recipe bioconductor-beachmat.hdf5

beachmat bindings for HDF5-backed matrices






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.

package bioconductor-beachmat.hdf5

(downloads) docker_bioconductor-beachmat.hdf5



depends bioconductor-beachmat:


depends bioconductor-beachmat:


depends bioconductor-delayedarray:


depends bioconductor-delayedarray:


depends bioconductor-hdf5array:


depends bioconductor-hdf5array:


depends bioconductor-rhdf5lib:


depends bioconductor-rhdf5lib:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends libstdcxx-ng:


depends r-base:


depends r-rcpp:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-beachmat.hdf5

and update with::

   mamba update bioconductor-beachmat.hdf5

To create a new environment, run:

mamba create --name myenvname bioconductor-beachmat.hdf5

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-beachmat.hdf5/tags`_ for valid values for ``<tag>``)

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