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

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

bioconductor-esatac
===================

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

   An Easy\-to\-use Systematic pipeline for ATACseq data analysis

   :homepage: https://bioconductor.org/packages/3.22/bioc/html/esATAC.html
   :license: GPL-3 | file LICENSE
   :recipe: /`bioconductor-esatac <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-esatac>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-esatac/meta.yaml>`_
   :links: biotools: :biotools:`esATAC`

   This package provides a framework and complete preset pipeline for quantification and analysis of ATAC\-seq Reads. It covers raw sequencing reads preprocessing \(FASTQ files\)\, reads alignment \(Rbowtie2\)\, aligned reads file operations \(SAM\, BAM\, and BED files\)\, peak calling \(F\-seq\)\, genome annotations \(Motif\, GO\, SNP analysis\) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end\-to\-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results\, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.


.. conda:package:: bioconductor-esatac

   |downloads_bioconductor-esatac| |docker_bioconductor-esatac|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.32.0-0</code>,  <code>1.24.0-1</code>,  <code>1.24.0-0</code>,  <code>1.22.0-0</code>,  <code>1.20.0-1</code>,  <code>1.20.0-0</code>,  <code>1.16.0-2</code>,  <code>1.16.0-1</code>,  <code>1.16.0-0</code>,  </span></summary>
      

      ``1.32.0-0``,  ``1.24.0-1``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.16.0-2``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.8.0-1``,  ``1.6.1-0``,  ``1.4.3-0``,  ``1.4.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends on bioconductor-annotationdbi: ``>=1.72.0,<1.73.0``
   :depends on bioconductor-annotationdbi: ``>=1.72.0,<1.73.0a0``
   :depends on bioconductor-biocgenerics: ``>=0.56.0,<0.57.0``
   :depends on bioconductor-biocgenerics: ``>=0.56.0,<0.57.0a0``
   :depends on bioconductor-biostrings: ``>=2.78.0,<2.79.0``
   :depends on bioconductor-biostrings: ``>=2.78.0,<2.79.0a0``
   :depends on bioconductor-bsgenome: ``>=1.78.0,<1.79.0``
   :depends on bioconductor-bsgenome: ``>=1.78.0,<1.79.0a0``
   :depends on bioconductor-chipseeker: ``>=1.46.0,<1.47.0``
   :depends on bioconductor-chipseeker: ``>=1.46.1,<1.47.0a0``
   :depends on bioconductor-clusterprofiler: ``>=4.18.0,<4.19.0``
   :depends on bioconductor-clusterprofiler: ``>=4.18.4,<4.19.0a0``
   :depends on bioconductor-genomicalignments: ``>=1.46.0,<1.47.0``
   :depends on bioconductor-genomicalignments: ``>=1.46.0,<1.47.0a0``
   :depends on bioconductor-genomicfeatures: ``>=1.62.0,<1.63.0``
   :depends on bioconductor-genomicfeatures: ``>=1.62.0,<1.63.0a0``
   :depends on bioconductor-genomicranges: ``>=1.62.0,<1.63.0``
   :depends on bioconductor-genomicranges: ``>=1.62.1,<1.63.0a0``
   :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0``
   :depends on bioconductor-iranges: ``>=2.44.0,<2.45.0a0``
   :depends on bioconductor-jaspar2018: ``>=1.1.0,<1.2.0``
   :depends on bioconductor-jaspar2018: ``>=1.1.1,<1.2.0a0``
   :depends on bioconductor-motifmatchr: ``>=1.32.0,<1.33.0``
   :depends on bioconductor-motifmatchr: ``>=1.32.0,<1.33.0a0``
   :depends on bioconductor-pipeframe: ``>=1.26.0,<1.27.0``
   :depends on bioconductor-pipeframe: ``>=1.26.0,<1.27.0a0``
   :depends on bioconductor-rbowtie2: ``>=2.16.0,<2.17.0``
   :depends on bioconductor-rbowtie2: ``>=2.16.0,<2.17.0a0``
   :depends on bioconductor-rsamtools: ``>=2.26.0,<2.27.0``
   :depends on bioconductor-rsamtools: ``>=2.26.0,<2.27.0a0``
   :depends on bioconductor-rtracklayer: ``>=1.70.0,<1.71.0``
   :depends on bioconductor-rtracklayer: ``>=1.70.1,<1.71.0a0``
   :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0``
   :depends on bioconductor-s4vectors: ``>=0.48.0,<0.49.0a0``
   :depends on bioconductor-seqinfo: ``>=1.0.0,<1.1.0``
   :depends on bioconductor-seqinfo: ``>=1.0.0,<1.1.0a0``
   :depends on bioconductor-shortread: ``>=1.68.0,<1.69.0``
   :depends on bioconductor-shortread: ``>=1.68.0,<1.69.0a0``
   :depends on bioconductor-tfbstools: ``>=1.48.0,<1.49.0``
   :depends on bioconductor-tfbstools: ``>=1.48.0,<1.49.0a0``
   :depends on libblas: ``>=3.9.0,<4.0a0``
   :depends on libgcc: ``>=14``
   :depends on liblapack: ``>=3.9.0,<4.0a0``
   :depends on liblzma: ``>=5.8.2,<6.0a0``
   :depends on libstdcxx: ``>=14``
   :depends on libzlib: ``>=1.3.1,<2.0a0``
   :depends on r-base: ``>=4.5,<4.6.0a0``
   :depends on r-biocmanager: 
   :depends on r-corrplot: 
   :depends on r-digest: 
   :depends on r-ggplot2: 
   :depends on r-igraph: 
   :depends on r-knitr: 
   :depends on r-magrittr: 
   :depends on r-r.utils: 
   :depends on r-rcpp: ``>=0.12.11``
   :depends on r-rjava: 
   :depends on r-rmarkdown: 
   :depends on r-venndiagram: 

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code></span>
      

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-esatac

to add into an existing workspace instead, run::

    pixi add bioconductor-esatac

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-esatac

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

    conda create -n envname bioconductor-esatac

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-esatac:<tag>

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


.. raw:: html

    <script>
        var package = "bioconductor-esatac";
        var versions = ["1.32.0","1.24.0","1.24.0","1.22.0","1.20.0"];
    </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-esatac/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-esatac/README.html