sigminer: Extract, Analyze and Visualize 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: 1.0.16
Depends: R (≥ 3.5)
Imports: cli (≥ 2.0.0), cowplot, data.table, dplyr, foreach, furrr, 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, doFuture, flexmix, GenomicRanges, GenSA, ggalluvial, ggfittext, ggplotify, IRanges, knitr, markdown, nnls, patchwork, pheatmap, quadprog, R.utils, RColorBrewer, reticulate, rmarkdown, roxygen2, testthat, tibble, ggrepel
Published: 2020-09-12
Author: Shixiang Wang ORCID iD [aut, cre], Xue-Song Liu ORCID iD [aut, ctb], Tao Wu [aut, ctb], Ziyu Tao [aut, ctb], Geoffrey Macintyre [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
NeedsCompilation: yes
Citation: sigminer citation info
Materials: README NEWS
CRAN checks: sigminer results

Downloads:

Reference manual: sigminer.pdf
Vignettes: sigminer vignette
Package source: sigminer_1.0.16.tar.gz
Windows binaries: r-devel: sigminer_1.0.16.zip, r-release: sigminer_1.0.16.zip, r-oldrel: sigminer_1.0.16.zip
macOS binaries: r-release: not available, r-oldrel: not available
Old sources: sigminer archive

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