ICAMS

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


License
GPL-3.0

Documentation

ICAMS

Travis build status CRAN_Status_Badge

In-depth Characterization and Analysis of Mutational Signatures (‘ICAMS’)

Purpose

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, https://doi.org/10.1101/gr.230219.117. ‘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.

Installation

Install the stable version of ICAMS from CRAN with the R command line:

install.packages("ICAMS")

After that, install the necessary dependency package from Bioconductor in order to successfully load ICAMS:

install.packages("BiocManager")
BiocManager::install("BSgenome")

Development version

To use new features, you can install ICAMS from the master branch on GitHub, which may not be stable:

install.packages("devtools")
devtools::install_github("steverozen/ICAMS")

Reference manual

https://github.com/steverozen/ICAMS/blob/master/data-raw/ICAMS_2.1.2.pdf