scirpy Analysis (bioSkills)

A Claude Code skill that analyzes single-cell paired TCR/BCR repertoires alongside gene expression in an AnnData/MuData object using scirpy.

   
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 workflow locally (Bash/Python), not as an MCP tool
Verified works · 2026-07-20
Security cleared · 2026-07-20 — provenance matches GPTomics/bioSkills, MIT, no advisories, read-only local scirpy workflow

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/scirpy-analysis ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). The skill declares its Python dependencies (scirpy, scanpy, mudata) in SKILL.md; install them when prompted on first use.

What it does

Runs a full single-cell immune-repertoire pipeline with scirpy (v0.24+) integrated with scanpy/mudata:

  • Data ingestion — loads 10x VDJ, AIRR TSV, dandelion, or BD Rhapsody formats and pairs receptor data with gene expression.
  • Quality control — chain-pairing categorization and doublet detection via chain_qc (multichain doublets, orphan dropout, extra-VJ dual-TCR).
  • Clonotype definition — receptor-specific strategies: exact CDR3-nt identity for TCR (define_clonotypes) versus nucleotide-distance clustering for BCR (define_clonotype_clusters with normalized Hamming + same V/J gene, because somatic hypermutation shatters identity clonotypes).
  • Clonal analysis — expansion binning, alpha diversity, repertoire overlap across groups, and clonotype modularity.
  • Integration — overlaying clonality onto the transcriptomic UMAP.

The skill works on the awkward-array AIRR model (adata.obsm['airr'], accessed via get.airr after pp.index_chains), not legacy per-chain obs columns, and covers tuning receptor_arms, dual_ir, and within_group.

Primary use cases: single-cell TCR/BCR clonotype analysis, clonal-expansion mapping onto transcriptomes, repertoire diversity and specificity annotation.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally via Bash/Python rather than as an MCP server. The upstream skill front-matter name is bio-tcr-bcr-analysis-scirpy-analysis; if you invoke it as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /scirpy-analysis. Complements bulk-repertoire skills (mixcr-analysis, immcantation-analysis) and VDJdb specificity lookup. Upstream directory: tcr-bcr-analysis/scirpy-analysis.

Sources

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