rhdf5
This is the development version of rhdf5; for the stable release version, see rhdf5.
R Interface to HDF5
Bioconductor version: Development (3.24)
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:
, Maintainer from 2017 to 2025), Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb], Hugo Gruson [cre]
, German Network for Bioinformatics Infrastructure - de.NBI [fnd] (ROR: <https://ror.org/01vmpm840>)
Maintainer: Hugo Gruson <hugo.gruson at embl.de>
citation("rhdf5")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Software |
| Version | 2.57.5 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | Artistic-2.0 |
| Depends | methods, R (>= 4.0.0) |
| Imports | rhdf5filters(>= 1.25.4), Rhdf5lib(>= 1.33.3) |
| System Requirements | GNU make |
| 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 |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rhdf5_2.57.5.tar.gz |
| Windows Binary (x86_64) | rhdf5_2.57.1.zip |
| macOS Binary (big-sur-x86_64) | rhdf5_2.57.5.tgz |
| macOS Binary (sonoma-arm64) | rhdf5_2.57.5.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 |