Tutorial
========

This section contains various tutorials showcasing use cases in the context of a typical perturbation analysis workflow.

The notebooks demonstrate how to prepare data, train PerturbGen models, generate in silico perturbations, and perform post-perturbation analyses. 
They are intended as practical example references, and assume familiarity with Python-based scientific computing and single-cell or high-dimensional biological data.

.. toctree::

   examples/01_preprocessing_curation
   examples/02_tokenization_pairing
   examples/03_train_perturbgen
   examples/04_GeneEmbedding_Extraction
   examples/05_GeneProgram_Discovery
   examples/06_perturbation
   examples/07_PostPerturbation_Analyses