README.md

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

mutSignatures

Thank you for your interest in mutSignatures!

• version: latest (dev) version, 2.1.5
• previous versions are available as alternative branches

Notes about the R library

• integrated R-based computational framework aimed at deciphering DNA mutational signatures

• provides advanced functions for importing DNA variants, computing mutation types, and extracting mutational signatures via non-negative matrix factorization (NMF)

• I/O: accepts multiple types of input data (VCF, MAF), is compatible with non-human genomes, and supports the analysis of non-standard mutation types, such as tetra-nucleotide mutation types.

Important differences with previous versions

• the latest version of mutSignatures (available here on GitHub) fixes a known compatibility issue between older versions of mutSignatures and more recent versions of BSgenome objects. If you get an error while running the attachContext() function, please re-install the latest version of mutSignatures (from GitHub, see below!) and try again.

• compared to mutSignatures version 1.3.1-7, the latest mutSignature version replaced the plot() method with the msigPlot() method. Please, make sure to use mutSignatures::msigPlot() to build plots (as shown in the vignette attached to the package) especially when reproducing examples from older vignettes. Thanks!

Links

• Vignette on CRAN: https://cran.r-project.org/web/packages/mutSignatures/vignettes/get_sarted_with_mutSignatures.html

• Peer-reviewed paper (Sci Rep. 2020 Oct 26;10(1):18217): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589488/

Installation from GitHub

In R, you can run:

devtools::install_github("dami82/mutSignatures", force = TRUE, build_vignettes = TRUE)

Authors

• Damiano Fantini, Vania Vidimar, Yanni Yu, Salvatore Condello, Joshua J Meeks
• The package was developed at Northwestern University, Chicago, IL (Department of Urology, 2017-2020)
• The package is still maintained by Damiano Fantini in his free time (Damiano has left academia). Therefore, please be patient when asking for help of submitting new issues! Thanks.

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.