:orphan:



.. _sphx_glr_auto_examples:

Example Gallery
=======================


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Plot single molecules centered at regions of interest defined in bed file and produce aggregate...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_enrichment_profile_single_example_thumb.png
     :alt: Enrichment Profile mA only

     :ref:`sphx_glr_auto_examples_enrichment_profile_single_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/enrichment_profile_single_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Plot overall fraction of methylated bases within multiple sets of regions of interest specified...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_enrichment_multi_bed_example_thumb.png
     :alt: Enrichment Plot Comparison Across BEDs

     :ref:`sphx_glr_auto_examples_enrichment_multi_bed_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/enrichment_multi_bed_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Aggregate and single molecule plots colored by modification and centered at regions of interest...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_enrichment_profile_ma_mc_example_thumb.png
     :alt: Enrichment Profile mA & mCG

     :ref:`sphx_glr_auto_examples_enrichment_profile_ma_mc_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/enrichment_profile_ma_mc_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Plot overall fraction of methylated bases within regions of interest specified by bed file acro...">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_enrichment_multi_bam_example_thumb.png
     :alt: Enrichment Plot Comparison Across BAMs

     :ref:`sphx_glr_auto_examples_enrichment_multi_bam_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/enrichment_multi_bam_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Aggregate fraction of methylated bases centered at regions of interest defined in bed files.">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_enrichment_profile_overlay_example_thumb.png
     :alt: Enrichment Profile Overlay

     :ref:`sphx_glr_auto_examples_enrichment_profile_overlay_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/enrichment_profile_overlay_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Plot single molecules with colored base modifications in a region of interest">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_browser_example_thumb.png
     :alt: Single-Molecule Browser Plot

     :ref:`sphx_glr_auto_examples_browser_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/browser_example

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Outputs quality control report from given bam files.">

.. only:: html

 .. figure:: /auto_examples/images/thumb/sphx_glr_qc_report_example_thumb.png
     :alt: QC Report

     :ref:`sphx_glr_auto_examples_qc_report_example.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/qc_report_example
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-gallery


  .. container:: sphx-glr-download sphx-glr-download-python

    :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`



  .. container:: sphx-glr-download sphx-glr-download-jupyter

    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_