Package: mSigSpectra
Type: Package
Title: Build Mutational-Spectrum Catalogs from Variant Call Format
        Files
Version: 0.1.3
Authors@R: c(person(given = "Steve",
                    family = "Rozen",
                    role = c("aut", "cre"),
                    email = "steverozen@pm.me"),
             person(given = "Nanhai",
                    family = "Jiang",
                    role = "aut"),
             person(given = "Arnoud",
                    family = "Boot",
                    role = "aut"),
             person(given = "Mo",
                    family = "Liu",
                    role = "aut"),
             person(given = "Yang",
                    family = "Wu",
                    role = "aut"),
             person(given = c("Mi", "Ni"),
                    family = "Huang",
                    role = "aut"),
             person(given = c("Jia", "Geng"),
                    family = "Chang",
                    role = "aut"))
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>.
License: GPL-3
URL: https://github.com/steverozen/mSigSpectra,
        https://steverozen.github.io/mSigSpectra/
BugReports: https://github.com/steverozen/mSigSpectra/issues
Encoding: UTF-8
LazyData: true
Language: en-US
biocViews:
Imports: BSgenome, data.table, fastrc, GenomeInfoDb, GenomicRanges,
        IRanges, Rcpp, S4Vectors, stats, stringi, tools
Depends: R (>= 4.1)
LinkingTo: Rcpp
Suggests: BSgenome.Hsapiens.1000genomes.hs37d5,
        BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
        knitr, mSigPlot, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
NeedsCompilation: yes
Packaged: 2026-09-16 17:38:49 UTC; steve
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@pm.me>
Repository: CRAN
Date/Publication: 2026-09-27 16:40:24 UTC
