MutationalPatterns - Comprehensive genome-wide analysis of mutational processes
Mutational processes leave characteristic footprints in
genomic DNA. This package provides a comprehensive set of
flexible functions that allows researchers to easily evaluate
and visualize a multitude of mutational patterns in base
substitution catalogues of e.g. healthy samples, tumour
samples, or DNA-repair deficient cells. The package covers a
wide range of patterns including: mutational signatures,
transcriptional and replicative strand bias, lesion
segregation, genomic distribution and association with genomic
features, which are collectively meaningful for studying the
activity of mutational processes. The package works with single
nucleotide variants (SNVs), insertions and deletions (Indels),
double base substitutions (DBSs) and larger multi base
substitutions (MBSs). The package provides functionalities for
both extracting mutational signatures de novo and determining
the contribution of previously identified mutational signatures
on a single sample level. MutationalPatterns integrates with
common R genomic analysis workflows and allows easy association
with (publicly available) annotation data.