immuneML & Galaxy

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:

To get started using immuneML in Galaxy, you will need to add your dataset to Galaxy, which is explained in this tutorial:

Remote datasets may be fetched from VDJdb or the iReceptor Plus Gateway, see:

If you do not want to use experimental data and just want to try something out quickly, you can simulate an immune dataset:

Synthetic immune signals (representing antigen binding or disease) can be implanted in an existing dataset:

Once an immuneML dataset has been created in Galaxy, immunology experts without machine learning background can follow these instructions:

Alternatively, CLI equivalent tools based on the YAML specification can be run using the following instructions:

Galaxy tutorials:

Dataset tutorials:

Analysis tutorials: