Bya, P.; Tran, D.; Nguyen, K.; Draghici, S.; Nguyen, T.

Single-cell technologies have revolutionized our ability to study cellular heterogeneity and dynamics at unprecedented resolutions. In this fast-growing field, it becomes increasingly challenging to navigate the vast amount of tools and steps for analysis. It is particularly difficult to integrate and analyze large datasets that require extensive collaborations and customized pipelines to obtain robust results. We present CytoAnalyst, a web-based platform that offers a number of important advantages over existing tools for single-cell analysis. First, the platform enables custom pipeline configuration using an efficient study management system and a broad range of analysis modules. Second, the platform supports parallel analysis instances, facilitating the comprehensive comparison of different methods or parameter settings available at each analysis step. Third, the advanced sharing system facilitates real-time synchronization among team members and seamless analysis continuation across different devices. Finally, the multi-grid visualization system supports simultaneous display of different data aspects, allowing for the comparison of multiple labels and plots side-by-side for comprehensive data insights, with the ability to save and reload visualization settings at any analysis step. The platform incorporates multiple blending modes, allowing users to combine plots in various ways for comprehensive data exploration. CytoAnalyst supports a high level of analytical rigor while providing user-friendly and flexible operations through its carefully designed interface and extensive documentation. The platform supports all major web browsers and is freely available at https://cytoanalyst.tinnguyen-lab.com.