scProtocol: a user-friendly Shiny application for interactive scRNA-seq analysis

This is a Docker-based Shiny platform that integrates a complete single-cell RNA-seq analysis pipeline, from data import, quality control, normalization, dimensionality reduction, batch correction, clustering, cell type annotation, to differential expression and functional enrichment. Compared with existing tools, scProtocol requires only one command to launch, completely eliminates software environment configuration, and provides LLM models for automated cell type annotation. Our software and user interface are designed to enable biologists and clinicians without any programming experience to independently complete end-to-end scRNA-seq analysis and generate high-quality results ready for publication.

scProtocol will be online soon.