Mutational Signature Comprehensive Analysis Toolkit

Introduction

A variety of exogenous exposures or endogenous biological processes can contribute to the overall mutational load observed in human tumors. Many different mutational patterns, or “mutational signatures”, have been identified across different tumor types. These signatures can provide a record of environmental exposure and can give clues about the etiology of carcinogenesis. The Mutational Signature Comprehensive Analysis Toolkit (musicatk) has utilities for extracting variants from a variety of file formats, contains multiple methods for discovery of novel signatures or prediction of known signatures, as well as many types of downstream visualizations for exploratory analysis. This package has the ability to parse and combine multiple motif classes in the mutational signature discovery or prediction processes. Mutation motifs include single base substitutions (SBS), double base substitutions (DBS), insertions (INS) and deletions (DEL).

Installation

Currently musicatk can be installed from on Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly=TRUE)){
    install.packages("BiocManager")}
BiocManager::install("musicatk")

To install the latest version from Github, use the following code:

if (!requireNamespace("devtools", quietly=TRUE)){
    install.packages("devtools")}

library(devtools)
install_github("campbio/musicatk")

The package can be loaded using the library command.

library(musicatk)

Tutorials

Detailed usage tutorials are available on the Camplab website under the 'Vignettes' drop-down.