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

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

bioconductor-spotclean
======================

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

   SpotClean adjusts for spot swapping in spatial transcriptomics data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/SpotClean.html
   :license: GPL-3
   :recipe: /`bioconductor-spotclean <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-spotclean>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-spotclean/meta.yaml>`_

   SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot\-specific barcodes that bind mRNA. Ideally\, unique molecular identifiers at a spot measure spot\-specific expression\, but this is often not the case due to bleed from nearby spots\, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect\, thus increase the sensitivity and precision of downstream analyses.


.. conda:package:: bioconductor-spotclean

   |downloads_bioconductor-spotclean| |docker_bioconductor-spotclean|

   :versions:
      
      

      ``1.4.1-0``,  ``1.2.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-spatialexperiment: ``>=1.12.0,<1.13.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-matrix: 
   :depends r-rcolorbrewer: 
   :depends r-readbitmap: 
   :depends r-rjson: 
   :depends r-rlang: 
   :depends r-seurat: 
   :depends r-tibble: 
   :depends r-viridis: 
   :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-spotclean

   and update with::

      mamba update bioconductor-spotclean

  To create a new environment, run::

      mamba create --name myenvname bioconductor-spotclean

  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-spotclean:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-spotclean";
        var versions = ["1.4.1","1.2.0","1.0.0"];
    </script>






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

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

Link to this page
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