Use case examples

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

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

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

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

1. Integration use case: post-analysis of sequences with Immcantation

2. Integration use case: post-analysis of sequences with immunarch

3. Integration use case: Performing analysis on immuneSIM-generated repertoires