.. Test documentation master file, created by
   sphinx-quickstart on Mon Mar 23 15:27:57 2009.

.. _peakcallingpipeline:

======================
Peak calling pipeline
======================

The following pages contain automatically created tables and 
plots from the ChIP-Seq pipeline.

Contents:

.. toctree::
   :maxdepth: 2

   pipeline/Methods.rst
   pipeline/Status.rst
   pipeline/IntervalsRegions.rst
   pipeline/IntervalsSummits.rst
   pipeline/Mapping.rst
   pipeline/Callers.rst
   pipeline/Peaks.rst	
   pipeline/Reproducibility.rst

..   pipeline/Mapping.rst
..   pipeline/Binding.rst
..   pipeline/IntervalLists.rst
..   pipeline/Correlations.rst
..   pipeline/Overlaps.rst
..   pipeline/Annotations.rst
..   pipeline/Repeats.rst
..   pipeline/TSS.rst
   python/Trackers.rst
 
.. errorlist::
  
.. glossary::

region
	A larger region called by a peak caller.

peak 
	A shorter region as called by a peak caller.

summit
	A local maximum within a region/peak.

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`



.. Test documentation master file, created by
   sphinx-quickstart on Mon Mar 23 15:27:57 2009.

.. _peakcallingpipeline:

======================
Peak calling pipeline
======================

The following pages contain automatically created tables and 
plots from the ChIP-Seq pipeline.

Contents:

.. toctree::
   :maxdepth: 2

   pipeline/Methods.rst
   pipeline/Status.rst
   pipeline/IntervalsPeaks.rst
   pipeline/IntervalsRegions.rst
   pipeline/IntervalsSummits.rst
   pipeline/Mapping.rst
   pipeline/Callers.rst
   pipeline/Peaks.rst	
   pipeline/Reproducibility.rst

..   pipeline/Mapping.rst
..   pipeline/Binding.rst
..   pipeline/IntervalLists.rst
..   pipeline/Correlations.rst
..   pipeline/Overlaps.rst
..   pipeline/Annotations.rst
..   pipeline/Repeats.rst
..   pipeline/TSS.rst
   python/Trackers.rst
 
.. errorlist::
  
.. glossary::

region
	A larger region called by a peak caller.

peak 
	A shorter region as called by a peak caller.

summit
	A local maximum within a region/peak.

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`



Refactor peak reporting into pages on (1) Peaks - as arising from point binding factors, (2) Regions - as arising from more diffuse signals such as chromatin marks and (3) Summits, as the positions of maxima located within peaks or regions.
Refactor peak reporting into pages on (1) Peaks - as arising from point binding factors, (2) Regions - as arising from more diffuse signals such as chromatin marks and (3) Summits, as the positions of maxima located within peaks or regions.
