Immcantation BCR Analysis (bioSkills)

A Claude Code skill that reconstructs B-cell clonal families, measures somatic hypermutation and antigen-driven selection, and infers antibody lineage trees from AIRR-format repertoire-sequencing data.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT)
Capabilities Read/Write — Claude runs the skill’s R/Python workflow locally (Bash), not as an MCP tool
Verified works · 2026-07-20
Security cleared · 2026-07-20 — provenance matches GPTomics/bioSkills, MIT, skill directory confirmed this run, local R/Python workflow wrapping the open-source Immcantation suite no credentials

How to install

bioSkills is not an npm package — 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 --list to preview and --dry-run to see what would be copied.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/tcr-bcr-analysis/immcantation-analysis ~/.claude/skills/

    (run from inside your clone; otherwise replace bioSkills/ with the absolute path of your clone). The skill uses the Immcantation R suite (alakazam, shazam, scoper, dowser, tigger) plus IgBLAST/Change-O/IgPhyML — install these when prompted; the Immcantation Docker image is the simplest way to get the full toolchain.

What it does

Runs a full BCR clonal-analysis pipeline on AIRR-format sequences using five Immcantation R packages:

  • shazam — data-derived distance thresholding and mutation quantification.
  • scoper — clonal clustering into families.
  • alakazam — diversity metrics (Hill numbers).
  • dowser — germline reconstruction and lineage-tree inference.
  • tigger — personalized V-gene genotyping.

Key workflows: clonal partitioning using a derived (bimodal-valley) threshold rather than a hardcoded constant; replacement-vs-silent mutation profiling by CDR/FWR region; BASELINe selection testing; and germline-rooted, codon-aware lineage trees tracing affinity maturation and class switching.

Primary use cases: BCR clonal-family reconstruction, somatic-hypermutation profiling, selection testing, antibody lineage/affinity-maturation analysis.

Notes

Distributed as a SKILL.md in the bioSkills collection — Claude executes the R/Python workflow locally via Bash rather than as an MCP server. Upstream front-matter name: bio-tcr-bcr-analysis-immcantation-analysis. This is the first Claude-installable wrapper for the Immcantation framework the catalog has surfaced (previously a tracked gap). Requires AIRR-formatted input (e.g., from IgBLAST or TRUST4). Upstream directory: tcr-bcr-analysis/immcantation-analysis.

Sources

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