beachmat.hdf5

DOI: 10.18129/B9.bioc.beachmat.hdf5  

beachmat bindings for HDF5-backed matrices

Bioconductor version: Release (3.18)

Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("beachmat.hdf5")

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("beachmat.hdf5")

 

HTML	R Script	User guide
PDF		Reference Manual

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends
Imports	methods, beachmat, HDF5Array, DelayedArray, Rcpp
LinkingTo	Rcpp, beachmat, Rhdf5lib
Suggests	testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
SystemRequirements	C++17, GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	beachmat.hdf5_1.0.0.tar.gz
Windows Binary	beachmat.hdf5_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	beachmat.hdf5_1.0.0.tgz
macOS Binary (arm64)	beachmat.hdf5_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/beachmat.hdf5
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/beachmat.hdf5
Bioc Package Browser	https://code.bioconductor.org/browse/beachmat.hdf5/
Package Short Url	https://bioconductor.org/packages/beachmat.hdf5/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive