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

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

bioconductor-isanalytics
========================

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

   Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/ISAnalytics.html
   :license: CC BY 4.0
   :recipe: /`bioconductor-isanalytics <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-isanalytics>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-isanalytics/meta.yaml>`_

   In gene therapy\, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus\-host DNA junctions allows the identification of insertion sites \(IS\)\, essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at \(1\) supporting automation of IS workflow\, \(2\) performing base and advance analysis for IS tracking \(clonal abundance\, clonal expansions and statistics for insertional mutagenesis\, etc.\)\, \(3\) providing basic biology insights of transduced stem cells in vivo.


.. conda:package:: bioconductor-isanalytics

   |downloads_bioconductor-isanalytics| |docker_bioconductor-isanalytics|

   :versions:
      
      

      ``1.12.0-0``,  ``1.10.1-0``,  ``1.8.0-0``,  ``1.4.1-0``,  ``1.2.0-0``,  ``1.0.0-1``

      

   
   :depends r-base: ``>=4.3,<4.4.0a0``
   :depends r-bslib: 
   :depends r-datamods: 
   :depends r-dplyr: 
   :depends r-dt: 
   :depends r-forcats: 
   :depends r-fs: 
   :depends r-ggplot2: 
   :depends r-ggrepel: 
   :depends r-glue: 
   :depends r-lifecycle: 
   :depends r-lubridate: 
   :depends r-purrr: 
   :depends r-readr: 
   :depends r-readxl: 
   :depends r-rlang: 
   :depends r-shiny: 
   :depends r-shinywidgets: 
   :depends r-stringr: 
   :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-isanalytics

   and update with::

      mamba update bioconductor-isanalytics

  To create a new environment, run::

      mamba create --name myenvname bioconductor-isanalytics

  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-isanalytics:<tag>

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


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


.. raw:: html

    <script>
        var package = "bioconductor-isanalytics";
        var versions = ["1.12.0","1.10.1","1.8.0","1.4.1","1.2.0"];
    </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-isanalytics/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-isanalytics/README.html