Package: sigminer
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
        Variations
Version: 2.3.1
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, 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, 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
RoxygenNote: 7.3.1
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2024-05-11 04:07:34 UTC; wsx
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
  Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
  Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
  Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
  Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
  Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Repository: CRAN
Date/Publication: 2024-05-11 08:50:02 UTC
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-15 16:47:25 UTC; windows
Archs: x64
