Package: sigminer
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
    Variations
Version: 2.1.7
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
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,
    purrr,
    Rcpp,
    rlang (>= 0.1.2),
    stats,
    tidyr
Suggests:
    Biobase,
    Biostrings,
    BSgenome,
    BSgenome.Hsapiens.UCSC.hg19,
    circlize,
    cluster,
    copynumber,
    covr,
    digest,
    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,
    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: 7.2.1