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.
Version: 2.3.1 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 LinkingTo: Rcpp 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 Published: 2024-05-11 DOI: 10.32614/CRAN.package.sigminer Author: Shixiang Wang [aut, cre], Ziyu Tao [aut], Huimin Li [aut], Tao Wu [aut], Xue-Song Liu [aut, ctb], Anand Mayakonda [ctb] Maintainer: Shixiang Wang <w_shixiang at 163.com> BugReports: https://github.com/ShixiangWang/sigminer/issues License: MIT + file LICENSE URL: https://github.com/ShixiangWang/sigminer, https://shixiangwang.github.io/sigminer/, https://shixiangwang.github.io/sigminer-book/ NeedsCompilation: yes Citation: sigminer citation info Materials: README NEWS In views: Omics CRAN checks: sigminer results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=sigminer to link to this page.
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