ABSTRACT
One of the fields of cancer bioinformatics aims to use cancer genomics data to better understand cancer biology by discovering new driver genes and characterizing mutational signatures associated with specific types of cancer. This type of analysis generally investigates large cohorts of patients rather than individual samples. The search for recurrently mutated genes relies mostly on the idea that driver mutations accumulate in tumor-relevant genes due to positive selection. Driver genes and pathways (DrGaP) is a tool which incorporates knowledge of biological pathways to identify both individual driver genes and entire driver pathways. The chapter discusses DrGaP because it identifies both driver genes and driver pathways and requires minimal input. SomaticSignatures, one of the few available methods for the discovery of mutational signatures, is an R/Bioconductor package requires only a Variant Call Format (VCF) file and a reference genome as input. These are loaded as VRanges and BSgenome objects, respectively.
