Single-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) and single-cell RNA sequencing (scRNA-seq) provide a transformative approach to profiling immune responses at unprecedented resolution across diverse pathophysiologic contexts. This work presents scRepertoire 2, a substantial update to our R package for analyzing and visualizing single-cell immune receptor data. This new version introduces an array of features designed to enhance both the depth and breadth of immune receptor analysis, including improved workflows for clonotype tracking, repertoire diversity metrics, and novel visualization modules that facilitate longitudinal and comparative studies. Additionally, scRepertoire 2 offers seamless integration with contemporary single-cell analysis frameworks like Seurat and SingleCellExperiment, allowing users to conduct end-to-end single-cell immune profiling with transcriptomic data. Performance optimizations in scRepertoire 2 resulted in a 85.1% increase in speed and a 91.9% reduction in memory usage from the first version over the range repertoire size tested in benchmarking, addressing the demands of the ever-increasing size and scale of single-cell studies. This release marks an advancement in single cell immunogenomics, equipping researchers with a robust toolset to uncover immune dynamics in health and disease.
Copyright: © 2025 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.