Description: Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software was described by Fantini D et al (2020) <doi:10.1038/s41598-020-75062-0> and is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.
Suggests: dplyr, reshape2, kableExtra, gridExtra, knitr, rmarkdown

Description: Mutable prototype based objects with multiple inheritance.
Collate: 'ancestors.r' 'core.r' 'object.r' 'object-inheritance.r'

Title: GUI and wrappers for multiple testing procedures
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten
Dickhaus, Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Description: The Mutoss package and accompanying mutossGUI package are
designed to ease the application and comparison of multiple
Depends: R (>= 2.8.0), multcomp (>= 1.1-0), methods, plotrix
Suggests: fdrtool, multtest (>= 2.2.0), mvtnorm, qvalue

Title: Unified Multiple Testing Procedures
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Suggests: fdrtool, qvalue, RUnit, lattice
Imports: plotrix, multtest (>= 2.2.0), multcomp (>= 1.1-0), methods

Description: Designed to ease the application and comparison of multiple
hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are
standardized and usable by the accompanying 'mutossGUI'.
Suggests: fdrtool, qvalue, testthat, lattice