last modified: July. 18 2020
CESanal_prepare.R: data preparation (using cancereffectsizeR package)
mutrate_scatter.R: scatter plot for mutation rate comparison between different tumor sizes/stages
selection_intensity_plot.R: bar plot of selection intensity of genes/variants (highlight genes with multiple variants)
common_var.R: extract common/similar variants between different tumor sizes/stages
dendro_heatmap_base.R: generate heatmap with dendrogram for tumor and signatures
trinuc_YL.R: heatmap for upstream & downstream trinucleotide mutation weights
summary_gene_info.R: summarise information of genes with multiple variants (output table with columns: gene, #variant, mean SI, sd, TopVariant, format)
scatter_linear.R: linear-scatter plot of gene mutation rate by stages/sizes (highlight genes of interest)
si_box.R: box plot for gene selection intensity by stages/sizes
epistasis_plot.R: epistasis plot for individual pair of genes