Immunogenicity Scoring (bioSkills)

A Claude Code skill that prioritizes neoantigen and epitope candidates by the likelihood of an actual T-cell response, rather than by binding affinity alone.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — NeoFox, PRIME2.0, BigMHC-IM, MixMHCpred and pVACtools are separately installed and carry their own (in some cases academic-only) terms
Capabilities Read/Write — Claude runs the skill’s workflow locally (Python), not as an MCP tool
Verified works · 2026-08-03
Security caution · 2026-08-03 — skill MIT/clean, but bundled MixMHCpred/PRIME predictors are academic-use-only

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "immunoinformatics"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/immunoinformatics/immunogenicity-scoring ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). Install NeoFox and the chosen recognition predictors when prompted on first use.

What it does

Turns a candidate epitope list into an auditable, feature-annotated shortlist:

  • Workflow — NeoFox annotates ~16 presentation and recognition features without ranking; non-negotiable expression and clonality filters are applied first (gene TPM ≥ 1, RNA VAF ≥ 0.25); PRIME2.0 or BigMHC-IM scores class-I immunogenicity; agretopicity (mutant-vs-wild-type binding gain) and foreignness are computed defensively; candidates are ranked within a patient by presentation strength, abundance and quality; pVACtools rule-based tiers quarantine anchor-position artifacts and subclonal traps; the output is presented for human curation with uncertainty stated.
  • Method panel — NeoFox (DAI, foreignness, dissimilarity, PRIME, PHBR), PRIME2.0 (presentation × TCR recognition, requires MixMHCpred v3.0+), BigMHC-IM (pan-allelic transfer-learned immunogenicity), pVACtools (tiering), and IEDB as a reference database that the skill treats as a weak standalone predictor.

Primary use cases: personalized cancer-vaccine candidate selection, TCR-therapy target triage, ranking a pVACseq/NeoFox candidate list.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-immunoinformatics-immunogenicity-scoring; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /immunogenicity-scoring. This is the ranking stage downstream of the catalogued Neoantigen Prediction, MHC Binding Prediction and Epitope Prediction skills, which generate the candidates it scores. Several bundled predictors (notably MixMHCpred/PRIME) are distributed under academic-use licenses by their own authors — check each before commercial use; the MIT grant covers the bioSkills skill text only.

Sources

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