Specificity Annotation (bioSkills)

A Claude Code skill that maps immune-receptor sequences to candidate antigen specificities and clusters repertoires by shared-specificity signal — explicitly treating database matches and cluster labels as hypotheses, not calls.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — the wrapped databases and tools (VDJdb, tcrdist3, OLGA, …) are separately installed OSS
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified works · 2026-07-27 — GPTomics/bioSkills resolves; clone + copy install path current
Security cleared · 2026-07-27 — provenance matches GPTomics/bioSkills, MIT, maintained, no OSV advisories

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 "tcr-bcr-analysis"

    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/tcr-bcr-analysis/specificity-annotation ~/.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 the referenced databases/tools when prompted on first use.

What it does

Assigns candidate antigen specificity to TCR/BCR clonotypes and groups them into specificity clusters, with statistical guardrails to avoid over-interpretation:

  • Database annotation — VDJdb, McPAS-TCR, IEDB, and TCRMatch, merging on CDR3 plus V-gene (never CDR3 alone), filtering to VDJdb confidence ≥1, and verifying donor HLA carriage.
  • Sequence clustering — tcrdist3 meta-clonotypes (primary), GLIPH2, GIANA, clusTCR, iSMART, CoNGA; runs ≥2 independent methods and reports agreement plus the reference repertoire.
  • Generation-probability nulls — OLGA (Pgen), IGoR, SONIA/soNNia (Ppost) to distinguish enrichment from convergent recombination.
  • ML predictors (optional) — DeepTCR, ERGO-II, NetTCR-2.0, pMTnet, TITAN.
  • BCR support — hands off to immcantation-analysis and scirpy for paired single-cell.

Primary use cases: antigen-specificity annotation of TCR/BCR repertoires, meta-clonotype clustering, generation-probability control for convergence claims.

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-tcr-bcr-analysis-specificity-annotation; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /specificity-annotation. The skill is deliberately conservative: database matches and cluster labels are reported as hypotheses with confidence levels, not definitive antigen assignments. Complements mixcr-analysis/scirpy-analysis (assembly), repertoire-visualization (figures), and vdjtools-analysis (diversity). Upstream directory: tcr-bcr-analysis/specificity-annotation.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.