Designing scFlowVis: Visual Analytics for Single-Cell RNA Sequencing Analysis

The advent of single-cell RNA sequencing (scRNA-seq) technologies has increased the demand for accessible analysis tools. Although a standard multi-stage scRNA-seq workflow is well established, existing visualization systems typically support only isolated stages or data types, leaving full-pipeline exploration under-addressed. Supporting the complete workflow introduces a broad problem and design space, requiring diverse analytical tasks and interactions to be systematically organized into a cohesive analytical process. To address this challenge, we conducted a design study with visualization and bioinformatics experts. From this process, we derived a 'Task-to-Interface' strategy for translating workflow-oriented tasks into coordinated interface structures. scFlowVis realizes this strategy as a unified visual analytics environment for exploration, comparison, and workflow tracking across the scRNA-seq pipeline. By detailing our design process and insights, we aim to inform the design of future visual analytics systems involving complex analytical workflows and integrated interfaces. The source code is available at https:// github.com/ EavanXing0416/ scFlowVis.