├── .Rapp.history ├── .gitignore ├── DESCRIPTION ├── EvoFreq.Rproj ├── LICENSE ├── NAMESPACE ├── R ├── Animate_funcs.R ├── Dendro_funcs.R ├── EvoFreq_Parsers.R ├── EvoFreq_funcs.R ├── Example.Easy.Wide.R ├── Example.Long.Clone.History.R ├── Example.Long.Edges.R ├── Example.Wide.R ├── cmap_hex_list.R ├── color_funcs.R ├── example.easy.long.edges.R ├── example.easy.long.sizes.R ├── example.easy.wide.with.attributes.R └── idx_funcs.R ├── README.md ├── data ├── cmap_hex_list.rdata ├── example.easy.long.edges.rdata ├── example.easy.long.sizes.rdata ├── example.easy.wide.rdata ├── example.easy.wide.with.attributes.rdata ├── example.long.clones.rdata ├── example.long.edges.rdata └── example.wide.rdata ├── img ├── CancerResearchCover.png ├── easy.long.image.png ├── easy.wide.image.png └── readme.img.code.R ├── man ├── animate_evogram.Rd ├── cmap_hex_list.Rd ├── example.easy.long.edges.Rd ├── example.easy.long.sizes.Rd ├── example.easy.wide.Rd ├── example.easy.wide.with.attributes.Rd ├── example.long.clones.Rd ├── example.long.edges.Rd ├── example.wide.Rd ├── get_evofreq.Rd ├── get_evofreq_labels.Rd ├── get_evogram.Rd ├── get_mutation_df.Rd ├── long_to_wide_freq_ready.Rd ├── parse_calder.Rd ├── parse_phylowgs.Rd ├── plot_evofreq.Rd ├── plot_evogram.Rd ├── read.HAL.Rd └── update_colors.Rd └── tests └── testthat ├── test.example.get_freq_dynamics.R ├── test.example.labels.R └── test.example.plotting.R /.Rapp.history: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MathOnco/EvoFreq/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 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