.. CIPHER documentation master file, created by
   sphinx-quickstart on Thu Jul 9 13:17:53 2026.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to the documentation of CIPHER!
===================================================

CIPHER `(link to preprint) <https://doi.org/10.1101/2025.06.27.661814>`_ uses linear response theory to predict the perturbed profile of a cell given a perturbation. It is a computational framework that can be used to predict the effects of genetic and chemical perturbations on gene expression profiles. CIPHER can also infer the causal perturbation from the observed perturbed profile of a cell.

.. toctree::
   :maxdepth: 1
   
   Perturbation in Biology <PerturbationInfo>
   CIPHER<CIPHER>
   Results <Results>
   Implementing CIPHER on your data <usageInformation>
   CIPHER PyPI Package <packageDocumentation>
   Dataset Information <datasetsInfo>
   Repositories <repositories>
   Contact <Contact>
   Link to paper <https://doi.org/10.1101/2025.06.27.661814>
   Goyal Lab website <https://www.goyallab.org/>

.. figure:: /images/Figure1.png
   :scale: 50 %
   :align: center

.. toctree::
   :maxdepth: 1

      
.. Contents
.. ==================

.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`
.. * source/about