Abstract
Single-cell adaptive immune receptor repertoire sequencing, combined with single-cell transcriptomics, offers a powerful way to interrogate T and B cell responses. This article presents scRepertoire 2, a major update of the R toolkit for analyzing single-cell immune receptor data. The new version expands support for clonotype tracking, repertoire diversity quantification, and visualization, and it integrates more tightly with Seurat and SingleCellExperiment workflows for joint immune receptor and transcriptomic analysis. Substantial performance optimizations yield marked gains in speed and memory efficiency compared with the first release, enabling routine analysis of much larger datasets. scRepertoire 2 therefore provides a flexible and scalable framework for dissecting adaptive immune dynamics in health and disease.