@@ -185,54 +185,54 @@ $ tree -a ptc-explorer/
185185├── user_interface/ < - UI components for each page
186186│ ├── cite_us_ui.R < - Citation information page layout
187187│ ├── contact_ui.R < - Team information page layout
188- │ ├── developer_guide_ui.R < - Developer documentation page layout
188+ │ ├── developer_guide_ui.R < - Developer documentation page layout
189189│ ├── download_ui.R < - Data download page layout
190190│ ├── gene_search_ui.R < - Gene search page layout
191191│ ├── home_ui.R < - Home/landing page layout
192- │ ├── rna_downstream_ui.R < - RNA downstream analysis page layout
193- │ ├── rna_fusion_ui.R < - RNA fusion analysis page layout
192+ │ ├── rna_downstream_ui.R < - RNA downstream analysis page layout
193+ │ ├── rna_fusion_ui.R < - RNA fusion analysis page layout
194194│ ├── user_guide_ui.R < - User documentation page layout
195- │ ├── wes_additional_ui.R < - Additional WES analysis page layout
195+ │ ├── wes_additional_ui.R < - Additional WES analysis page layout
196196│ └── wes_variant_ui.R < - WES variant analysis page layout
197197│
198- ├── modules/ < - Reusable UI and server modules
199- │ ├── dt_mod.R < - Enhanced DataTable components
200- │ ├── enrichr_mod.R < - Pathway enrichment analysis
201- │ ├── fusion_filter_mod.R < - RNA fusion filtering
202- │ ├── gene_info_mod.R < - Gene annotation services
203- │ ├── gene_search_mod.R < - Gene search functionality
204- │ ├── meta_plots_mod.R < - Clinical metadata visualization
205- │ ├── profile_mod.R < - Team photo and social media display
206- │ ├── reactable_mod.R < - Modern interactive tables
207- │ ├── variant_filter_mod.R < - Genomic variant filtering
208- │ └── volcano_mod.R < - Interactive volcano plots
209- │
210- ├── data/ < - Sample datasets
211- │ ├── app_data_pack_* .rds < - Main application datasets
212- │ └── ptc_onco_obj_list_* .rds < - Oncoplot object data
213- │
214- ├── R/ < - Utility functions
215- │ ├── load_components.R < - Component loading functions
216- │ └── utils.R < - General utility functions
217- │
218- ├── docs/ < - Documentation files
219- │ ├── DYNAMIC_DATA_LOADING.md < - Dynamic data loading guide
220- │ ├── LINTING_GUIDE.md < - Code linting and formatting guide
221- │ ├── MODULES_COMPONENTS.md < - Module and component reference
222- │ ├── TECHNICAL_REFERENCE.md < - Developer technical reference
223- │ └── USER_GUIDE.md < - Comprehensive user guide
224- │
225- ├── www/ < - Static web assets
226- │ ├── css/ < - Stylesheets
227- │ ├── img/ < - Images and figures
228- │ └── js/ < - JavaScript files
229- │
230- ├── docker/ < - Docker build helper scripts
231- │ ├── install_bioc.R < - Installs Bioconductor packages
232- │ ├── install_cran.R < - Installs CRAN packages
233- │ └── install_github.R < - Installs GitHub packages
234- │
235- └── Dockerfile < - For containerization
198+ ├── modules/ < - Reusable UI and server modules
199+ │ ├── dt_mod.R < - Enhanced DataTable components
200+ │ ├── enrichr_mod.R < - Pathway enrichment analysis
201+ │ ├── fusion_filter_mod.R < - RNA fusion filtering
202+ │ ├── gene_info_mod.R < - Gene annotation services
203+ │ ├── gene_search_mod.R < - Gene search functionality
204+ │ ├── meta_plots_mod.R < - Clinical metadata visualization
205+ │ ├── profile_mod.R < - Team photo and social media display
206+ │ ├── reactable_mod.R < - Modern interactive tables
207+ │ ├── variant_filter_mod.R < - Genomic variant filtering
208+ │ └── volcano_mod.R < - Interactive volcano plots
209+ │
210+ ├── data/ < - Sample datasets
211+ │ ├── app_data_pack_* .rds < - Main application datasets
212+ │ └── ptc_onco_obj_list_* .rds < - Oncoplot object data
213+ │
214+ ├── R/ < - Utility functions
215+ │ ├── load_components.R < - Component loading functions
216+ │ └── utils.R < - General utility functions
217+ │
218+ ├── docs/ < - Documentation files
219+ │ ├── DYNAMIC_DATA_LOADING.md < - Dynamic data loading guide
220+ │ ├── LINTING_GUIDE.md < - Code linting and formatting guide
221+ │ ├── MODULES_COMPONENTS.md < - Module and component reference
222+ │ ├── TECHNICAL_REFERENCE.md < - Developer technical reference
223+ │ └── USER_GUIDE.md < - Comprehensive user guide
224+ │
225+ ├── www/ < - Static web assets
226+ │ ├── css/ < - Stylesheets
227+ │ ├── img/ < - Images and figures
228+ │ └── js/ < - JavaScript files
229+ │
230+ ├── docker/ < - Docker build helper scripts
231+ │ ├── install_bioc.R < - Installs Bioconductor packages
232+ │ ├── install_cran.R < - Installs CRAN packages
233+ │ └── install_github.R < - Installs GitHub packages
234+ │
235+ └── Dockerfile < - For containerization
236236```
237237
238238## Contributing
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