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

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

bioconductor-cellscore
======================

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

   Tool for Evaluation of Cell Identity from Transcription Profiles

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/CellScore.html
   :license: GPL-3
   :recipe: /`bioconductor-cellscore <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-cellscore>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-cellscore/meta.yaml>`_

   The CellScore package contains functions to evaluate the cell identity of a test sample\, given a cell transition defined with a starting \(donor\) cell type and a desired target cell type. The evaluation is based upon a scoring system\, which uses a set of standard samples of known cell types\, as the reference set. The functions have been carried out on a large set of microarray data from one platform \(Affymetrix Human Genome U133 Plus 2.0\). In principle\, the method could be applied to any expression dataset\, provided that there are a sufficient number of standard samples and that the data are normalized.


.. conda:package:: bioconductor-cellscore

   |downloads_bioconductor-cellscore| |docker_bioconductor-cellscore|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.26.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-1</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  </span></summary>
      

      ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.2.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-biobase: ``>=2.66.0,<2.67.0``
   :depends on bioconductor-summarizedexperiment: ``>=1.36.0,<1.37.0``
   :depends on r-base: ``>=4.4,<4.5.0a0``
   :depends on r-gplots: ``>=3.0.1``
   :depends on r-lsa: ``>=0.73.1``
   :depends on r-rcolorbrewer: ``>=1.1-2``
   :depends on r-squash: ``>=1.0.8``

   :additional platforms:
      

Installation
------------

You need a conda-compatible package manager
(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
and the Bioconda channel already activated (see :ref:`bioconda_setup`).
Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi
""""

With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
to install globally, run::

    pixi global install bioconductor-cellscore

to add into an existing workspace instead, run::

    pixi add bioconductor-cellscore

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::

    pixi workspace channel add conda-forge
    pixi workspace channel add bioconda

Conda
"""""

With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::

    conda install bioconductor-cellscore

Alternatively, to install into a new environment, run::

    conda create -n envname bioconductor-cellscore

with ``envname`` being the name of the desired environment.

Container
"""""""""

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
For e.g. docker, run::

    docker pull quay.io/biocontainers/bioconductor-cellscore:<tag>

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

Integrated deployment
"""""""""""""""""""""

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency.
Check the documentation of your workflow management system to find out about the integration.

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


.. raw:: html

    <script>
        var package = "bioconductor-cellscore";
        var versions = ["1.26.0","1.22.0","1.20.0","1.18.0","1.14.0"];
    </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-cellscore/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-cellscore/README.html