recipe bioconductor-hcatonsildata

Provide programmatic access to the tonsil cell atlas datasets






This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

package bioconductor-hcatonsildata

(downloads) docker_bioconductor-hcatonsildata



depends bioconductor-data-packages:


depends bioconductor-experimenthub:


depends bioconductor-hdf5array:


depends bioconductor-s4vectors:


depends bioconductor-singlecellexperiment:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends curl:

depends r-base:


depends r-base64enc:

depends r-htmltools:

depends r-rmarkdown:



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-hcatonsildata

and update with::

   mamba update bioconductor-hcatonsildata

To create a new environment, run:

mamba create --name myenvname bioconductor-hcatonsildata

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

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