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.