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LIgO 1.0.11 documentation
LIgO 1.0.11 documentation
  • Quickstart
    • How to use LIgO for receptor-level simulation
    • How to use LIgO for repertoire-level simulation
    • Overview of LIgO simulation parameters
  • Installing LIgO
  • 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
  • Use case examples
    • 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
  • YAML specification
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