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

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

bioconductor-easier
===================

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

   Estimate Systems Immune Response from RNA\-seq data

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

   This package provides a workflow for the use of EaSIeR tool\, developed to assess patients\' likelihood to respond to ICB therapies providing just the patients\' RNA\-seq data as input. We integrate RNA\-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view\, including composition of the immune repertoire\, and activity of intra\- and extra\-cellular communications. Then\, we use multi\-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state\-of\-the\-art hallmarks of anti\-cancer immune response. In this way we derive cancer\-specific models and identify cancer\-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti\-PD1 or anti\-PDL1 therapy.


.. conda:package:: bioconductor-easier

   |downloads_bioconductor-easier| |docker_bioconductor-easier|

   :versions:
      
      

      ``1.8.0-0``,  ``1.6.3-0``,  ``1.4.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-decoupler: ``>=2.8.0,<2.9.0``
   :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0``
   :depends bioconductor-dorothea: ``>=1.14.0,<1.15.0``
   :depends bioconductor-easierdata: ``>=1.8.0,<1.9.0``
   :depends bioconductor-progeny: ``>=1.24.0,<1.25.0``
   :depends bioconductor-quantiseqr: ``>=1.10.0,<1.11.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-coin: 
   :depends r-dplyr: 
   :depends r-ggplot2: 
   :depends r-ggpubr: 
   :depends r-ggrepel: 
   :depends r-magrittr: 
   :depends r-matrixstats: 
   :depends r-reshape2: 
   :depends r-rlang: 
   :depends r-rocr: 
   :depends r-rstatix: 
   :depends r-tibble: 
   :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-easier

   and update with::

      mamba update bioconductor-easier

  To create a new environment, run::

      mamba create --name myenvname bioconductor-easier

  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-easier:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-easier";
        var versions = ["1.8.0","1.6.3","1.4.0","1.0.0"];
    </script>






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

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

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