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

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

bioconductor-infercnv
=====================

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

   Infer Copy Number Variation from Single\-Cell RNA\-Seq Data

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/infercnv.html
   :license: BSD_3_clause + file LICENSE
   :recipe: /`bioconductor-infercnv <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-infercnv>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-infercnv/meta.yaml>`_

   Using single\-cell RNA\-Seq expression to visualize CNV in cells.


.. conda:package:: bioconductor-infercnv

   |downloads_bioconductor-infercnv| |docker_bioconductor-infercnv|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.18.1-1</code>,  <code>1.18.1-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.10.0-0</code>,  <code>1.8.0-0</code>,  <code>1.6.0-1</code>,  <code>1.6.0-0</code>,  <code>1.4.0-0</code>,  </span></summary>
      

      ``1.18.1-1``,  ``1.18.1-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.3-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-edger: ``>=4.0.0,<4.1.0``
   :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends jags: ``4.*.*``
   :depends r-ape: 
   :depends r-argparse: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-catools: 
   :depends r-coda: 
   :depends r-coin: 
   :depends r-digest: 
   :depends r-doparallel: 
   :depends r-dplyr: 
   :depends r-fastcluster: 
   :depends r-fitdistrplus: 
   :depends r-foreach: 
   :depends r-futile.logger: 
   :depends r-future: 
   :depends r-ggplot2: 
   :depends r-gplots: 
   :depends r-gridextra: 
   :depends r-hiddenmarkov: 
   :depends r-htmltools: ``>=0.5.7``
   :depends r-igraph: 
   :depends r-matrix: 
   :depends r-paralleldist: 
   :depends r-phyclust: 
   :depends r-rann: 
   :depends r-rcolorbrewer: 
   :depends r-reshape2: 
   :depends r-rjags: 
   :depends r-seurat: 
   :depends r-tidyr: 
   :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-infercnv

   and update with::

      mamba update bioconductor-infercnv

  To create a new environment, run::

      mamba create --name myenvname bioconductor-infercnv

  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-infercnv:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-infercnv";
        var versions = ["1.18.1","1.18.1","1.16.0","1.14.0","1.10.0"];
    </script>






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

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

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/bioconductor-infercnv/README.html