Code for Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the classical Hodgkin Lymphoma Tumor Microenvironment

Overview of Code The following is an overview of the code in this repository. Please note that since this repository doesn't contain the necessary data that was used for the analysis, if one wishes to reproduce the result, one will need to download the data and change the file path accordingly in the code. File Name Description Figure2.rmd Produces Figure 2A, 2B, 2C, 2E Figure3.rmd Produces Figure 3A, 3B, 3C, 3D, 3E MESA.ipynb Produces the spatial diversity heatmap and violin plots in Figure 3A Figure4.rmd Produces Figure 4B, 4C Figure5/ Includes scripts that produce Figure 5C, 5D, 5F, and related supplementary figures Figure6.rmd Produces Figure 6A, 6B, 6C, 6D, 6E Figure7.rmd Produces Figure 7B, 7D, 7E, 7F Supplementary.rmd Produces supplementary figures for Figures 2, 3, and 4 multi_test_correction.R Conducts all the statistical tests in the paper and corrects for multiple comparisons using the Benjamini-Hochberg procedure Batch effect correction and evaluation.R This script is to adjust and assess data for batch effects based on GeoMX data