recipe bioconductor-singlecellexperiment

S4 Classes for Single Cell Data






Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

package bioconductor-singlecellexperiment

(downloads) docker_bioconductor-singlecellexperiment



depends bioconductor-biocgenerics:


depends bioconductor-delayedarray:


depends bioconductor-genomicranges:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:




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-singlecellexperiment

and update with::

   mamba update bioconductor-singlecellexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-singlecellexperiment

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

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