rhdf5

DOI: 10.18129/B9.bioc.rhdf5  

R Interface to HDF5

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DataImport, Infrastructure, Software
Version	2.42.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods
Imports	Rhdf5lib(>= 1.13.4), rhdf5filters
LinkingTo	Rhdf5lib
Suggests	bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2, mockery
SystemRequirements	GNU make
Enhances
URL	https://github.com/grimbough/rhdf5
BugReports	https://github.com/grimbough/rhdf5/issues
Depends On Me	GSCA, HDF5Array, HiCBricks, LoomExperiment, MuData, octad
Imports Me	BayesSpace, BgeeCall, biomformat, bnbc, bsseq, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DmelSGI, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HiCcompare, HiCDOC, HiContacts, IONiseR, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, MethylSeqData, MOFA2, NxtIRFcore, phantasus, ptairData, ptairMS, PureCN, recountmethylation, ribor, scCB2, scone, signatureSearch, signatureSearchData, SpliceWiz, SpotClean, trackViewer
Suggests Me	edgeR, rhdf5filters, SCArray, slalom, Spectra, SummarizedExperiment, TENxIO, tximport, zellkonverter
Links To Me
Build Report

Package Archives

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

Source Package	rhdf5_2.42.1.tar.gz
Windows Binary	rhdf5_2.42.1.zip
macOS Binary (x86_64)	rhdf5_2.42.1.tgz
macOS Binary (arm64)	rhdf5_2.42.1.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 3.16	Source Archive