antigenomics

Run QC scripts on a VDJdb chunk, report every error with a suggested fix, verify the output of previous /extract and /format steps, estimate confidence scores, and flag gaps in current py_src QC coverage.

Identify and classify duplicate TCR records across all VDJdb chunks at three resolution levels (beta-only, paired, and same-epitope multi-MHC), categorise by publication source, author overlap, and flag spurious high-frequency records.

Harmonize antigen.gene and antigen.species fields in a VDJdb chunk to canonical VDJdb naming. Detects spurious gene/species names, resolves inconsistencies (same epitope → multiple names), and warns about epitopes that are exact substrings of longer epitopes. Invoked standalone or from /proofread when spurious values are detected.

For each new or changed chunk in chunks/ (by git), find or create a GitHub issue for its PMID, then commit the chunk with "Fixes

Extract TCR:pMHC specificity data from raw source files (papers, supplementary tables, XLS, PDF, 10X output, AIRR-format) and produce a VDJdb-formatted TSV chunk ready for /format and /proofread.

Standardise a raw or partially-formatted VDJdb TSV chunk — normalising species names, IMGT V/D/J gene IDs, IMGT-HLA MHC alleles, and method vocabulary — and produce a properly-named chunk file ready for proofreading.

Fast TCR/BCR FR/CDR region annotation (Antigen Receptor Domain Annotation). Use whenever the user wants to annotate immune-receptor sequences with framework/CDR regions, V/D/J gene calls, constant-region isotype (c_call/c_class), junction/CDR3 boundaries, or AIRR output — for TCR (TRA/TRB/TRG/TRD) or BCR (IGH/IGK/IGL), nucleotide or amino acid, single sequences or large FASTA/FASTQ. Also use for: marking up, validating or REPAIRING a bare (CDR3 amino acid, V, J) record that has no read behind it — a VDJdb-style row — including locating where it disagrees with germline and restoring a missing Cys104 / Phe118 anchor; calling the D gene (and tandem D-D) on a bare junction, or inferring it from junction length when the protein shows none of it; extracting the receptor repertoire (clonotypes, isotype usage) from bulk RNA-seq; getting germline FR1-FR3/CDR1-CDR2 (V) or FR4 (J) subsequences for individual alleles; building or rebuilding the reference database from IMGT germlines via IgBLAST; or diagnosing mmseqs2 set

tcren — TCR-pMHC contact potential (TCRen) pipeline; conventions and public API

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.