rhdf5
R Interface to HDF5
Bioconductor version: 3.24 · Package version: 2.57.18
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rhdf5")Details
| Maintainer | Hugo Gruson <hugo.gruson@embl.de> |
| Author | Bernd Fischer [aut], Mike Smith [aut] (ORCID: <https://orcid.org/0000-0002-7800-3848>, Maintainer from 2017 to 2025), Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb], Hugo Gruson [aut, cre] (ORCID: <https://orcid.org/0000-0002-4094-1476>), German Network for Bioinformatics Infrastructure - de.NBI [fnd] (ROR: <https://ror.org/01vmpm840>) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | GNU make |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/rhdf5/ |
Citation
From within R, enter citation("rhdf5"):
Bernd Fischer, Mike Smith, Gregoire Pau, Hugo Gruson. rhdf5: R Interface to HDF5. doi:10.18129/B9.bioc.rhdf5, R package version 2.57.18, https://bioconductor.org/packages/rhdf5.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | rhdf5_2.57.18.tar.gz |
| Windows binary (x86_64) | rhdf5_2.57.18.zip |
| macOS binary (arm64) | rhdf5_2.57.18.tgz |
| macOS binary (x86_64) | rhdf5_2.57.18.tgz |
Dependencies
Depends: methods, R (>= 4.0.0)
Imports: rhdf5filters (>= 1.25.4), Rhdf5lib (>= 1.33.3)
LinkingTo: Rhdf5lib
Suggests: bench, BiocParallel, BiocStyle, bit64, curl, dplyr, ggplot2, knitr, rmarkdown, testthat, withr
Reverse dependencies
Depends On Me (6): GSCA, h5mread, HiCBricks, LoomExperiment, MuData, octad
Imports Me (68): alabaster.base, alabaster.bumpy, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.spatial, BayesSpace, BgeeCall, bioRad, bnbc, bsseq, chihaya, CiteFuse, cmapR, CoGAPS, CONCERTDR, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DropletUtils, ebvcube, epigraHMM, EventPointer, file2meco, FRASER, GenomicScores, gep2pep, h5vc, HDF5Array, HicAggR, HiCcompare, HiCExperiment, HiCPotts, ImageArray, 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
Suggests Me (35): anndataR, beachmat.hdf5, biomformat, CLAMP, CLAMPData, ClustAssess, conos, CRMetrics, edgeR, getRad, HiCDOC, HiCParser, imageFeatureTCGA, imageTCGAutils, io, mia, MicrobiotaProcess, MplusAutomation, neonstore, neonUtilities, pairedGSEA, phantasusLite, rhdf5filters, SCArray, SignacX, slalom, SpatialFeatureExperiment, spatialHeatmap, Spectra, strollur, SummarizedExperiment, tximport, Voyager, xcms, zellkonverter