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tooluniverse-immune-repertoire-analysis

TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification. Use for adaptive immune response characterization, post-treatment immune monitoring, antigen-specific clone tracking, and clonal-expansion analysis in immunotherapy or vaccination studies.

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# 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.

## LOOK UP DON'T GUESS

- Clonotype frequency thresholds, CDR3 length ranges, and convergence ratios: query IEDB or VDJdb; do not assume values from memory.
- Epitope specificities for expanded clones: search `iedb_search_tcell_assays` and `BVBRC_search_epitopes`; never infer antigen identity from CDR3 alone.
- V gene family usage biases in healthy donors: retrieve published reference data or query ImmPort; do not assume baseline distributions are uniform.
- Sequencing depth adequacy: compute rarefaction curves from the actual data; do not guess whether depth is sufficient.