Use case examples
====================

.. meta::

   :twitter:card: summary
   :twitter:site: @immuneml
   :twitter:title: immuneML use cases: get started with immuneML by following one of the tutorials
   :twitter:description: See tutorials covering different analysis (instructions) covered by immuneML.
   :twitter:image: https://docs.immuneml.uio.no/_images/receptor_classification_overview.png


In the immuneML manuscript, we showcase immuneMLs functionalities based on three use cases.
The following three sections describe how to reproduce these three use cases:

1. :ref:`Manuscript use case 1: Reproduction of a published study inside immuneML`

2. :ref:`Manuscript use case 2: Extending immuneML with a deep learning component for predicting antigen specificity of paired receptor data`

3. :ref:`Manuscript use case 3: Benchmarking ML methods on ground-truth synthetic data`

..
    immuneML supports import from multiple different data formats and export into AIRR-C format (MIAIRR standard), which enables post analysis by AIRR-compliant third-party tools.

To see how immuneML can be used in combination with other tools, see the following examples:

#. :ref:`Integration use case: post-analysis of sequences with Immcantation`

#. :ref:`Integration use case: post-analysis of sequences with immunarch`

#. :ref:`Integration use case: Performing analysis on immuneSIM-generated repertoires`


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

  usecases/emerson_reproduction
  usecases/extendability_use_case
  usecases/benchmarking_use_case
  usecases/immcantation_use_case
  usecases/immunarch_use_case
  usecases/immunesim_use_case