rhdf5

This is thereleased version of rhdf5; for the devel version, seerhdf5.

R Interface to HDF5

DOI: 10.18129/B9.bioc.rhdf5

Bioconductor version: Release (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, entercitation("rhdf5")):

Installation

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

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("rhdf5")

For older versions of R, please refer to the appropriateBioconductor 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	2.54.1
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,methodical,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,BigDataStatMeth,bioRad,ebvcube,file2meco,karyotapR,LOMAR,NEONiso,OmicFlow,rDataPipeline
Suggests Me	anndataR,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
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	rhdf5_2.54.1.tar.gz
Windows Binary (x86_64)	rhdf5_2.54.0.zip
macOS Binary (x86_64)	rhdf5_2.54.1.tgz
macOS Binary (arm64)	rhdf5_2.54.1.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 3.22	Source Archive

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