I have found the JACoP Plugin to be very useful in colocalization (coloc) analysis. However, I have had a lot of trouble trying to figure out its method for coloc calculations when using stacks. Let’s say I want to get the Pearson’s coefficient using JACoP. If I input two stacks of any length, JACoP will return one Pearson’s coefficient. This global value is not an average but something else. Does anyone know how JACoP works with stacks in this context?