Repertoire Visualization (bioSkills)

A Claude Code skill that renders publication-quality TCR/BCR repertoire figures and advises on which visualization and comparison metric to use for depth-robust conclusions.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — VDJtools and R/Python dependencies are separately installed OSS
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/R/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/repertoire-visualization ~/.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 R/Python/CLI dependencies (below) when prompted on first use.

What it does

Turns an assembled repertoire table (native or AIRR) into interpretable figures, with built-in guidance on metric choice so comparisons are not confounded by sequencing depth:

  • Figure types — V-J usage chord/circos diagrams, CDR3 spectratypes, clonal-space stratification, clonal tracking across timepoints, rarefaction/extrapolation curves, overlap heatmaps, and clonotype-similarity networks.
  • Tools — VDJtools (PlotFancyVJUsage, RarefactionPlot, CalcSpectratype); R circlize for chord diagrams and iNEXT for Hill-number rarefaction/extrapolation; Python matplotlib/seaborn/networkx/rapidfuzz.
  • Metric guidance — Morisita-Horn (depth-robust overlap) vs. Jaccard (presence/absence); Hamming/Levenshtein for sequence-similarity networks; frequency-weighted vs. clonotype-weighted views.
  • Correct-comparison workflow — clonotype definition → depth normalization → figure selection → metric choice → distance-threshold setting → interpretation at shared x-values with all parameters stated.

Primary use cases: TCR/BCR repertoire figure generation, depth-robust cross-sample overlap/diversity comparison, clonal tracking across timepoints.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally via Bash/R/Python rather than as an MCP server. The upstream skill front-matter name is bio-tcr-bcr-analysis-repertoire-visualization; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /repertoire-visualization. External dependencies: matplotlib 3.8+, seaborn 0.13+, pandas 2.2+, numpy 1.26+, R circlize 0.4+, R iNEXT 3.0+, and VDJtools 1.2. Upstream repertoire assembly is handled by mixcr-analysis (bulk) or scirpy-analysis (single-cell); diversity/overlap statistics by vdjtools-analysis. Upstream directory: tcr-bcr-analysis/repertoire-visualization.

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.