.. FitHiChIP_Doc documentation master file, created by
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.. :caption: Contents:

Welcome to FitHiChIP!
=======================

**Developers**: Sourya Bhattacharyya, Ferhat Ay

**Institution**: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA


Utilities of FitHiChIP at a glance
------------------------------------

	- FitHiChIP derives the statistically significant CIS interactions from a given **HiChIP / PLAC-seq**, and now for **Hi-C** data as well.
		- CIS Interactions within a specified distance range (default = 20 Kb to 2 Mb: can be user defined) and for a specified fixed size bin size, are computed. 
		- Distance decay model proposed in the method FitHiC (Ay and Noble, Genome Research  2014) together with a novel bias (coverage / ICE) regression model is used to find the statistical significant interactions.
	
	- Processing HiChIP / PLAC-seq requires specifying ChIP-seq peaks corresponding to the target protein or histone modifications of interest. 
		- Either user can provide ChIP-seq peak files from ENCODE, ROADMAP, or any other reference. 
		- Alternatively, **FitHiChIP supports calling peaks from HiChIP data**, which can be used to find out the interactions involving peaks (enriched) segments.
	
	- FitHiChIP also supports finding **differential HiChIP contacts** between two different categories of HiChIP data, having one or more replicates.

	- FitHiChIP also proposes a basic implementation of **simulating HiChIP contact map given a reference HiC contact map and a ChIP-seq alignment file**, with respect to specified number of reads. (**Note**: this implementation is still in basic stage; output HiChIP heatmap shows explicit bias towards low range contacts.)	

Repository 
-----------

FitHiChIP is hosted in https://github.com/ay-lab/FitHiChIP


Execution
----------

Details of execution commands and parameters are provided in the below mentioned links:

.. toctree::
	:maxdepth: 2
	
	usage/installation
	usage/quickstart
	usage/configuration
	usage/output	
	usage/DiffLoops
	usage/Utilities
	usage/FAQ

.. usage/optional


Citation
-----------
FitHiChIP is now published at Nature Communications (<https://www.nature.com/articles/s41467-019-11950-y>)

If you are using FitHiChIP, please cite:

Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, and Ferhat Ay, *Identification of significant chromatin contacts from HiChIP data by FitHiChIP*, Nature Communications, Vol 10, No 4221, 2019, DOI:  <https://doi.org/10.1038/s41467-019-11950-y>

	
Support
-----------

For any queries or problems, user can report an issue in GitHub (<https://github.com/ay-lab/FitHiChIP>). Alternatively, user can mail us in:

- Sourya Bhattacharyya <sourya@lji.org>
- Ferhat Ay <ferhatay@lji.org>

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

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