Examples
=============
This section contains examples to show how to prepare the data for UNAGI running, analyse the UNAGI outcomes, perform perturbations and visualize the reuslts using the example IPF dataset.

Running UNAGI on the example dataset
------------------------------------

.. toctree::
    dataset_preparation
    run_UNAGI_using_example_dataset
    visualize_UNAGI_results_example_dataset

    

UNAGI ablations
------------------------------------

.. toctree::
    ablation_study

Using UNAGI to predict post-treatment gene expressions
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.. toctree::
    PCLS_data_post_treatment_prediction

Using UNAGI with a customized pathway or drug database for in-silico perturbation
------------------------------------

.. toctree::
    Customize_pathway_database_for_perturbation
    Customize_drug_database_for_perturbation

UNAGI walkthrough
------------------------------------

.. toctree::
    walkthrough_example