Protocol for deep-learning-driven cell type label transfer in single-cell RNA sequencing data

Here, we present a protocol for using SIMS (scalable, interpretable machine learning for single cell) to transfer cell type labels in single-cell RNA sequencing data. This protocol outlines data preparation, model training with labeled data or inference using pretrained models, and methods for visualizing, downloading, and interpreting predictions. We provide stepwise instructions for accessing SIMS through the application programming interface (API), GitHub Codespaces, and a web application. For complete details on the use and execution of this protocol, please refer to Gonzalez-Ferrer et al.(1).