Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.

Abstract

Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data. Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy. Supplementary data are available at Bioinformatics online.