recipe bioconductor-merfishdata

Collection of public MERFISH datasets






MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

package bioconductor-merfishdata

(downloads) docker_bioconductor-merfishdata



depends bioconductor-annotationhub:


depends bioconductor-bumpymatrix:


depends bioconductor-data-packages:


depends bioconductor-ebimage:


depends bioconductor-experimenthub:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends curl:

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-merfishdata

and update with::

   mamba update bioconductor-merfishdata

To create a new environment, run:

mamba create --name myenvname bioconductor-merfishdata

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

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