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

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

bioconductor-bayesspace
=======================

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

   Clustering and Resolution Enhancement of Spatial Transcriptomes

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

   Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low\-dimensional representation of the gene expression matrix\, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low\-dimensional representation into \"sub\-spots\"\, for which features such as gene expression or cell type composition can be imputed.


.. conda:package:: bioconductor-bayesspace

   |downloads_bioconductor-bayesspace| |docker_bioconductor-bayesspace|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.20.2-0</code>,  <code>1.12.0-0</code>,  <code>1.10.1-0</code>,  <code>1.8.0-1</code>,  <code>1.8.0-0</code>,  <code>1.4.1-1</code>,  <code>1.4.1-0</code>,  <code>1.4.0-0</code>,  <code>1.2.0-0</code>,  </span></summary>
      

      ``1.20.2-0``,  ``1.12.0-0``,  ``1.10.1-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.4.1-1``,  ``1.4.1-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocfilecache: ``>=3.0.0,<3.1.0``
   :depends bioconductor-biocfilecache: ``>=3.0.0,<3.1.0a0``
   :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0``
   :depends bioconductor-biocparallel: ``>=1.44.0,<1.45.0a0``
   :depends bioconductor-biocsingular: ``>=1.26.0,<1.27.0``
   :depends bioconductor-biocsingular: ``>=1.26.1,<1.27.0a0``
   :depends bioconductor-rhdf5: ``>=2.54.0,<2.55.0``
   :depends bioconductor-rhdf5: ``>=2.54.1,<2.55.0a0``
   :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0``
   :depends bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0``
   :depends bioconductor-scater: ``>=1.38.0,<1.39.0``
   :depends bioconductor-scater: ``>=1.38.0,<1.39.0a0``
   :depends bioconductor-scran: ``>=1.38.0,<1.39.0``
   :depends bioconductor-scran: ``>=1.38.0,<1.39.0a0``
   :depends bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0``
   :depends bioconductor-singlecellexperiment: ``>=1.32.0,<1.33.0a0``
   :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.40.0,<1.41.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc: ``>=14``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends liblzma: ``>=5.8.2,<6.0a0``
   :depends libstdcxx: ``>=14``
   :depends libzlib: ``>=1.3.1,<2.0a0``
   :depends r-arrow: 
   :depends r-assertthat: 
   :depends r-base: ``>=4.5,<4.6.0a0``
   :depends r-coda: 
   :depends r-dirichletreg: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-magrittr: 
   :depends r-matrix: 
   :depends r-mclust: 
   :depends r-microbenchmark: 
   :depends r-purrr: 
   :depends r-rcpp: ``>=1.0.4.6``
   :depends r-rcpparmadillo: 
   :depends r-rcppdist: 
   :depends r-rcppprogress: 
   :depends r-rcurl: 
   :depends r-rjson: 
   :depends r-rlang: 
   :depends r-scales: 
   :depends r-tibble: 
   :depends r-tidyr: 
   :depends r-xgboost: ``>=3.0.0``
   :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-bayesspace

   and update with::

      mamba update bioconductor-bayesspace

  To create a new environment, run::

      mamba create --name myenvname bioconductor-bayesspace

  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-bayesspace:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-bayesspace";
        var versions = ["1.20.2","1.12.0","1.10.1","1.8.0","1.8.0"];
    </script>






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

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

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