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beachmat.hdf5

This is the development version of beachmat.hdf5; for the stable release version, see beachmat.hdf5.

beachmat bindings for HDF5-backed matrices


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("beachmat.hdf5")):

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("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")
User guide HTML R Script
Reference Manual PDF

Details

biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3
Depends
Imports methods, beachmat, HDF5Array, DelayedArray, Rcpp
System Requirements C++17, GNU make
URL
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
Linking To Rcpp, beachmat, Rhdf5lib
Enhances
Depends On Me
Imports Me
Suggests Me sketchR
Links To Me
Build Report Build Report

Package Archives

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

Source Package beachmat.hdf5_1.1.0.tar.gz
Windows Binary beachmat.hdf5_1.1.0.zip (64-bit only)
macOS Binary (x86_64) beachmat.hdf5_1.1.0.tgz
macOS Binary (arm64) beachmat.hdf5_1.1.0.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