API reference

Ranking neoantigens and Command-line reference are the narrative and the command-line walkthroughs; this page is the full per-module reference, grouped by pipeline stage rather than alphabetically — the same order a candidate moves through: load a store, score presentation, score complementarity, rank, then (optionally) design a cassette.

Core

The four pages below carry the entry points almost every caller needs. If you are looking for something and do not know where it lives, it is very likely here.

• Store, search and reference data
• Presentation -- the P of EPIC
• Ranking neoantigens
• Cassette design

Advanced

Narrower questions, optional dependencies, and internals that are useful but are not the way in. Complementarity — the I and C of EPIC is the exception worth knowing about: it documents the C_phys_* and C_corpus_* channels the shipped scorer is fitted on, so it is reference material for reading a coefficient rather than an entry point you call.

• Complementarity -- the I and C of EPIC
• Structure and visualization
• Vendored data
• Optional extras