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

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

bioconductor-biotmle
====================

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

   Targeted Learning with Moderated Statistics for Biomarker Discovery

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

   Tools for differential expression biomarker discovery based on microarray and next\-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and inference of the \(marginal\) average treatment effects of potential biomarkers are computed by targeted minimum loss\-based estimation\, with joint\, stable inference constructed across all biomarkers using a generalization of moderated statistics for use with the estimated efficient influence function. The procedure accommodates the use of ensemble machine learning for the estimation of nuisance functions.


.. conda:package:: bioconductor-biotmle

   |downloads_bioconductor-biotmle| |docker_bioconductor-biotmle|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.26.0-0</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.18.0-0</code>,  <code>1.16.0-0</code>,  <code>1.14.0-1</code>,  <code>1.14.0-0</code>,  <code>1.12.0-0</code>,  <code>1.10.0-0</code>,  </span></summary>
      

      ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.6.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0``
   :depends bioconductor-limma: ``>=3.58.0,<3.59.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0``
   :depends r-assertthat: 
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-dplyr: 
   :depends r-drtmle: ``>=1.0.4``
   :depends r-ggplot2: 
   :depends r-ggsci: 
   :depends r-superheat: 
   :depends r-tibble: 
   :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-biotmle

   and update with::

      mamba update bioconductor-biotmle

  To create a new environment, run::

      mamba create --name myenvname bioconductor-biotmle

  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-biotmle:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-biotmle";
        var versions = ["1.26.0","1.24.0","1.22.0","1.18.0","1.16.0"];
    </script>






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

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

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