Example use of Polaris 
======================

Loop Annotation
-----------------
See the `Loop Annotation tutorial`_ for detailed information.

.. figure:: _static/logo03.png
   :alt: Polaris Logo03
   :width: 700px
   :height: 175px
   :align: center

   Pre-training, fine-tuning, and application on bulk contact maps of Polaris.

.. figure:: _static/logo04.png
   :alt: Polaris Logo04
   :width: 509px
   :height: 90px
   :align: center


   Application on single-cell contact maps of Polaris.

-------------------------------------------------------------------------------------

.. Single-cell Hi-C data
.. ---------------------
.. See the `Single-cell Hi-C tutorial`_ for detailed information.

.. .. figure:: _static/logo04.png
..    :alt: Polaris Logo04
..    :width: 509px
..    :height: 90px
..    :align: center


..    Application on single-cell contact maps of Polaris.

.. --------------------------------------------------------------------------------------

Aggregate peak analysis
---------------------------
See the `Aggregate Peak Analysis tutorial`_ for detailed information.

.. figure:: _static/apa.png
   :alt: APA
   :width: 250px
   :height: 125px
   :align: center

   Aggregate peak analysis of bulk Hi-C (GM12878 with 250M validate read pairs at 5kb) (left) and aggregated scHi-C (400 mESCs) (right).


.. _Loop Annotation tutorial: https://github.com/ai4nucleome/Polaris/blob/master/example/loop_annotation/loop_annotation.ipynb
.. _Aggregate Peak Analysis tutorial: https://github.com/ai4nucleome/Polaris/blob/master/example/APA/APA_example.ipynb