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

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

bioconductor-eegc
=================

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

   Engineering Evaluation by Gene Categorization \(eegc\)

   :homepage: https://bioconductor.org/packages/3.17/bioc/html/eegc.html
   :license: GPL-2
   :recipe: /`bioconductor-eegc <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-eegc>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-eegc/meta.yaml>`_

   This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion \(transdifferentiation\) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. The package takes gene expression profiles as inputs from three types of samples\: \(i\) somatic or stem cells to be \(trans\)differentiated \(input of the engineering process\)\, \(ii\) induced cells to be evaluated \(output of the engineering process\) and \(iii\) target primary cells \(reference for the output\). The package performs differential gene expression analysis for each pair\-wise sample comparison to identify and evaluate the transcriptional differences among the 3 types of samples \(input\, output\, reference\). The ideal goal is to have induced and primary reference cell showing overlapping profiles\, both very different from the original cells.


.. conda:package:: bioconductor-eegc

   |downloads_bioconductor-eegc| |docker_bioconductor-eegc|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-1</code>,  </span></summary>
      

      ``1.26.0-0``,  ``1.24.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.8.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationdbi: ``>=1.62.0,<1.63.0``
   :depends bioconductor-clusterprofiler: ``>=4.8.0,<4.9.0``
   :depends bioconductor-deseq2: ``>=1.40.0,<1.41.0``
   :depends bioconductor-dose: ``>=3.26.0,<3.27.0``
   :depends bioconductor-edger: ``>=3.42.0,<3.43.0``
   :depends bioconductor-limma: ``>=3.56.0,<3.57.0``
   :depends bioconductor-org.hs.eg.db: ``>=3.17.0,<3.18.0``
   :depends bioconductor-org.mm.eg.db: ``>=3.17.0,<3.18.0``
   :depends bioconductor-s4vectors: ``>=0.38.0,<0.39.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-ggplot2: 
   :depends r-gplots: 
   :depends r-igraph: 
   :depends r-pheatmap: 
   :depends r-r.utils: 
   :depends r-sna: 
   :depends r-wordcloud: 
   :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-eegc

   and update with::

      mamba update bioconductor-eegc

  To create a new environment, run::

      mamba create --name myenvname bioconductor-eegc

  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-eegc:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-eegc";
        var versions = ["1.26.0","1.24.0","1.20.0","1.18.0","1.16.0"];
    </script>






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

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

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