├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── compute_complexes.R ├── compute_gene_localization.R ├── create_TDAmut_object.R ├── filter_genes.R ├── objects.R └── plot_mapper.R ├── README.md ├── TDA.TCGA.Rproj ├── TDAmut_Tutorial.Rmd ├── TDAmut_Tutorial_files ├── figure-gfm │ ├── mut_load-1.png │ ├── mut_load-2.png │ ├── plots-1.png │ ├── plots-2.png │ ├── plots-3.png │ └── plots-4.png ├── figure-html │ ├── mut_load-1.png │ ├── mut_load-2.png │ ├── plots-1.png │ ├── plots-2.png │ └── plots-3.png └── updated_images │ └── text.txt ├── data ├── LGG_Full_TPM_matrix.csv ├── LGG_Muts.txt ├── LGG_NonSynMuts.txt ├── LGG_NonSynMuts_Binary.txt ├── LGG_SynMuts.txt └── create_mut_table.R └── man ├── TDAmut-class.Rd ├── compute_complexes.Rd ├── compute_gene_localization.Rd ├── create_TDAmut_object.Rd ├── filter_genes.Rd └── plot_mapper.Rd /.gitignore: -------------------------------------------------------------------------------- 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