1. Script: QC_DNA_intensity_FISH_cooks_dis: The codes added here are for demonstrating how to filter out nuclei with low intensity on both ORION and FISH assys. This also contains calculating cook's distance to filter out the outliers.
2. script: QC_FISH_score: The single cell table followed by cycif importer package was used to calculate the categories for diploid and aneuploid cells based on spotiflow FISH score. This is not a mandatory step and the scripts are also incoreporated in script 3 prior to neighborhood analysis. Categorising cells based on FISH score depends on the questions and projects.
3. script: local_neighborhoods_distance: neighborhood script was used to calculate a local neighborhood (50 um radius in any direction) of any epithelial cells. GLMM model was used for statistical analysis.