Borcherding Nicholas, Bormann Nicholas L, Kraus Gloria
Department of Pathology, University of Iowa, Iowa City, IA, USA.
Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA.
F1000Res. 2020 Jan 27;9:47. doi: 10.12688/f1000research.22139.2. eCollection 2020.
Single-cell sequencing is an emerging technology in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. A number of workflows and software packages have been created to process and analyze single-cell transcriptomic data. These packages allow users to take the vast dimensionality of the data generated in single-cell-based experiments and distill the data into novel insights. Unlike the transcriptomic field, there is a lack of options for software that allow for single-cell immune receptor profiling. Enabling users to easily combine mRNA and immune profiling, scRepertoire was built to process data derived from 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with a number of popular R packages for single-cell expression, such as Seurat. The scRepertoire R package and processed data are open source and available on GitHub and provides in-depth tutorials on the capability of the package.
单细胞测序是免疫学和肿瘤学领域的一项新兴技术，它使研究人员能够在单个细胞水平上结合RNA定量分析和其他方法，如免疫细胞受体分析。目前已经创建了许多工作流程和软件包来处理和分析单细胞转录组数据。这些软件包允许用户处理基于单细胞实验产生的海量数据，并从中提炼出新的见解。与转录组学领域不同，目前缺乏用于单细胞免疫受体分析的软件选项。为了让用户能够轻松地将mRNA和免疫分析结合起来，scRepertoire被开发出来，用于处理来自10x Genomics Chromium免疫分析的T细胞受体（TCR）和免疫球蛋白（Ig）富集工作流程的数据，并随后与一些用于单细胞表达的流行R软件包（如Seurat）进行交互。scRepertoire R软件包和处理后的数据是开源的，可在GitHub上获取，并提供了关于该软件包功能的深入教程。
