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" catalogs of mutational spectra or signatures.

Version: 2.2.4
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: 2020-09-22
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
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
Materials: README NEWS
CRAN checks: ICAMS results

Downloads:

Reference manual: ICAMS.pdf
Package source: ICAMS_2.2.4.tar.gz
Windows binaries: r-devel: ICAMS_2.2.4.zip, r-release: ICAMS_2.2.4.zip, r-oldrel: ICAMS_2.2.4.zip
macOS binaries: r-release: ICAMS_2.2.4.tgz, r-oldrel: not available
Old sources: ICAMS archive

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