Ma Wei Feng, Turner Adam W, Gancayco Christina, Wong Doris, Song Yipei, Mosquera Jose Verdezoto, Auguste Gaëlle, Hodonsky Chani J, Prabhakar Ajay, Ekiz H Atakan, van der Laan Sander W, Miller Clint L
Medical Scientist Training Program, University of Virginia, Charlottesville, VA, United States.
Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States.
Front Cardiovasc Med. 2022 Aug 8;9:969421. doi: 10.3389/fcvm.2022.969421. eCollection 2022.
Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
单细胞RNA测序（scRNA-seq）是一种强大的基因组学技术，用于探究复杂系统的细胞组成和行为。虽然scRNA-seq数据集的数量和可用的计算分析工具呈指数级增长，但用于快速探索和重新分析单细胞数据集的系统数据共享策略有限，尤其是在心血管领域。我们之前推出了PlaqView，这是一个用于探索和分析已发表的动脉粥样硬化单细胞数据集的开源门户网站。现在，我们推出了PlaqView 2.0（www.plaqview.com），它提供了扩展的功能以及更多的心血管单细胞数据集。我们展示了PlaqView改进后的功能、后端数据处理、用户界面和能力。PlaqView带来了新的或改进的工具来探索scRNA-seq数据，包括基因查询、元数据浏览器、细胞身份预测、RNA轨迹分析和药物-基因相互作用预测。PlaqView是心血管单细胞数据集最大的中央存储库之一，现在包括来自人类主动脉瘤、基因特异性小鼠基因敲除和健康对照的数据。PlaqView 2.0无需任何编程知识即可直接为用户带来先进的工具和高性能计算。最后，我们概述了将PlaqView框架推广并重新用于其他领域单细胞数据集的步骤。
