User Guide
==========

For comprehensive tutorials and guides, visit the `Single-Cell <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell>`_ section of `TileDB Academy <https://cloud.tiledb.com/academy/>`_.

.. toctree::
   :maxdepth: 2

   Introduction <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/introduction/>
   Quickstart <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/quickstart/>

Foundation
~~~~~~~~~~

* `Data Model <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/data-model/>`_
* `Key Concepts <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/key-concepts/>`_

  * `Data Structures <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/key-concepts/data-structures/>`_
  * `Use of Apache Arrow <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/key-concepts/data-types/>`_
  * `Join IDs <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/key-concepts/joinids/>`_
  * `State Management <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/key-concepts/state-management/>`_

* `Configuration Options <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/configure/>`_
* `SOMA API Spec <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/foundation/specification/>`_

Tutorials
~~~~~~~~~

* `Data Ingestion <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/data-ingestion/>`_
* `Bulk Ingestion <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/bulk-ingest/>`_
* `Data Access <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/data-access/>`_
* `Distributed Compute <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/distributed-compute/>`_
* `Basic S3 Example <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/basic-s3/>`_
* `Multi-Experiment Queries <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/multi-experiment-queries/>`_
* `Append Data <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/append-data/>`_
* `Add Measurements <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/add-measurement/>`_
* `Update Axis DataFrames <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/update-axis-dataframes/>`_
* `Running Locally <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/running-locally/>`_
* `Shapes in TileDB-SOMA <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/shapes/>`_
* `Distributed Scanpy <https://cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/distributed-scanpy/>`_