: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/3.22/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>1.24.0-0</code>,  <code>1.20.0-0</code>,  <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>,  </span></summary>
      

      ``1.24.0-0``,  ``1.20.0-0``,  ``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 on bioconductor-annotationhub: ``>=4.0.0,<4.1.0``
   :depends on bioconductor-biocfilecache: ``>=3.0.0,<3.1.0``
   :depends on bioconductor-data-packages: ``>=20260207``
   :depends on bioconductor-experimenthub: ``>=3.0.0,<3.1.0``
   :depends on curl: 
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-curl: 
   :depends on r-dplyr: 
   :depends on r-httr2: 
   :depends on r-tibble: 

   :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-depmap

to add into an existing workspace instead, run::

    pixi add bioconductor-depmap

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-depmap

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

    conda create -n envname bioconductor-depmap

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-depmap:<tag>

(see `bioconductor-depmap/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-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 = ["1.24.0","1.20.0","1.16.0","1.14.0","1.12.0"];
    </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-depmap/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-depmap/README.html