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

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

bioconductor-aucell
===================

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

   AUCell\: Analysis of \'gene set\' activity in single\-cell RNA\-seq data \(e.g. identify cells with specific gene signatures\)

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

   AUCell allows to identify cells with active gene sets \(e.g. signatures\, gene modules...\) in single\-cell RNA\-seq data. AUCell uses the \"Area Under the Curve\" \(AUC\) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking\-based\, AUCell is independent of the gene expression units and the normalization procedure. In addition\, since the cells are evaluated individually\, it can easily be applied to bigger datasets\, subsetting the expression matrix if needed.


.. conda:package:: bioconductor-aucell

   |downloads_bioconductor-aucell| |docker_bioconductor-aucell|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.1-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-1</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  </span></summary>
      

      ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.1-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.4.1-0``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0``
   :depends bioconductor-delayedmatrixstats: ``>=1.24.0,<1.25.0``
   :depends bioconductor-gseabase: ``>=1.64.0,<1.65.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-matrix: 
   :depends r-mixtools: 
   :depends r-r.utils: 
   :depends r-shiny: 
   :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-aucell

   and update with::

      mamba update bioconductor-aucell

  To create a new environment, run::

      mamba create --name myenvname bioconductor-aucell

  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-aucell:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-aucell";
        var versions = ["1.24.0","1.22.0","1.20.1","1.16.0","1.14.0"];
    </script>






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

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

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