DDR-EpiTOF dataset and analysis code

This record contains the data and analysis scripts used for the DDR-EpiTOF study, including gated FCS files exported from Cytobank, compensation bead FCS files, metadata files, panel information files, cluster-merging tables, and R Markdown scripts used for the analysis of ovarian cancer cell lines. The scripts should be run in the following order:1. DDR-EpiTOF_Part1.Rmd2. DDR-EpiTOF_Part2.Rmd3. DDR-EpiTOF_Part3.Rmd4. DDR-EpiTOF_Part4.Rmd DDR-EpiTOF_Part1.Rmd contains the initial preprocessing steps for CyTOF data analysis, including data import, compensation, conversion to a SingleCellExperiment object, and normalization steps required for downstream analysis. DDR-EpiTOF_Part2.Rmd contains additional functions used in the analysis. DDR-EpiTOF_Part3.Rmd contains the analysis of the control population used for steady-state evaluation and includes the code used to generate Figures 2, 3, and 4, as well as Supplementary Figures 2 and 3. DDR-EpiTOF_Part4.Rmd contains the analysis of samples from all conditions used to evaluate the response to irradiation and includes the code used to generate Figures 5 and 6, as well as Supplementary Figures 4 and 5. Version 2 update:Supplementary Fig. 3D was corrected because an incorrect figure had been shown in the previous version. No changes were made to the underlying data, analysis results, or study conclusions.