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

作者：Gregor Sturm, Tamás Szabó, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello · 发表于：Bioinformatics · 年份：2020 · DOI：10.1093/bioinformatics/btaa611 · 被引用次数：231 · 研究领域：Single-cell and spatial transcriptomics、T-cell and B-cell Immunology、vaccines and immunoinformatics approaches

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.