rhdf5

This is the released version of rhdf5; for the devel version, see rhdf5.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

R Interface to HDF5

Bioconductor version: Release (3.23)

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 , German Network for Bioinformatics Infrastructure - de.NBI [fnd]

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

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

Bernd Fischer, Mike Smith, Gregoire Pau. rhdf5: R Interface to HDF5. doi:10.18129/B9.bioc.rhdf5, R package version 2.56.1, https://bioconductor.org/packages/rhdf5.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, Software
Version	2.56.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 years)
License	Artistic-2.0
Depends	methods, R (>= 4.0.0)
Imports	rhdf5filters (>= 1.15.5), Rhdf5lib (>= 1.33.3)
System Requirements	GNU make
URL	https://huber-group-embl.github.io/rhdf5/ https://github.com/Huber-group-EMBL/rhdf5
Bug Reports	https://github.com/Huber-group-EMBL/rhdf5/issues

Suggests	bench, BiocParallel, BiocStyle, bit64, curl, dplyr, ggplot2, knitr, rmarkdown, testthat, withr
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, bioRad, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DropletUtils, ebvcube, epigraHMM, EventPointer, file2meco, FRASER, GenomicScores, gep2pep, 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	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
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	rhdf5_2.56.1.tar.gz
Windows Binary (x86_64)	rhdf5_2.56.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	rhdf5_2.56.1.tgz
macOS Binary (sonoma-arm64)	rhdf5_2.56.1.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
Old Source Packages for BioC 3.23	Source Archive