Package: sigminer
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
        Variations
Version: 2.4.0
Authors@R: c(
    person("Shixiang", "Wang", , "w_shixiang@163.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9855-7357")),
    person("Ziyu", "Tao", , "taozy@shanghaitech.edu.cn", role = "aut",
           comment = c(ORCID = "0000-0003-3272-1227")),
    person("Huimin", "Li", , "lihm@shanghaitech.edu.cn", role = "aut",
           comment = c(ORCID = "0000-0003-1683-9057")),
    person("Tao", "Wu", , "wutao2@shanghaitech.edu.cn", role = "aut",
           comment = c(ORCID = "0000-0002-8999-9628")),
    person("Xue-Song", "Liu", role = c("aut", "ctb"),
           comment = c(ORCID = "0000-0002-7736-0077")),
    person("Anand", "Mayakonda", role = "ctb")
  )
Description: Genomic alterations including single nucleotide
        substitution, copy number alteration, etc. are the major force
        for cancer initialization and development. Due to the
        specificity of molecular lesions caused by genomic alterations,
        we can generate characteristic alteration spectra, called
        'signature' (Wang, Shixiang, et al. (2021)
        <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et
        al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher
        D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>).  This
        package helps users to extract, analyze and visualize
        signatures from genomic alteration records, thus providing new
        insight into cancer study.
License: MIT + file LICENSE
URL: https://github.com/ShixiangWang/sigminer,
        https://shixiangwang.github.io/sigminer/,
        https://shixiangwang.github.io/sigminer-book/
BugReports: https://github.com/ShixiangWang/sigminer/issues
Depends: R (>= 3.5)
Imports: cli (>= 2.0.0), cowplot, data.table, dplyr, furrr (>= 0.2.0),
        future, ggplot2 (>= 3.3.0), ggpubr, maftools, magrittr,
        methods, NMF, parallelly, purrr, Rcpp, rlang (>= 0.1.2), stats,
        tidyr
Suggests: Biobase, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
        circlize, cluster, covr, digest, doParallel, GenomicRanges,
        GenSA, ggalluvial, ggcorrplot, ggfittext, ggplotify, ggrepel,
        IRanges, knitr, lpSolve, markdown, matrixStats, nnls, parallel,
        patchwork, pheatmap, quadprog, R.utils, RColorBrewer,
        reticulate, rmarkdown, roxygen2, scales, synchronicity,
        testthat (>= 3.0.0), tibble, UCSCXenaTools
LinkingTo: Rcpp
VignetteBuilder: knitr
biocViews:
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace",
        "rd", "roxytest::testthat_roclet"))
RoxygenNote: 7.3.3
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        xz-utils zlib1g-dev
Repository: https://shixiangwang.r-universe.dev
Date/Publication: 2026-10-20 08:27:23 UTC
RemoteUrl: https://github.com/ShixiangWang/sigminer
RemoteRef: HEAD
RemoteSha: 63ad31682ec9c84979c979a25e35f1926c572a5a
NeedsCompilation: yes
Packaged: 2026-10-20 10:39:15 UTC; root
Author: Shixiang Wang [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9855-7357>),
  Ziyu Tao [aut] (ORCID: <https://orcid.org/0000-0003-3272-1227>),
  Huimin Li [aut] (ORCID: <https://orcid.org/0000-0003-1683-9057>),
  Tao Wu [aut] (ORCID: <https://orcid.org/0000-0002-8999-9628>),
  Xue-Song Liu [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-7736-0077>),
  Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>