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Tutorial

This section provides a hands-on guide to using OptiMHC effectively.

What You Will Learn

  • Examples — Walk through complete configuration files for MHC Class I, Class II, and experiment-mode analyses.
  • Pipeline Workflow — Understand each stage of the pipeline from input parsing through rescoring to visualization.
  • Features — Deep dive into every feature: what it computes, the underlying formulas, and how to configure it.

Prerequisites

Before starting the tutorials, make sure you have installed OptiMHC and verified it with optimhc --help. If you plan to use advanced features (SpectralSimilarity, DeepLC, MHCflurry, NetMHCpan), ensure their external dependencies are also installed.