.. 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 scmatcher

**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`

