scX: a user-friendly tool for scRNAseq exploration

Abstract

Abstract Motivation Single-cell RNA sequencing (scRNAseq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. Results In this article, we present scX, an R package built on the Shiny framework that streamlines the analysis, exploration, and visualization of single-cell experiments. With an interactive graphic interface, implemented as a web application, scX provides easy access to key scRNAseq analyses, including marker identification, gene expression profiling, and differential gene expression analysis. Additionally, scX seamlessly integrates with commonly used single-cell Seurat and SingleCellExperiment R objects, resulting in efficient processing and visualization of varied datasets. Overall, scX serves as a valuable and user-friendly tool for effortless exploration and sharing of single-cell data, simplifying some of the complexities inherent in scRNAseq analysis. Availability and implementation Source code can be downloaded from https://github.com/chernolabs/scX. A docker image is available from dockerhub as chernolabs/scx.