Global Statistical and Data Sciences, Teva Pharmaceuticals, West Chester, PA 19380, USA.
Cells. 2023 May 27;12(11):1489. doi: 10.3390/cells12111489.
Single-cell RNA sequencing (scRNA-seq) is an attractive technology for researchers to gain valuable insights into the cellular processes and cell type diversity present in all tissues. The data generated by the scRNA-seq experiment are high-dimensional and complex in nature. Several tools are now available to analyze the raw scRNA-seq data from public databases; however, simple and easy-to-explore single-cell gene expression visualization tools focusing on differential expression and co-expression are lacking. Here, we present scViewer, an interactive graphical user interface (GUI) R/Shiny application designed to facilitate the visualization of scRNA-seq gene expression data. With the processed Seurat RDS object as input, scViewer utilizes several statistical approaches to provide detailed information on the loaded scRNA-seq experiment and generates publication-ready plots. The major functionalities of scViewer include exploring cell-type-specific gene expression, co-expression analysis of two genes, and differential expression analysis with different biological conditions considering both cell-level and subject-level variations using negative binomial mixed modeling. We utilized a publicly available dataset (brain cells from a study of Alzheimer's disease to demonstrate the utility of our tool. scViewer can be downloaded from GitHub as a Shiny app with local installation. Overall, scViewer is a user-friendly application that will allow researchers to visualize and interpret the scRNA-seq data efficiently for multi-condition comparison by performing gene-level differential expression and co-expression analysis on the fly. Considering the functionalities of this Shiny app, scViewer can be a great resource for collaboration between bioinformaticians and wet lab scientists for faster data visualizations.
单细胞 RNA 测序 (scRNA-seq) 是一种很有吸引力的技术,可让研究人员深入了解所有组织中存在的细胞过程和细胞类型多样性。scRNA-seq 实验产生的数据具有高度的维度和复杂性。现在有几种工具可用于分析来自公共数据库的原始 scRNA-seq 数据;然而,缺乏简单易用的单细胞基因表达可视化工具,这些工具侧重于差异表达和共表达。在这里,我们介绍了 scViewer,这是一个交互式图形用户界面 (GUI) R/Shiny 应用程序,旨在促进 scRNA-seq 基因表达数据的可视化。scViewer 以处理后的 Seurat RDS 对象作为输入,利用几种统计方法提供有关加载的 scRNA-seq 实验的详细信息,并生成可发表的图形。scViewer 的主要功能包括探索细胞类型特异性基因表达、两个基因的共表达分析,以及考虑到细胞水平和个体水平的变化,使用负二项混合模型对不同的生物学条件进行基因水平的差异表达分析。我们使用了一个公开可用的数据集(阿尔茨海默病研究中的脑细胞)来演示我们工具的实用性。scViewer 可以从 GitHub 作为 Shiny 应用程序下载,并进行本地安装。总的来说,scViewer 是一个用户友好的应用程序,它允许研究人员通过对基因水平的差异表达和共表达分析进行快速数据分析,有效地可视化和解释 scRNA-seq 数据,以便进行多条件比较。考虑到这个 Shiny 应用程序的功能,scViewer 可以成为生物信息学家和湿实验室科学家之间进行协作的重要资源,以实现更快的数据可视化。