Use case examples

This page provides examples on how LIgO can be used to validate AIRR-ML approaches. All use cases assume you have LIgO already installed. For details on how to do that, see Installing LIgO.

The LIgO manuscript showcases LIgO on two use cases. The following sections provide a description of how to reproduce these use cases.

1. Manuscript use case 1: Out-of-distribution receptor-level simulation using LIgO

2. Manuscript use case 2: Limitations of conventional encoding schemes for repertoire-level binary classification when immune signals co-occur within the same AIR

The following group of use cases is inspired by the manucript “Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance” (biorxiv). From these use cases you can learn how to define LIgO motifs inspired by VDJdb database, simulate epitope-specific TCRs based on these motifs, and inspect the simulated TCRs compared to experimental data.

1. Constructing LIgO motifs inspired by a database of TCR sequences with known antigen specificities

2. Simulating epitope-specific TCRs and validating their properties

List of all usecases

• Manuscript use case 1: Out-of-distribution receptor-level simulation using LIgO
• Manuscript use case 2: Limitations of conventional encoding schemes for repertoire-level binary classification when immune signals co-occur within the same AIR
• Constructing LIgO motifs inspired by a database of TCR sequences with known antigen specificities
• Simulating epitope-specific TCRs and validating their properties