:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'bioconductor-hcatonsildata'
.. highlight: bash

bioconductor-hcatonsildata
==========================

.. conda:recipe:: bioconductor-hcatonsildata
   :replaces_section_title:
   :noindex:

   Provide programmatic access to the tonsil cell atlas datasets

   :homepage: https://bioconductor.org/packages/3.18/data/experiment/html/HCATonsilData.html
   :license: MIT + file LICENSE
   :recipe: /`bioconductor-hcatonsildata <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-hcatonsildata>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-hcatonsildata/meta.yaml>`_

   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.


.. conda:package:: bioconductor-hcatonsildata

   |downloads_bioconductor-hcatonsildata| |docker_bioconductor-hcatonsildata|

   :versions:
      
      

      ``1.0.0-0``

      

   
   :depends bioconductor-data-packages: ``>=20231203``
   :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0``
   :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-spatialexperiment: ``>=1.12.0,<1.13.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends curl: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-base64enc: 
   :depends r-htmltools: 
   :depends r-rmarkdown: 
   :requirements:

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ 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 <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/bioconductor-hcatonsildata:<tag>

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


.. |downloads_bioconductor-hcatonsildata| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-hcatonsildata.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-hcatonsildata
   :alt:   (downloads)
.. |docker_bioconductor-hcatonsildata| image:: https://quay.io/repository/biocontainers/bioconductor-hcatonsildata/status
   :target: https://quay.io/repository/biocontainers/bioconductor-hcatonsildata
.. _`bioconductor-hcatonsildata/tags`: https://quay.io/repository/biocontainers/bioconductor-hcatonsildata?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-hcatonsildata";
        var versions = ["1.0.0"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-hcatonsildata/README.html