recipe bioconductor-zellkonverter

Conversion Between scRNA-seq Objects






Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

package bioconductor-zellkonverter

(downloads) docker_bioconductor-zellkonverter



depends bioconductor-basilisk:


depends bioconductor-delayedarray:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-cli:

depends r-matrix:

depends r-reticulate:



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-zellkonverter

and update with::

   mamba update bioconductor-zellkonverter

To create a new environment, run:

mamba create --name myenvname bioconductor-zellkonverter

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

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