RT Journal Article
SR Electronic
T1 MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 071761
DO 10.1101/071761
A1 Francis Blokzijl
A1 Roel Janssen
A1 Ruben van Boxtel
A1 Edwin Cuppen
YR 2016
UL http://biorxiv.org/content/early/2016/10/17/071761.abstract
AB Summary Mutational processes leave characteristic footprints in genomic DNA. The MutationalPatterns R package provides an easy-to-use toolset for the characterization and visualization of mutational patterns in base substitution catalogues of e.g. tumour samples or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional strand bias, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of and molecular mechanisms behind mutational processes. The package provides functionalities for both extracting mutational signatures de novo and inferring the contribution of previously identified mutational signatures in a given sample. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.Availability and implementation The MutationalPatterns R package is freely available for download at https://github.com/CuppenResearch/MutationalPatterns. The package documentation provides a detailed description of typical analysis workflows.Contact ecuppen{at}umcutrecht.nl