MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues

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Description

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns from base substitution catalogues. These patterns include: mutational signatures, transcriptional strand bias, genomic distribution and association with genomic features.

Details

The package provides functionalities for both extracting mutational signatures de novo and inferring the contribution of previously identified mutational signatures. Furthermore, MutationalPatterns allows for easy exploration and visualization of other types of patterns such as transcriptional strand asymmetry, genomic distribution and associations with (publically available) annotations such as chromatin organization. In addition to identification of active mutation-inducing processes, this approach also allows for determining the involvement of specific DNA repair pathways. For example, presence of a transcriptional strand bias in genic regions may indicate activity of transcription coupled repair.

Author(s)

Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen Maintainers: Francis Blokzijl, UMC Utrecht <f.blokzijl@umcutrecht.nl> Roel Janssen, UMC Utrecht <R.R.E.Janssen-10@umcutrecht.nl>

References

Alexandrov,L.B. et al. (2013) Signatures of mutational processes in human cancer. Nature, 500, 415–21.

Blokzijl,F. et al. (2016) Tissue-specific mutation accumulation in human adult stem cells during life. Nature, in press.

Borchers,H.W. (2016) pracma: Practical Numerical Math Functions.

Durinck,S. et al. (2005) BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis. Bioinformatics, 21, 3439–3440.

Gaujoux,R. and Seoighe,C. (2010) A flexible R package for nonnegative matrix factorization. BMC Bioinformatics, 11, 367.

Haradhvala,N.J. et al. (2016) Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell, 1–12.

Helleday,T. et al. (2014) Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet., 15, 585–598.

Lawrence,M. et al. (2013) Software for computing and annotating genomic ranges. PLoS Comput. Biol., 9, e1003118.

Pleasance,E.D. et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191–196.

See Also

https://github.com/CuppenResearch/MutationalPatterns

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