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rhdf5

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

R Interface to HDF5


Bioconductor version: Development (3.19)

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, cre] , Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb]

Maintainer: Mike Smith <mike.smith at embl.de>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews DataImport, Infrastructure, Software
Version 2.47.4
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods
Imports Rhdf5lib(>= 1.13.4), rhdf5filters
System Requirements GNU make
URL https://github.com/grimbough/rhdf5
Bug Reports https://github.com/grimbough/rhdf5/issues
See More
Suggests bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel
Linking To Rhdf5lib
Enhances
Depends On Me GSCA, HDF5Array, 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, CRISPRseek, cTRAP, cytomapper, diffHic, DmelSGI, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HiCcompare, HiCExperiment, IONiseR, MafH5.gnomAD.v3.1.2.GRCh38, mariner, methodical, MethylSeqData, MOFA2, MoleculeExperiment, phantasus, ptairData, ptairMS, PureCN, recountmethylation, ribor, scCB2, scMultiome, scone, scRNAseqApp, signatureSearch, signatureSearchData, SpliceWiz, SpotClean, SurfR, trackViewer, TumourMethData
Suggests Me beachmat.hdf5, edgeR, HiCDOC, pairedGSEA, phantasusLite, rhdf5filters, SCArray, scviR, slalom, SpatialFeatureExperiment, spatialHeatmap, Spectra, SummarizedExperiment, TENxIO, tximport, Voyager, zellkonverter
Links To Me
Build Report Build Report

Package Archives

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

Source Package rhdf5_2.47.4.tar.gz
Windows Binary rhdf5_2.47.4.zip
macOS Binary (x86_64) rhdf5_2.47.4.tgz
macOS Binary (arm64)
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