Analysis and visualization of experimentally elucidated mutational signatures – the kind of analysis and visualization in Boot et al., "In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors", Genome Research 2018, <doi:10.1101/gr.230219.117> and "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types", Genome Research 2020 <doi:10.1101/gr.255620.119>. 'ICAMS' stands for In-depth Characterization and Analysis of Mutational Signatures. 'ICAMS' has functions to read in variant call files (VCFs) and to collate the corresponding catalogs of mutational spectra and to analyze and plot catalogs of mutational spectra and signatures. Handles both "counts-based" and "density-based" (i.e. representation as mutations per megabase) mutational spectra or signatures.
| Version: | 3.0.11 |
| Depends: | R (≥ 3.5) |
| Imports: | Biostrings, BSgenome, data.table, dplyr, fuzzyjoin, GenomeInfoDb, GenomicRanges, graphics, grDevices, IRanges, lifecycle, RColorBrewer, stats, stringi, utils, zip |
| Suggests: | BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, ggplot2, reshape2, rlang, testthat |
| Published: | 2025-06-15 |
| DOI: | 10.32614/CRAN.package.ICAMS |
| Author: | Steve Rozen [aut, cre], Nanhai Jiang [aut], Arnoud Boot [aut], Mo Liu [aut], Yang Wu [aut], Mi Ni Huang [aut], Jia Geng Chang [aut] |
| Maintainer: | Steve Rozen <steverozen at gmail.com> |
| BugReports: | https://github.com/steverozen/ICAMS/issues |
| License: | GPL-3 | file LICENSE |
| URL: | https://github.com/steverozen/ICAMS |
| NeedsCompilation: | no |
| Language: | en-US |
| Citation: | ICAMS citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | ICAMS results |
| Reference manual: | ICAMS.pdf |
| Package source: | ICAMS_3.0.11.tar.gz |
| Windows binaries: | r-devel: ICAMS_3.0.11.zip, r-release: ICAMS_3.0.11.zip, r-oldrel: ICAMS_3.0.11.zip |
| macOS binaries: | r-release (arm64): ICAMS_3.0.11.tgz, r-oldrel (arm64): ICAMS_3.0.11.tgz, r-release (x86_64): ICAMS_3.0.11.tgz, r-oldrel (x86_64): ICAMS_3.0.11.tgz |
| Old sources: | ICAMS archive |
| Reverse suggests: | cosmicsig, mSigTools |
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