ArticleMethods in molecular biology (Clifton, N.J.)2022
Flexible Distance-Based TCR Analysis in Python with tcrdist3.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion.bioRxiv : the preprint server for biology · 2026Article
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- CD8+ T cells cross-restricted by HLA-B*57 and HLA-E*01 recognize HIV Gag with different functional profiles.JCI insight · 2026Article
- T Cell Receptor Sharing in Hypersensitivity Pneumonitis.Computational and structural biotechnology journal · 2026Article
- A functionally validated TCR-pMHC database for TCR specificity model development.bioRxiv : the preprint server for biology · 2025Article
- A fingerprint approach to pioneer structure-based T cell receptor repertoire analysis and specificity prediction.Frontiers in immunology · 2025Article
- Predicting Antigen-Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Quantification of heterogeneity in human CD8Frontiers in immunology · 2024Article
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3 authors.
Funding
Abstract
Paired- and single-chain T cell receptor (TCR) sequencing are now commonly used techniques for interrogating adaptive immune responses. TCRs targeting the same epitope frequently share motifs consisting of critical contact residues. Here we illustrate the key features of tcrdist3, a new Python package for distance-based TCR analysis through a series of three interactive examples. In the first example, we illustrate how tcrdist3 can integrate sequence similarity networks, gene-usage plots, and background-adjusted CDR3 logos to identify TCR sequence features conferring antigen specificity among sets of peptide-MHC-multimer sorted receptors. In the second example, we show how the TCRjoin feature in tcrdist3 can be used to flexibly query receptor sequences of interest against bulk repertoires or libraries of previously annotated TCRs based on matching of similar sequences. In the third example, we show how the TCRdist metric can be leveraged to identify candidate polyclonal receptors under antigenic selection in bulk repertoires based on sequence neighbor enrichment testing, a statistical approach similar to TCRNET and ALICE algorithms, but with added flexibility in how the neighborhood can be defined.
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