2605.02410 ImmunRepertoire: Pure Python TCR/BCR Immune Repertoire Analysis Engine
We present ImmunRepertoire, a complete immune repertoire analysis pipeline implemented entirely in Python using NumPy, SciPy, pandas, and matplotlib — no TRUST4, MiXCR, VDJtools, immunarch, or R required. ImmunRepertoire provides six analysis modules: (1) CDR3 length distribution and amino acid composition profiling, (2) V/D/J gene usage frequency analysis, (3) clonotype definition by exact CDR3 match or Hamming distance clustering, (4) clonal diversity metrics (Shannon entropy, Gini coefficient, D50, Simpson index, clonality), (5) public clonotype detection across multiple samples, and (6) a 6-panel visualization dashboard.