This repository contains the data, code, and analyses used for "Cell-type specific epigenetic links to schizophrenia risk in brain"
1. DEG/ contains the codes and input data for analyises and visualization for the differential gene expression analysis (DEG) betweem schizophrenia and healthy controls.
2. DMP_ENRICHMENT/ contains data from WGBS analysis and downstream analysis for scDEGs and CellType DEGs.
3. EXTRA_DATA/ contains data from CMC and BrainSeq re-analysis and comparison with NeuN and OLIG2 data.
4. MAGMA/ contains code for the GWAS enrichment.
5. SHINY/ contains code and input data for exploratory shiny app based on boxplots/violin plots with statistics.
6. WGBS/ contains codes for the differential methylation analysis.