Package: sigminer
Title: Extract, Analyze and Visualize Mutational Signatures for
    Genomic Variations
Version: 2.1.0
Authors@R: 
    c(person(given = "Shixiang",
             family = "Wang",
             role = c("aut", "cre"),
             email = "w_shixiang@163.com",
             comment = c(ORCID = "0000-0001-9855-7357")),
      person(given = "Ziyu",
             family = "Tao",
             role = "aut",
             email = "taozy@shanghaitech.edu.cn",
             comment = c(ORCID = "0000-0003-3272-1227")),
      person(given = "Huimin",
             family = "Li",
             role = "aut",
             email = "lihm@shanghaitech.edu.cn",
             comment = c(ORCID = "0000-0003-1683-9057")),
      person(given = "Tao",
             family = "Wu",
             role = "aut",
             email = "wutao2@shanghaitech.edu.cn",
             comment = c(ORCID = "0000-0002-8999-9628")),
      person(given = "Xue-Song",
             family = "Liu",
             role = c("aut", "ctb"),
             comment = c(ORCID = "0000-0002-7736-0077")),
      person(given = "Anand",
             family = "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.  (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil
    B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>).  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,
    covr,
    digest,
    GenomicRanges,
    GenSA,
    ggalluvial,
    ggcorrplot,
    ggfittext,
    ggplotify,
    ggrepel,
    IRanges,
    knitr,
    lpSolve,
    markdown,
    matrixStats,
    nnls,
    patchwork,
    pheatmap,
    quadprog,
    R.utils,
    RColorBrewer,
    reticulate,
    rmarkdown,
    roxygen2,
    scales,
    synchronicity,
    testthat,
    tibble,
    UCSCXenaTools,
    copynumber
LinkingTo: 
    Rcpp
VignetteBuilder: 
    knitr
biocViews:
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c("collate",
    "namespace", "rd", "roxytest::testthat_roclet"))
RoxygenNote: 7.1.1.9001