This package contains the R code to reproduce the figures in the paper "Identifying Modulators of Cellular Responses by Heterogeneity-sequencing" currently available on bioRxiv. The Scifate.zip contains the R notebooks for preprocessing, the main analysis and the testing of Heterogeneity-seq via simulation of the Scifate data set. It also contains intermediary files to speed up rerunning the code. The MCMV.zip contains the R notebooks for preprocessing and the main analysis of the MCMV data set first presented in our manuscript. It also contains intermediary files to speed up rerunning the code. The functions.R files contains the Heterogeneity-seq functions, which will later be available as a standalone package.