ezSingleCell: An integrated one-stop single-cell and spatial omics analysis platform for bench scientists

Abstract ezSingleCell is an interactive and easy-to-use application for the analysis and integration of multiple single-cell and spatial omics data types. It integrates the best-performing publicly available methods and in-house novel algorithms for in-depth data analysis, integration, and interactive data visualization. By integrating the relevant tools to form a complete analysis pipeline, we save users from the hassles of choosing among the enormous diversity of available methods, installing individual packages, and reformatting the data for different analysis steps. ezSingleCell takes input data in a variety of formats such as text files or Cell Ranger/ Space Ranger output and produces publication ready figures and tables. Users can customize the relevant parameters to ensure the quality and accuracy of their data analysis. Users can also download and store the R objects from ezSingleCell to perform additional offline analyses. ezSingleCell’s streamlined interface can analyze a standard scRNA-seq dataset containing 3000 cells in less than five mins. ezSingleCell is also accompanied by an in-depth manual and video tutorials to guide users. Overall, these features make ezSingleCell a convenient and easy web service for single cell and spatial analysis without requiring prior programming knowledge. ezSingleCell is available in two forms: an installation-free web application (https://immunesinglecell.org/ezsc/) or a software package with a shinyApp interface (https://github.com/JinmiaoChenLab/ezSingleCell2) that runs on a personal computer with a low memory requirement of 8 Gb RAM.