.. MATCHER documentation master file, created by

   sphinx-quickstart on Wed Jun 29 15:17:06 2016.

   You can adapt this file completely to your liking, but it should at least

   contain the root `toctree` directive.



Welcome to MATCHER's documentation!

===================================



**Installation**



MATCHER is on the Python package index (PyPI). To install it using pip, simply type::



        pip install pymatcher



**MATCHER Input**



MATCHER takes in single cell datasets as Numpy ndarrays (produced by the genfromtxt function in the Numpy package, for example). Each row should contain the measured values for a single cell, and each column should contain the values of a feature across cells. See the sample data files and the `Jupyter notebook <https://github.com/jw156605/MATCHER/blob/master/MATCHER_demo.ipynb>`_ included with the package for more details.



.. toctree::

   :maxdepth: 2



.. autoclass:: matcher.MATCHER

   :members:

.. autoclass:: matcher.WarpFunction

   :members:



Indices and tables

==================



* :ref:`genindex`

* :ref:`modindex`

* :ref:`search`