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beachmat bindings for HDF5-backed matrices

Bioconductor version: Release (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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Imports methods, beachmat, HDF5Array, DelayedArray, Rcpp
System Requirements C++17, GNU make
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Suggests testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
Linking To Rcpp, beachmat, Rhdf5lib
Depends On Me
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Follow Installation instructions to use this package in your R session.

Source Package beachmat.hdf5_1.2.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) beachmat.hdf5_1.2.0.tgz
macOS Binary (arm64) beachmat.hdf5_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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