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.Rmd
2. DDR-EpiTOF_Part2.Rmd
3. DDR-EpiTOF_Part3.Rmd
4. 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.