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

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. Here, we present TCRscape, an open-source Python 3 tool tailored for BD Rhapsody™ data, which performs high-resolution TCR clonotype discovery and quantification. TCRscape integrates full-length TCR sequence data with gene expression profiles and V(D)J gene segment usage to enable multimodal clustering of αβ and γδ T-cell populations. It outputs Seurat-compatible matrices, facilitating downstream visualization and analysis in standard single-cell analysis environments. By bridging clonotype detection with immune cell transcriptome and proteome 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.