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mhcmatch 1.20.2

  • Getting started
  • Command-line reference
  • Running a cohort
  • Ranking neoantigens
    • The shipped models
    • Designing a cassette: what goes in, and what it is worth
    • Cassette composition
    • Safety, prior evidence, and what goes in the cassette
    • Notebooks
    • API reference
    • The amino-acid property basis
  • GitHub
  • Getting started
  • Command-line reference
  • Running a cohort
  • Ranking neoantigens
  • The shipped models
  • Designing a cassette: what goes in, and what it is worth
  • Cassette composition
  • Safety, prior evidence, and what goes in the cassette
  • Notebooks
  • API reference
  • The amino-acid property basis
  • GitHub

Start here

  • Getting started
  • Command-line reference
    • Commands, by axis
    • Reproducing the published analyses
    • Staging reference data
    • Environment
  • Running a cohort
    • Designing a cassette
    • Safety screen
    • Cassette composition

Scoring a candidate

  • Ranking neoantigens
    • E - Expression
    • P - Presentation
    • I - Immunogenicity features
    • I - the chemistry reduction
    • C - Complementarity
    • C - the corpus channels
  • The shipped models

Designing a cassette

  • Designing a cassette: what goes in, and what it is worth
  • Cassette composition
  • Safety, prior evidence, and what goes in the cassette

Worked examples

  • Notebooks

Reference

  • API reference
    • Store, search and reference data
    • Presentation -- the P of EPIC
    • Ranking neoantigens
    • Cassette design
    • Complementarity -- the I and C of EPIC
    • Structure and visualization
    • Vendored data
    • Optional extras
  • The amino-acid property basis
  • Overview: module code

All modules for which code is available

  • mhcmatch.affinity
  • mhcmatch.calibrate
  • mhcmatch.cassette
  • mhcmatch.complement
  • mhcmatch.diffusion
  • mhcmatch.expression
  • mhcmatch.immuno
  • mhcmatch.known
  • mhcmatch.ligand
  • mhcmatch.logo
  • mhcmatch.luksza
  • mhcmatch.mimicry
  • mhcmatch.mimics
  • mhcmatch.portfolio
  • mhcmatch.posbayes
  • mhcmatch.predict
  • mhcmatch.proteome
  • mhcmatch.pseudoseq
  • mhcmatch.rank
  • mhcmatch.recognition
  • mhcmatch.search
  • mhcmatch.store
  • mhcmatch.structure
  • mhcmatch.vector

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