Figure 10 is generated using compare_rna_dna_ranks.R
Recurrence analysis is done using recurrance_histogram.R
Master table generation and filtering is done using make_master_table.R followed by filter_master_table.R
Metadata needed for filtering and analysis:
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To account for gene_length: ensembl_gene_length_gc_path
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To translate gene names: ensembl_annot_path
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Filter out the genes from the ranked list that don't pass permutation test: filter_score_path
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Cancer Census genes used in this analysis: cancer_census_genes_path
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PCAWG driver genes used in this analysis: driver_gene_path
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HLA genes removed from recurrance analysis: hla_genes_path
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Genes with high enough expression to be included in the recurrance analysis: fpkm_pass_path