sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

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:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <doi:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <doi:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Version: 1.2.5
Depends: R (≥ 3.5)
Imports: cli (≥ 2.0.0), cowplot, data.table, dplyr, foreach, 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, doFuture, flexmix, 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
Published: 2021-02-20
Author: Shixiang Wang ORCID iD [aut, cre], Ziyu Tao ORCID iD [aut], Huimin Li ORCID iD [aut], Tao Wu ORCID iD [aut], Xue-Song Liu ORCID iD [aut, ctb], Geoffrey Macintyre [ctb], Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang at>
License: MIT + file LICENSE
NeedsCompilation: yes
Citation: sigminer citation info
Materials: README NEWS
CRAN checks: sigminer results


Reference manual: sigminer.pdf
Vignettes: A Quick Start of sigminer Package
Package source: sigminer_1.2.5.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: not available, r-oldrel: not available
Old sources: sigminer archive


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