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TCRscape: a single-cell multi-omic TCR profiling toolkit
Roman Perik-Zavodskii1, Olga Perik-Zavodskaia1, Marina Volynets1
1Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, 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 Seurat-compatible 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 TCR-engineered therapeutic development. TCRscape can be found at https://github.com/Perik-Zavodskii/TCRscape/.
