immuneML & Galaxy ================= .. meta:: :twitter:card: summary :twitter:site: @immuneml :twitter:title: immuneML & Galaxy :twitter:description: See tutorials on how to run immuneML through Galaxy. :twitter:image: https://docs.immuneml.uio.no/_images/receptor_classification_overview.png All of immuneMLs functionalities are also available through `a Galaxy web interface `_ as a collection of Galaxy tools. We provide a YAML-based Galaxy tool that is equivalent to the CLI (command-line interface), as well as repertoire and receptor-level classification tools with an intuitive graphical user interface aimed at immunology experts without a machine learning background. If you are unfamiliar with Galaxy, you may want to start here: - :ref:`Introduction to Galaxy` To get started using immuneML in Galaxy, you will need to add your dataset to Galaxy, which is explained in this tutorial: - :ref:`How to make an immuneML dataset in Galaxy` Remote datasets may be fetched from VDJdb or the iReceptor Plus Gateway, see: - :ref:`How to import remote AIRR datasets in Galaxy` If you do not want to use experimental data and just want to try something out quickly, you can simulate an immune dataset: - :ref:`How to simulate an AIRR dataset in Galaxy` Synthetic immune signals (representing antigen binding or disease) can be implanted in an existing dataset: - :ref:`How to simulate immune events into an existing AIRR dataset in Galaxy` Once an immuneML dataset has been created in Galaxy, immunology experts without machine learning background can follow these instructions: - :ref:`How to train immune repertoire classifiers using the simplified Galaxy interface` - :ref:`How to train immune receptor classifiers using the simplified Galaxy interface` Alternatively, CLI equivalent tools based on the YAML specification can be run using the following instructions: - :ref:`How to train ML models in Galaxy` - :ref:`How to run any AIRR ML analysis in Galaxy` .. toctree:: :maxdepth: 1 :caption: Galaxy tutorials: galaxy/galaxy_intro .. toctree:: :maxdepth: 1 :caption: Dataset tutorials: galaxy/galaxy_dataset galaxy/galaxy_import_remote_data galaxy/galaxy_simulate_dataset galaxy/galaxy_simulate_signals .. toctree:: :maxdepth: 1 :caption: Analysis tutorials: galaxy/galaxy_simple_repertoires galaxy/galaxy_simple_receptors galaxy/galaxy_train_ml_models galaxy/galaxy_general_yaml