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

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

bioconductor-depmap
===================

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

   Cancer Dependency Map Data Package

   :homepage: https://bioconductor.org/packages/3.18/data/experiment/html/depmap.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-depmap <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-depmap>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-depmap/meta.yaml>`_

   The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available\, including RNAI and CRISPR\-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines\, protein expression of cell lines as measured by reverse phase protein lysate microarray \(RPPA\)\, \'Transcript Per Million\' \(TPM\) data\, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug\_dependency dataset\, that contains cancer cell line dependency data with respect to drug and drug\-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license \(Attribution 4.0 International \(CC BY 4.0\)\).


.. conda:package:: bioconductor-depmap

   |downloads_bioconductor-depmap| |docker_bioconductor-depmap|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.16.0-0</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.8.0-1</code>,  <code>1.8.0-0</code>,  <code>1.6.0-0</code>,  <code>1.4.0-1</code>,  <code>1.4.0-0</code>,  <code>1.2.0-0</code>,  </span></summary>
      

      ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-annotationhub: ``>=3.10.0,<3.11.0``
   :depends bioconductor-data-packages: ``>=20231203``
   :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0``
   :depends curl: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :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-depmap

   and update with::

      mamba update bioconductor-depmap

  To create a new environment, run::

      mamba create --name myenvname bioconductor-depmap

  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-depmap:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-depmap";
        var versions = ["1.16.0","1.14.0","1.12.0","1.8.0","1.8.0"];
    </script>






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

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

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