├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── allele-specific.R ├── clonealign.R ├── inference-tflow.R ├── plotting.R └── preprocess.R ├── README.md ├── data ├── df_cnv.rda ├── example_clonealign_fit.rda └── example_sce.rda ├── docs ├── index.html ├── introduction_to_clonealign.html └── preparing_copy_number_data.html ├── inst ├── clonealign_figure.png └── create_model3_synthetic.R ├── man ├── clone_assignment.Rd ├── clonealign.Rd ├── compute_ca_fit_mse.Rd ├── compute_correlations.Rd ├── construct_ai_likelihood.Rd ├── df_cnv.Rd ├── example_clonealign_fit.Rd ├── example_sce.Rd ├── get_outlying_genes.Rd ├── inference_tflow.Rd ├── plot_clonealign.Rd ├── preprocess_for_clonealign.Rd ├── print.clonealign_fit.Rd ├── process_cnv_data.Rd ├── process_gene_expression_data.Rd ├── recompute_clone_assignment.Rd ├── round2.Rd ├── run_clonealign.Rd └── saturate.Rd ├── tests ├── testthat.R └── testthat │ └── test_clonealign.R └── 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