├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── data.R ├── data.import.R ├── deprecated.data.import.R ├── deprecated.mutation.factor.R ├── deprecated.utils.R ├── signatures.assignment.lasso.R ├── signatures.discovery.lasso.R └── visualization.R ├── README.md ├── _pkgdown.yml ├── data ├── background.rda ├── background2.rda ├── cv_example.rda ├── imported_data.rda ├── lambda_range_example.rda ├── mutation_categories.rda ├── nmf_LassoK_example.rda ├── patients.rda ├── ssm560_reduced.rda └── starting_betas_example.rda ├── inst └── NEWS.Rd ├── man ├── background.Rd ├── background2.Rd ├── cv_example.Rd ├── import.trinucleotides.counts.Rd ├── imported_data.Rd ├── lambdaRangeAlphaEvaluation.Rd ├── lambdaRangeBetaEvaluation.Rd ├── lambda_range_example.Rd ├── mutation_categories.Rd ├── nmfLasso.Rd ├── nmfLassoBootstrap.Rd ├── nmfLassoCV.Rd ├── nmf_LassoK_example.Rd ├── patients.Rd ├── 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