mutSignatures-package: Decipher Mutational Signatures from Somatic Mutational...

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair pro-cesses. mutSignatures is a computational framework that is aimed at deciphering DNA mutational signatures oper-ating in cancer. The input is a numeric matrix of DNA mutation counts de-tected in a panel of cancer samples. The framework performs Non-negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. The framework relies on parallelization and is optimized for use on multi-core systems. This framework was described by Fantini D et al (2020) https://www.nature.com/articles/s41598-020-75062-0/ and is built upon a custom R-based implementation of the original MATLAB WTSI frame-work by Alexandrov LB et al (2013) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/. The mutSignatures framework has been described in peer-reviewed publications, including Fantini D et al (2018) https://www.nature.com/articles/s41388-017-0099-6/ and Fantini D et al (2019) https://www.sciencedirect.com/science/article/abs/pii/S1078143918303818/. The framework includes three modules that support raw data import and pre-processing, mutation counts deconvolution, and data visualization.

References

More info, examples and vignettes:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. 2020 Sci Rep paper describing the latest version of mutSignatures: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper: Mutational Signatures operative in bladder cancer: https://www.nature.com/articles/s41388-017-0099-6/

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.