zip
macOS Binary (x86_64)	rhdf5_2.53.6.tgz
macOS Binary (arm64)	rhdf5_2.53.6.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