How matheuscortez04/reposicionamento-farmacos-tdm-tb works
PDPD is an interactive R application for network-based drug repurposing in major depressive disorder and bipolar disorder. The user enters through the console menu, then can generate PPI kernels, score and rank drugs against disease gene modules, validate rankings against RepoDB, enrich top candidates with OpenTargets clinical information, inspect disease-network components, and run biological enrichment analyses. The README documents these workflows, but no source excerpts were provided, so the graph follows documented relationships and does not infer unverified internal calls.
Main entry points: PDPD.R Console menus · drug.R Drug scoring and ranking · evaluation.R Ranking evaluation · enrichment.R Enrichment analyses
Components 16
Application entry
- Console menus
src/PDPD.R - Shared utilities
src/Utils/utils.R
Network analysis
- PPI network
src/Data/PPI_gysi.csv - Kernel generation
src/Utils/kernels.R - Disease graph metrics
src/Utils/graph_metrics.R
Drug prioritization
- Drug targets
src/Data/Drug/drug_targets_DrugBank_Gysi.csv - Drug scoring and ranking
src/Utils/drug.R - Disease gene associations
src/Utils/utils.R
Evaluation and evidence
- MDD RepoDB
src/Data/REPODB/MDD_REPODB.tsv - Bipolar RepoDB
src/Data/REPODB/BIPOLAR_REPODB.tsv - Ranking evaluation
src/Utils/evaluation.R - OpenTargets client
src/Utils/open_targets_requests.R
Biological interpretation
- Enrichment analyses
src/Utils/enrichment.R
Other components
- Analyst
- OpenTargets API
- Pathway gene sets
Connections 19
- Analyst → Console menus: selects menu
- Console menus → Kernel generation: dispatches
- Console menus → Drug scoring and ranking: dispatches
- Console menus → Ranking evaluation: dispatches
- Console menus → Disease graph metrics: dispatches
- Console menus → Enrichment analyses: dispatches
- Kernel generation → PPI network: reads network
- Drug scoring and ranking → Drug targets: reads targets
- Drug scoring and ranking → Kernel generation: uses kernels
- Drug scoring and ranking → Disease gene associations: uses disease genes
- Disease graph metrics → PPI network: reads network
- Disease graph metrics → Disease gene associations: uses disease genes
- Ranking evaluation → MDD RepoDB: validates MDD
- Ranking evaluation → Bipolar RepoDB: validates bipolar
- Ranking evaluation → OpenTargets client: requests candidate details
- OpenTargets client → OpenTargets API: queries GraphQL
- Enrichment analyses → Pathway gene sets: uses pathway sets
- Enrichment analyses → Disease gene associations: uses disease genes
- Enrichment analyses → Drug scoring and ranking: uses drug rankings