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. (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:

Reference manual:	sigminer.pdf
Vignettes:	Analyze Copy Number Signatures with sigminer A Quick Start of sigminer Package

Downloads:

Package source:	sigminer_2.3.1.tar.gz
Windows binaries:	r-devel: sigminer_2.3.1.zip, r-release: sigminer_2.3.1.zip, r-oldrel: sigminer_2.3.1.zip
macOS binaries:	r-release (arm64): sigminer_2.3.1.tgz, r-oldrel (arm64): sigminer_2.3.1.tgz, r-release (x86_64): sigminer_2.3.1.tgz, r-oldrel (x86_64): sigminer_2.3.1.tgz
Old sources:	sigminer archive

Linking:

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