🎯 Motivation

The book is written as a guide for extracting, analyzing and visualizing mutational signatures with R/CRAN packagesigminer. TheREADME andReference list ofsigminer have given users overview and the very details of specific points (e.g., functions) insigminer. This book will help users focus on quickly getting the mutational signature analysis done to make life easy.

In this book, we assume you have already known how to operateR.

📝 Citation

If you usesigminer or its pipeline versionsigflow in published research, please cite the most appropriate paper(s):

1. Wang, S., Li, H., Song, M., Tao, Z., Wu, T., He, Z., … & Liu, X. S. (2021). Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.PLoS genetics, 17(5), e1009557.https://doi.org/10.1371/journal.pgen.1009557
2. Wang, S., Tao, Z., Wu, T., & Liu, X. S. (2021). Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.Bioinformatics, 37(11), 1590-1592.https://doi.org/10.1093/bioinformatics/btaa895

Please properly cite the following references when you are using anycorresponding features. The references are also listed in the functiondocumentation. Very thanks to the works,sigminer cannot be createdwithout the giants.

1. Mayakonda, Anand, et al. “Maftools: efficient and comprehensiveanalysis of somatic variants in cancer.”Genome research 28.11(2018): 1747-1756.
2. Gaujoux, Renaud, and Cathal Seoighe. “A Flexible R Package forNonnegative Matrix Factorization.””BMC Bioinformatics 11, no. 1(December 2010).
3. Wickham, Hadley. “ggplot2.”Wiley Interdisciplinary Reviews: Computational Statistics 3.2 (2011): 180-185.
4. Kim, Jaegil, et al. “Somatic ERCC2 mutations are associated with adistinct genomic signature in urothelial tumors.”Nature Genetics48.6 (2016): 600.
5. Alexandrov, Ludmil B., et al. “Deciphering signatures of mutationalprocesses operative in human cancer.”Cell Reports 3.1 (2013):246-259.
6. Degasperi, Andrea, et al. “A practical framework and online tool formutational signature analyses show intertissue variation and driverdependencies.”Nature Cancer 1.2 (2020): 249-263.
7. Alexandrov, Ludmil B., et al. “The repertoire of mutationalsignatures in human cancer.”Nature 578.7793 (2020): 94-101.
8. Macintyre, Geoff, et al. “Copy number signatures and mutationalprocesses in ovarian carcinoma.”Nature Genetics 50.9 (2018): 1262.
9. Tan, Vincent YF, and Cédric Févotte. “Automatic relevancedetermination in nonnegative matrix factorization with the/splbeta/-divergence.”IEEE Transactions on Pattern Analysis and Machine Intelligence 35.7 (2012): 1592-1605.
10. Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG,Alexandrov LB: SigProfilerMatrixGenerator: a tool for visualizingand exploring patterns of small mutational events.BMC Genomics2019, 20:685https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6041-2

📚 Book structure

• Part 1 (Background and Prerequisite) describes the basic concepts of mutational signature and how to install/loadsigminer.
• Part 2 (Workflows) introduces how to prepare your input data and run mutational signature analysis for different mutation data types (SBS, DBS, INDEL, Genome rearrangement, CNV) with different methods provided bysigminer.
• Part 3 (Miscellaneous topics) describes useful utilities including builtin datasets, SBS signature conversion.

💖 Want to help?

The book’s source code is hosted on GitHub, athttps://github.com/ShixiangWang/sigminer-book. Any feedback on the book is very welcome. Feel free toopen an issue on GitHub or send me a pull request if you notice typos or other issues (I’m not a native English speaker ;) ).

🐜 Bug report or feature request

If you find any bugs or want to have a new feature, pleasefile an issue.

🌵 Acknowlegment

I built this book website by imitatingBiomedical knowledge mining using GOSemSim and clusterProfiler and reusing its configurations, I would like to thankGuangchuang Yu here.