shinyDeepGxP: A user-friendly R Shiny app for Predicting Surface Protein Abundance from scRNA-seq Expression Using Deep Learning in Blood Cells

Abstract Motivation Understanding accurate immune cell heterogeneity and function in single-cell datasets requires access to protein-level information, which is often unavailable due to experimental limitations. Results We present shinyDeepGxP, an interactive web application featuring our deep learning model, DeepGxP, for predicting surface protein abundance from single-cell RNA-sequencing (scRNA-seq) data. This platform makes DeepGxP accessible to researchers without programming skills. Users can upload scRNA-seq count matrices and use “Predict Protein” to predict the abundance of 224 biologically relevant surface proteins. shinyDeepGxP provides visualizations to help identify distinct cell populations based on predicted protein profiles. Moreover, users can choose “Explore Model” to reveal key RNA predictors and their associated biological pathways for each protein. Overall, shinyDeepGxP is a user-friendly, freely available web tool that provides protein-level detail for RNA-only single-cell datasets, enabling multimodal discovery without additional experiments. Availability and implementation shinyDeepGxP can be launched on https://shiny.crc.pitt.edu/deepgxp/.