.. phippery documentation master file, created by
   sphinx-quickstart on Mon Sep 27 17:42:02 2021.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


Welcome to phippery's documentation!
====================================

.. toctree::
   :maxdepth: 2
   :caption: Overview:

   introduction
   installation
   examples

.. toctree::
   :maxdepth: 1
   :caption: Nextflow Pipeline:

   alignments-pipeline

.. toctree::
   :maxdepth: 1
   :caption: Python API:

   phippery.utils
   phippery.normalize
   phippery.modeling
   phippery.eigen
   phippery.escprof

.. toctree::
   :maxdepth: 1
   :caption: Command Line Interface:

   command-line-interface

.. toctree::
   :maxdepth: 2
   :caption: Streamlit Viz App

   streamlit-app

.. toctree::
   :maxdepth: 2
   :caption: Methods Descriptions

   esc-prof
   bkg-model

.. toctree::
   :maxdepth: 2
   :caption: The Rest of It

   the-rest-of-it

.. interactive-visualization
   annotation-tables
   under-the-hood

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

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



.. todolist::