recipe bioconductor-tenxvisiumdata

Visium spatial gene expression data by 10X Genomics






Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.

package bioconductor-tenxvisiumdata

(downloads) docker_bioconductor-tenxvisiumdata



depends bioconductor-data-packages:


depends bioconductor-experimenthub:


depends bioconductor-spatialexperiment:


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-tenxvisiumdata

and update with::

   mamba update bioconductor-tenxvisiumdata

To create a new environment, run:

mamba create --name myenvname bioconductor-tenxvisiumdata

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

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