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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 |
| 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 |
| Reference manual: | mSigSpectra.html , mSigSpectra.pdf |
| Vignettes: |
Reading VCFs and Building Mutational-Spectrum Catalogs (source, R code) |
| Package source: | mSigSpectra_0.1.3.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): mSigSpectra_0.1.3.tgz, r-oldrel (arm64): mSigSpectra_0.1.3.tgz, r-release (x86_64): mSigSpectra_0.1.3.tgz, r-oldrel (x86_64): mSigSpectra_0.1.3.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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