Tooluniverse Immune Repertoire Analysis

This handles TCR and BCR repertoire sequencing analysis through an eight phase workflow covering clonotype definition, diversity metrics (Shannon entropy, Simpson index, clonality scoring), V(D)J gene usage patterns, CDR3 characterization, and clonal expansion tracking. The real value is in phase 7, where it queries IEDB and BVBRC to match expanded clones against known epitope specificities, which is exactly what you need when trying to figure out what antigen is driving a response post-vaccination or in tumor infiltrating lymphocytes. It integrates with single-cell data to link clonotypes to phenotypes and includes a sensible evidence grading system for interpreting results. One caution: the documentation correctly emphasizes computing rarefaction curves from your actual data rather than guessing whether sequencing depth is adequate.

skills.sh installs: 361
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

$ npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-immune-repertoire-analysis --agent claude-code

Installs into .claude/skills of the current project.

Files

ToolUniverse Immune Repertoire Analysis

Comprehensive skill for analyzing T-cell receptor (TCR) and B-cell receptor (BCR) repertoire sequencing data to characterize adaptive immune responses, clonal expansion, and antigen specificity.

Domain Reasoning

Repertoire diversity reflects immune history. High clonality — a few clones dominating — indicates antigen-driven expansion, as seen in active infection, tumor-infiltrating lymphocytes, or chronic stimulation. Low diversity points to immunodeficiency or treatment-induced lymphopenia. Always compare observed metrics against healthy donor reference distributions before drawing conclusions; a Shannon entropy of 7 is unremarkable in a healthy adult but alarming post-chemotherapy.