Function reference • PANACEA

PANACEA

PANACEA package

PANACEA PANACEA-package: PANACEA: Personalized Network-based Anti-Cancer Therapy Evaluation

Main functions

Main functions of PANACEA

score_drugs(): Scoring of Drugs via Network-based Methods

score_drugs_distance_based(): Distance-based Scoring of Drugs

score_drugs_RWR_based(): RWR-based Scoring of Drugs

Utility Functions

Utility functions

add_drugs_as_nodes(): Add Drugs as Nodes

convert2alias(): Convert Input Gene Symbols to Alias

network_propagation(): Network Propagation (Random-walk with Restart)

process_drug_target_interactions(): Process Drug-Target Interactions

adj_list2mat(): Turn Adjacency List into Adjacency Matrix

Laplacian.norm(): Graph Laplacian Normalization

Built-in Data

Data within the package

DGIdb_interactions_df: DGIdb Interactions Expert-curated Sources

STRING_adj_df: Adjacency List for STRING v11.5 - High Confidence Interactions

toy_W_mat: Toy Adjacency Matrix (for examples)

example_driveR_res: Example driveR Result

example_scores_dist: Example PANACEA "distance-based" Method Result

example_scores_RWR: Example PANACEA "RWR" Method Result