Programmable activators of cell signaling polarize macrophages to user-defined functional states

This project contains data and scripts associated with the paper, "Programmable activators of cell signaling polarize macrophages to user-defined functional states" (Lunger et al., 2026). Note: If you utilize any of the data or analyses found in this project, please cite our work. 1. Running the two-state model The Rds file phago_suma_combined.Rds contains the phagocytosis and surface marker data associated with Fig. 3 and used as input to run the two-state model associated with Fig. 5 and 6. The R markdown file run_two-state_model.Rmd contains the script which takes phago_suma_combined.Rds as input to fit the two-state model. Quality metrics, Predicted vs. Observed plots, and plots for the Km values associated with each motif are produced. 2. Datasets of interest The excel file RNAseq_DEGs.xlsx contains differentially expressed genes for each of the indicated comparisons, as presented in Figure 2, Figure S2, and Figure S3.