mirpy

Python library for AIRR-seq and immune repertoire analysis of T-cell (TCR) and B-cell (BCR) receptor sequences. Use when the user asks to: parse AIRR, VDJtools, Adaptive, or 10x repertoire files; compute diversity metrics (Shannon, Chao1, Hill curves, rarefaction); detect antigen-specific TCR clusters (ALICE Poisson enrichment, TCRNET MC-control, GLIPH k-mer motifs); compute TCREmp prototype embeddings or TCRdist distances; analyse pairwise sample overlap (Jaccard, D-metric, F-metric, Morisita-Horn); build CDR3 motif logos (IC or selection logos against OLGA background); load or analyse single-cell 10x VDJ ± CITE-seq data; compute Pgen via OLGA or Monte-Carlo pools; embed receptors with TCREmp (V+J+CDR3 or germline CDR1+CDR2+CDR3 via arda region annotations); or run VDJBet Pgen-matched overlap analysis. Load references/ files when detailed parameter tables, performance notes, or edge-case gotchas are needed.