rhdf5
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see rhdf5.
R Interface to HDF5
Bioconductor version: 3.13
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("rhdf5")):
Installation
To install this package, start R (version "4.1") 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")| 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 2.36.0 |
| 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, microbenchmark, dplyr, ggplot2 |
| Linking To | Rhdf5lib |
| Enhances | |
| Depends On Me | GenoGAM, GSCA, HDF5Array, HiCBricks, LoomExperiment |
| Imports Me | BayesSpace, BgeeCall, biomformat, bnbc, bsseq, CiteFuse, cmapR, CoGAPS, CopyNumberPlots, CRISPRseek, cTRAP, cytomapper, diffHic, DmelSGI, DropletUtils, epigraHMM, EventPointer, FRASER, GenomicScores, gep2pep, h5vc, HiCcompare, IONiseR, MafH5.gnomAD.r3.0.GRCh38, MafH5.gnomAD.v3.1.1.GRCh38, MethylSeqData, MOFA2, phantasus, ptairData, ptairMS, PureCN, recountmethylation, ribor, scCB2, scone, signatureSearch, signatureSearchData, slinky, trackViewer |
| Suggests Me | edgeR, rhdf5filters, slalom, Spectra, SummarizedExperiment, tximport, zellkonverter |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rhdf5_2.36.0.tar.gz |
| Windows Binary | rhdf5_2.36.0.zip |
| macOS 10.13 (High Sierra) | rhdf5_2.36.0.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 3.13 | Source Archive |