Package: decompTumor2Sig
Type: Package
Title: Decomposition of individual tumors into mutational signatures by
        signature refitting
Depends: R (>= 4.5), ggplot2
Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats,
        rlang, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors,
        plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg38,
        TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation,
        SummarizedExperiment, ggseqlogo, gridExtra, data.table,
        GenomeInfoDb, readxl
Suggests: knitr, rmarkdown, cosmicsig, BiocStyle
Version: 2.99.0
Date: 2026-07-07
Encoding: UTF-8
Authors@R: c(
    person("Rosario M.", "Piro", email = "rmpiro@gmail.com",
            role = c("aut", "cre"), comment=c(ORCID="0000-0002-3066-7397")),
    person("Sandra", "Krueger", role = c("ctb"))
    )
Description: Uses quadratic programming for signature refitting, i.e.,
        to decompose the mutation catalog from an individual tumor
        sample into a set of given mutational signatures (either
        Alexandrov-model signatures or Shiraishi-model signatures),
        computing weights that reflect the contributions of the
        signatures to the mutation load of the tumor.
License: GPL-2
URL: http://rmpiro.net/decompTumor2Sig/,
        https://github.com/rmpiro/decompTumor2Sig
BugReports: https://github.com/rmpiro/decompTumor2Sig/issues
biocViews: Software, SNP, Sequencing, DNASeq, GenomicVariation,
        SomaticMutation, BiomedicalInformatics, Genetics,
        BiologicalQuestion, StatisticalMethod
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-07 17:55:43 UTC
RemoteUrl: https://github.com/bioc/decompTumor2Sig
RemoteRef: HEAD
RemoteSha: 2ef41d46f6c87f1bd585968f102b891f37db8a9f
NeedsCompilation: no
Packaged: 2026-07-07 21:31:26 UTC; root
Author: Rosario M. Piro [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3066-7397>),
  Sandra Krueger [ctb]
Maintainer: Rosario M. Piro <rmpiro@gmail.com>
Built: R 4.6.1; ; 2026-07-07 21:35:33 UTC; windows
