{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T14:15:50Z","timestamp":1764080150699,"version":"3.44.0"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,5]],"date-time":"2025-09-05T00:00:00Z","timestamp":1757030400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["124112200103-3"],"award-info":[{"award-number":["124112200103-3"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Single-cell multi-omics has transformed T-cell biology by enabling the simultaneous analysis of T-cell receptor (TCR) sequences, transcriptomes, and surface proteins at the resolution of individual cells. These capabilities are critical for identifying antigen-specific T-cells and accelerating the development of TCR-based immunotherapies.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Here, we introduce TCRscape, an open-source Python 3 tool designed for high-resolution T-cell receptor clonotype discovery and quantification, optimized for BD Rhapsody\u2122 single-cell multi-omics data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>TCRscape integrates full-length TCR sequence data with gene expression profiles and surface protein expression to enable multimodal clustering of \u03b1\u03b2 and \u03b3\u03b4 T-cell populations. It also outputs Seurat-compatible matrices, facilitating downstream visualization and analysis in standard single-cell analysis environments.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>By bridging clonotype detection with immune cell transcriptome, proteome, and antigen specificity profiling, TCRscape supports rapid identification of dominant T-cell clones and their functional phenotypes, offering a powerful resource for immune monitoring and TCR-engineered therapeutic development. TCRscape can be found at <jats:ext-link>https:\/\/github.com\/Perik-Zavodskii\/TCRscape\/<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fbinf.2025.1641491","type":"journal-article","created":{"date-parts":[[2025,9,5]],"date-time":"2025-09-05T05:41:19Z","timestamp":1757050879000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["TCRscape: a single-cell multi-omic TCR profiling toolkit"],"prefix":"10.3389","volume":"5","author":[{"given":"Roman","family":"Perik-Zavodskii","sequence":"first","affiliation":[]},{"given":"Olga","family":"Perik-Zavodskaia","sequence":"additional","affiliation":[]},{"given":"Marina","family":"Volynets","sequence":"additional","affiliation":[]},{"given":"Saleh","family":"Alrhmoun","sequence":"additional","affiliation":[]},{"given":"Sergey","family":"Sennikov","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,9,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"4020","DOI":"10.3390\/cancers16234020","article-title":"Targeting precision in cancer immunotherapy: naturally-occurring antigen-specific TCR discovery with single-cell sequencing","volume":"16","author":"Alrhmoun","year":"2024","journal-title":"Cancers (Basel)"},{"key":"B2","doi-asserted-by":"publisher","first-page":"2805","DOI":"10.3390\/BIOMEDICINES11102805","article-title":"TCR-engineered lymphocytes targeting NY-ESO-1: in vitro assessment of cytotoxicity against tumors","volume":"11","author":"Alsalloum","year":"2023","journal-title":"Biomedicines"},{"key":"B3","doi-asserted-by":"publisher","first-page":"6916","DOI":"10.1038\/s41467-024-51252-6","article-title":"Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer","volume":"15","author":"Byrne","year":"2024","journal-title":"Nat. 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