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

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

bioconductor-rtcga
==================

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

   The Cancer Genome Atlas Data Integration

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/RTCGA.html
   :license: GPL-2
   :recipe: /`bioconductor-rtcga <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtcga>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-rtcga/meta.yaml>`_
   :links: biotools: :biotools:`rtcga`, doi: :doi:`10.1038/nmeth.3252`

   The Cancer Genome Atlas \(TCGA\) Data Portal provides a platform for researchers to search\, download\, and analyze data sets generated by TCGA. It contains clinical information\, genomic characterization data\, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key\, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients\' treatment. Furthermore\, RTCGA package transforms TCGA data to tidy form which is convenient to use.


.. conda:package:: bioconductor-rtcga

   |downloads_bioconductor-rtcga| |docker_bioconductor-rtcga|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.32.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-1</code>,  <code>1.20.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  </span></summary>
      

      ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.8.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends r-assertthat: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-data.table: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-ggthemes: 
   :depends r-htmltools: 
   :depends r-knitr: 
   :depends r-purrr: 
   :depends r-rcurl: 
   :depends r-rmarkdown: 
   :depends r-rvest: 
   :depends r-scales: 
   :depends r-stringi: 
   :depends r-survival: 
   :depends r-survminer: 
   :depends r-viridis: 
   :depends r-xml: 
   :depends r-xml2: 
   :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-rtcga

   and update with::

      mamba update bioconductor-rtcga

  To create a new environment, run::

      mamba create --name myenvname bioconductor-rtcga

  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-rtcga:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-rtcga";
        var versions = ["1.32.0","1.30.0","1.28.0","1.24.0","1.22.0"];
    </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-rtcga/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-rtcga/README.html