This repository contains the analysis code for Molecular Pixelation: Single cell spatial proteomics by sequencing by Karlsson et al.
- doublet_estimation.Rmd - Code for estimating doublets in a Jurkat/Daudi mixture experiment
- polarization.Rmd - Code for differential polarity analysis in a CD3 capping experiment and a Rituximab treatment experiment
- theme.R - Theme file for plotting
- unstimulated cells.Rmd - Code for analysis of unstimulated PBMC cells
- uropod analysis.Rmd - Code for analysis of T cells stimulated to form uropods, including differential polarity analysis, differential colocalization analysis
- utility.R - Utility scripts containing support functions