├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── VCFserver.R ├── VCFui.R └── runApp.R ├── README.md ├── VCFshiny.Rproj ├── inst ├── .DS_Store ├── Annovar │ ├── Annovar_Datebase_Table.CSV │ ├── annotate_variation.pl │ ├── coding_change.pl │ ├── convert2annovar.pl │ ├── retrieve_seq_from_fasta.pl │ ├── table_annovar.pl │ └── variants_reduction.pl ├── extdata │ ├── IntOGen_cancer_driver_gene.rds │ ├── VCFshiny_Circos_Chrom_hg38.txt │ └── example_data.rds ├── markdown │ ├── images │ │ ├── Fold_Format.png │ │ ├── Input File Format.png │ │ └── workflow.jpg │ ├── installation.html │ └── installation.md └── shiny │ ├── modules │ ├── 0.Introduction.R │ ├── 1.Upload_server.R │ ├── 1.Upload_ui.R │ ├── 10.mutational_signature_server.R │ ├── 10.mutational_signature_ui.R │ ├── 11.Annotation_server.R │ ├── 11.Annotation_ui.R │ ├── 2.Venn_server.R │ ├── 2.Venn_ui.R │ ├── 3.summarise_barplot_server.R │ ├── 3.summarise_barplot_ui.R │ ├── 4.SNP_Analysis_server.R │ ├── 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