mSigSpectra: Build Mutational-Spectrum Catalogs from Variant Call Format
Files
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>.
| Version: |
0.1.3 |
| Depends: |
R (≥ 4.1) |
| Imports: |
BSgenome, data.table, fastrc, GenomeInfoDb, GenomicRanges, IRanges, Rcpp, S4Vectors, stats, stringi, tools |
| LinkingTo: |
Rcpp |
| Suggests: |
BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, knitr, mSigPlot, rmarkdown, testthat (≥ 3.0.0), withr |
| Published: |
2026-09-27 |
| DOI: |
10.32614/CRAN.package.mSigSpectra (may not be active yet) |
| Author: |
Steve Rozen [aut, cre],
Nanhai Jiang [aut],
Arnoud Boot [aut],
Mo Liu [aut],
Yang Wu [aut],
Mi Ni Huang [aut],
Jia Geng Chang [aut] |
| Maintainer: |
Steve Rozen <steverozen at pm.me> |
| BugReports: |
https://github.com/steverozen/mSigSpectra/issues |
| License: |
GPL-3 |
| URL: |
https://github.com/steverozen/mSigSpectra,
https://steverozen.github.io/mSigSpectra/ |
| NeedsCompilation: |
yes |
| Language: |
en-US |
| Materials: |
README, NEWS |
| CRAN checks: |
mSigSpectra results |
Documentation:
Downloads:
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