recipe bioconductor-hdf5array

HDF5 backend for DelayedArray objects







biotools: hdf5array, doi: 10.1038/nmeth.3252

Implement the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.

package bioconductor-hdf5array

(downloads) docker_bioconductor-hdf5array



depends bioconductor-biocgenerics:


depends bioconductor-biocgenerics:


depends bioconductor-delayedarray:


depends bioconductor-delayedarray:


depends bioconductor-iranges:


depends bioconductor-iranges:


depends bioconductor-rhdf5:


depends bioconductor-rhdf5:


depends bioconductor-rhdf5filters:


depends bioconductor-rhdf5filters:


depends bioconductor-rhdf5lib:


depends bioconductor-rhdf5lib:


depends bioconductor-s4arrays:


depends bioconductor-s4arrays:


depends bioconductor-s4vectors:


depends bioconductor-s4vectors:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:


depends r-matrix:



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-hdf5array

and update with::

   mamba update bioconductor-hdf5array

To create a new environment, run:

mamba create --name myenvname bioconductor-hdf5array

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-hdf5array/tags`_ for valid values for ``<tag>``)

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