recipe bioconductor-singlecellmultimodal

Integrating Multi-modal Single Cell Experiment datasets






SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis.

package bioconductor-singlecellmultimodal

(downloads) docker_bioconductor-singlecellmultimodal



depends bioconductor-annotationhub:


depends bioconductor-biocbaseutils:


depends bioconductor-biocfilecache:


depends bioconductor-data-packages:


depends bioconductor-experimenthub:


depends bioconductor-hdf5array:


depends bioconductor-multiassayexperiment:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends curl:

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-singlecellmultimodal

and update with::

   mamba update bioconductor-singlecellmultimodal

To create a new environment, run:

mamba create --name myenvname bioconductor-singlecellmultimodal

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

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