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

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

bioconductor-visiumio
=====================

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

   Import Visium data from the 10X Space Ranger pipeline

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/VisiumIO.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-visiumio <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-visiumio>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-visiumio/meta.yaml>`_

   The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz\, h5\, and mtx files. Multiple files can be imported at once with \*List type of functions. The package represents data mainly as SpatialExperiment objects.


.. conda:package:: bioconductor-visiumio

   |downloads_bioconductor-visiumio| |docker_bioconductor-visiumio|

   :versions:
      
      

      ``1.2.0-0``

      

   
   :depends bioconductor-biocbaseutils: ``>=1.8.0,<1.9.0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0``
   :depends bioconductor-biocio: ``>=1.16.0,<1.17.0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0``
   :depends bioconductor-singlecellexperiment: ``>=1.28.0,<1.29.0``
   :depends bioconductor-spatialexperiment: ``>=1.16.0,<1.17.0``
   :depends bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0``
   :depends bioconductor-tenxio: ``>=1.8.0,<1.9.0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :depends r-jsonlite: 
   :requirements:

   :additional platforms:
      

   .. 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-visiumio

   and update with::

      mamba update bioconductor-visiumio

  To create a new environment, run::

      mamba create --name myenvname bioconductor-visiumio

  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-visiumio:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-visiumio";
        var versions = ["1.2.0"];
    </script>






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

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

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

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

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-visiumio/README.html)

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