Analysis code and processed data for "Identification of candidate markers for dry eye disease-associated corneal damage: mechanistic implications of IFN-γ response in macrophages"

This dataset contains the complete R scripts, raw input matrices, and processed Seurat objects used for the single-cell RNA-seq analysis, along with the exported metadata, for the manuscript: "Identification of candidate markers for dry eye disease-associated corneal damage: mechanistic implications of IFN-γ response in macrophages". Data Source: The raw single-cell RNA-seq data analyzed in this code were originally generated by Alam et al. (2024) and obtained from the Broad Institute Single Cell Portal (SCP2448). Contents of this repository: SCP2448.R: Complete R script containing all analysis steps. matrix/: Raw 10x Genomics matrix files for the SCP2448 dataset. input/: External input files, including the ImmGen reference dataset and the IFN-γ (IFNG) gene list. sc_Rds/: Seurat object files that allow direct reproduction of figures without re-running upstream steps. output/: Folder containing the exported metadata from our final analysis. When running the R script, all generated figures and intermediate tables will be automatically saved in this directory. README.txt: Detailed instructions on the directory structure and the order of script execution. This upload is provided to ensure full reproducibility of our findings in response to the reviewer's comments.