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
Roxygen: list(markdown = TRUE)
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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://steverozen.r-universe.dev
Date/Publication: 2026-09-16 17:38:58 UTC
RemoteUrl: https://github.com/steverozen/msigspectra
RemoteRef: HEAD
RemoteSha: 1848df872cd6455a554ca737a608bc11f233d8a7
NeedsCompilation: yes
Packaged: 2026-10-11 11:17:26 UTC; root
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>