MutationalPatterns: comprehensive genome-wide analysis of mutational processes

Base substitution catalogs represent historical records of mutational processes that have been active in a system. Such processes can be distinguished by typical characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, and distribution throughout the genome. MutationalPatterns is an R/Bioconductor package that characterizes this broad range of mutational patterns and potential relations with (epi-)genomic features. Furthermore, it offers an efficient method to quantify the contribution of known mutational signatures. Such analyses can be used to determine whether certain DNA repair mechanisms are perturbed and to further characterize the processes underlying known mutational signatures.