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mSigSpectra  

Build Mutational-Spectrum Catalogs from Variant Call Format Files
View on CRAN: Click here


Download and install mSigSpectra package within the R console
Install from CRAN:
install.packages("mSigSpectra")

Install from Github:
library("remotes")
install_github("cran/mSigSpectra")

Install by package version:
library("remotes")
install_version("mSigSpectra", "0.1.3")



Attach the package and use:
library("mSigSpectra")
Maintained by
Steve Rozen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-09-27
Latest Update: 2026-09-27
Description:
Reads variant call format (VCF) files in a caller-agnostic way, annotates variants with flanking sequence context and transcriptional strand, and builds mutational-spectrum catalogs of single base substitutions (SBS), doublet base substitutions (DBS), and small insertions and deletions (indels, ID) at several resolutions (SBS96, SBS192, SBS1536, DBS78, DBS136, DBS144, ID83, ID89, ID166, ID476) and in both counts and density representations. Successor to the numerical core of the 'ICAMS' package with plotting, 'shiny', and portable document format (PDF) reporting removed; plotting is provided separately by 'mSigPlot'. Used in the preparation of Rozen et al. (2026) <doi:10.5281/zenodo.18451842>.
How to cite:
Steve Rozen (2026). mSigSpectra: Build Mutational-Spectrum Catalogs from Variant Call Format Files. R package version 0.1.3, https://cran.r-project.org/web/packages/mSigSpectra. Accessed 25 Oct. 2026.
Previous versions and publish date:
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Complete documentation for mSigSpectra
Functions, R codes and Examples using the mSigSpectra R package
Full mSigSpectra package functions and examples
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