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 4.1.3; x86_64-pc-linux-gnu; 2024-05-23 23:15:03 UTC; unix
RemoteType: standard
RemotePkgRef: sigminer
RemoteRef: sigminer
RemoteRepos: https://cloud.r-project.org
RemoteReposName: CRAN
RemotePkgPlatform: source
RemoteSha: 2.3.1