TCRscape: A Single-Cell Multi-Omic TCR Profiling Toolkit

Roman Perik-Zavodskii^*Olga Perik-ZavodskaiaMarina VolynetsSaleh AlrhmounSergey Vital'evich Sennikov

• Research Institute for Fundamental and Clinical Immunology (NIIFKI), Novosibirsk, Russia

Introduction. 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. Methods. 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™ single-cell multi-omics data. Results. TCRscape integrates full-length TCR sequence data with gene expression profiles and surface protein expression to enable multimodal clustering of αβ and γδ T-cell populations. It also outputs Seuratcompatible matrices, facilitating downstream visualization and analysis in standard single-cell analysis environments. Discussion. 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 TCRengineered therapeutic development. TCRscape can be found at https://github.com/Perik-Zavodskii/TCRscape/.