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

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

bioconductor-banksy
===================

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

   Spatial transcriptomic clustering

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/Banksy.html
   :license: file LICENSE
   :recipe: /`bioconductor-banksy <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-banksy>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-banksy/meta.yaml>`_

   Banksy is an R package that incorporates spatial information to cluster cells in a feature space \(e.g. gene expression\). To incorporate spatial information\, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell\'s own expression to embed cells in a neighbor\-augmented product space which can then be clustered\, allowing for accurate and spatially\-aware cell typing and tissue domain segmentation.


.. conda:package:: bioconductor-banksy

   |downloads_bioconductor-banksy| |docker_bioconductor-banksy|

   :versions:
      
      

      

      

   
   :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-banksy

   and update with::

      mamba update bioconductor-banksy

  To create a new environment, run::

      mamba create --name myenvname bioconductor-banksy

  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-banksy:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-banksy";
        var versions = [];
    </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-banksy/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-banksy/README.html