ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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: 2.3.12
Depends: R (≥ 3.5)
Imports: Biostrings, BSgenome, data.table, dplyr, GenomeInfoDb, GenomicRanges, graphics, grDevices, IRanges, RColorBrewer, stats, stringi, utils, zip
Suggests: BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat
Published: 2024-02-09
DOI: 10.32614/CRAN.package.ICAMS
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu
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_2.3.12.tar.gz
Windows binaries: r-devel: ICAMS_2.3.12.zip, r-release: ICAMS_2.3.12.zip, r-oldrel: ICAMS_2.3.12.zip
macOS binaries: r-release (arm64): ICAMS_2.3.12.tgz, r-oldrel (arm64): ICAMS_2.3.12.tgz, r-release (x86_64): ICAMS_2.3.12.tgz, r-oldrel (x86_64): ICAMS_2.3.12.tgz
Old sources: ICAMS archive

Reverse dependencies:

Reverse suggests: cosmicsig, mSigTools


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