.. include:: README.rst

.. toctree::
   :hidden:
   :maxdepth: 1

   README.rst

Tutorial
========

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Tutorial:

   notebooks/Q1-singularity-preprocessing.ipynb
   notebooks/Q2-object-prep.ipynb
   notebooks/Q3-analysis.ipynb
   notebooks/Q4-singularity-changeo.ipynb
   notebooks/Q5-pseudobulk.ipynb


Base Backend: Notebooks
=======================

.. toctree::
   :maxdepth: 1
   :caption: Advanced Guide (Base):

   notebooks/base/1_dandelion_preprocessing-10x_data.ipynb
   notebooks/base/1b_dandelion_noreannotation-10x_data.ipynb
   notebooks/base/1c_dandelion_scirpy.ipynb
   notebooks/base/2_dandelion_filtering-10x_data.ipynb
   notebooks/base/3_dandelion_findingclones-10x_data.ipynb
   notebooks/base/4_dandelion_visualization-10x_data.ipynb
   notebooks/base/5_dandelion_diversity_and_mutation-10x_data.ipynb
   notebooks/base/7_dandelion_TCR_data_10x_data.ipynb
   notebooks/base/8-pseudobulk-trajectory.ipynb
   notebooks/base/0_dandelion_primer.ipynb

Polars Backend: Notebooks
==========================

.. toctree::
   :maxdepth: 1
   :caption: Advanced Guide (Polars):

   notebooks/polars/1_dandelion_preprocessing-10x_data_polars.ipynb
   notebooks/polars/1b_dandelion_noreannotation-10x_data_polars.ipynb
   notebooks/polars/1c_dandelion_scirpy_polars.ipynb
   notebooks/polars/2_dandelion_filtering-10x_data_polars.ipynb
   notebooks/polars/3_dandelion_findingclones-10x_data_polars.ipynb
   notebooks/polars/4_dandelion_visualization-10x_data_polars.ipynb
   notebooks/polars/5_dandelion_diversity_and_mutation-10x_data_polars.ipynb
   notebooks/polars/7_dandelion_TCR_data_10x_data_polars.ipynb
   notebooks/polars/8-pseudobulk-trajectory_polars.ipynb
   notebooks/polars/0_dandelion_polars_primer.ipynb

.. toctree::
   :maxdepth: 1
   :caption: API:
   :hidden:

   api