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] (<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 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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