Tutorials
==========

.. meta::

   :twitter:card: summary
   :twitter:site: @immuneml
   :twitter:title: immuneML tutorials: 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


This page provides an overview of tutorials on how to get started using immuneML and instructions on how to use immuneML for various different use cases.

All immuneML analyses are specified using a YAML specification file. To learn how to construct this file, see this tutorial:

  - :ref:`How to specify an analysis with YAML`

Each analysis begins with selecting the dataset that will be used. In immuneML, the user can choose to import an existing dataset, or to generate a
dataset made of random sequences (for example to test out some functionality without needing to use a specific dataset, or as a benchmarking dataset).
The respective tutorials can be found here:

  - :ref:`How to import data into immuneML`
  - :ref:`How to generate a random sequence, receptor or repertoire dataset`

Using the specified dataset, immuneML can be used for various purposes: one can train and assess an ML model for immune repertoire or receptor-level
classification, perform an exploratory analysis (to run preprocessings, encodings and reports without training a ML model), or simulate immune events
by implanting sequence motifs in the dataset. See the tutorials below:

  - :ref:`How to train and assess a receptor or repertoire-level ML classifier`
  - :ref:`How to apply previously trained ML models to a new dataset`
  - :ref:`How to perform an exploratory data analysis`
  - :ref:`How to simulate antigen or disease-associated signals in AIRR datasets`

.. toctree::
  :maxdepth: 1
  :caption: Tutorials:

  tutorials/how_to_specify_an_analysis_with_yaml
  tutorials/how_to_import_the_data_to_immuneML
  tutorials/how_to_generate_a_random_repertoire_dataset
  tutorials/how_to_train_and_assess_a_receptor_or_repertoire_classifier
  tutorials/how_to_apply_to_new_data
  tutorials/how_to_perform_exploratory_analysis
  tutorials/how_to_simulate_antigen_signals_in_airr_datasets
  tutorials/motif_recovery