- filtering_disco.R - script to filter the DISCO dataset
The original RDS from DISCO was filtered according to the following steps:
- excluded samples/projects that did not have sex metadata
- excluded projects that did not contain data from both sexes (at least 2-3/samples per sex)
- for each disease condition (normal/healthy, Alzheimer's disease, and multiple sclerosis) kept only the cell types that had samples from both sexes
- then excluded the cell types which had samples from only one project
- lastly, cell types with less than 100 cells per project and sex were not analyzed
- prep_DEG_files.R - script to prepare files for the DEG analysis, to be run BEFORE the DEGs analysis
- 01B_plot_num_genes_func.R - functions to extract the common DEGs among F and M DEGs per each subtype, and plot the results
- 01C_num_chr_func.R - functions to map the DEGs obtained from 01B to the genome and plot the fraction of DEGs belonging to X, Y or autosomial chromosome; it also plots a heatmap of the X- and Y-genes expression across the different subtypes
- 01D_Xpar1,2_func.R - script to calculate and plot the number of genes belonging to Xpar1 and Xpar2
- 01E_CellMarker_func.R - functions to calculate and plot the percentage of DEGs which are also markers (marker list retrieved from CellMarker)
- 02A_HyperGeom_func.R - functions to calculate the enrichment of sex chromosomes compared to autosomial genes - used in 01C to add significance to plot
- 02B_ARE_ERE_func.R - functions to calculate and plot the ARE and ERE sites percentages in the cell types, separated F and M, but in the individual projects instead of on the intersected DEGs
- 02C_Conservation_func.R - functions to plot the conserved fraction of DEGs across mammals and primates
- all_scripts_DISCO_proj_GSE157827.R - script sourcing and running the previous scripts, 01A-02C, on the DEGs in an individual project
- all_scripts_DISCO_proj_GSE174367.R - script sourcing and running the previous scripts, 01A-02C, on the DEGs in an individual project
- all_scripts_DISCO_proj_PRJNA544731.R - script sourcing and running the previous scripts, 01A-02C, on the DEGs in an individual project
The scripts should be run in the following order:
- filtering_disco.R
- prep_DEG_files.R
- all_scripts_DISCO_proj_GSE157827.R, all_scripts_DISCO_proj_GSE174367.R, all_scripts_DISCO_proj_PRJNA544731.R (among these three, no order has to be followed)