Tutorials¶
This page provides an overview of tutorials to get started with LIgO. All tutorials assume you have LIgO already installed. For details on how to do that, see Installing LIgO.
Each LIgO simulation begins with defining immune signals and immune events. To learn how to construct immune signals and events in the YAML specification file, see this tutorial:
When immune events and immune signals are defined, the user should choose between two simulation strategies — rejection sampling or signal implantation. Also we recommend users to assess feasibility of defined simulation parameters before running the main simulation. See the tutorials below:
These tutorials cover the more complex usage of LIgO simulations. For basic usage of LIgO simulation see Quickstart tutorials.
The following tutorials are inspired by the manucript “Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance” by Gielis et al (biorxiv). From these tutorials 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.
Constructing LIgO motifs inspired by a database of TCR sequences with known antigen specificities
Simulating epitope-specific TCRs and validating their properties
List of all tutorials¶
- How to define immune signals and immune events
- How to choose between rejection sampling and signal implantation
- How to check feasibility of the simulation parameters
- How to handle the maximum iterations were reached error
- Simulation with custom signal functions
- Paired chain simulations in LIgO
- How to simulate co-occuring immune signals
- Constructing LIgO motifs inspired by a database of TCR sequences with known antigen specificities
- Simulating epitope-specific TCRs and validating their properties