Package: PANACEA 1.0.1.9000
PANACEA: Personalized Network-Based Anti-Cancer Therapy Evaluation
Identification of the most appropriate pharmacotherapy for each patient based on genomic alterations is a major challenge in personalized oncology. 'PANACEA' is a collection of personalized anti-cancer drug prioritization approaches utilizing network methods. The methods utilize personalized "driverness" scores from 'driveR' to rank drugs, mapping these onto a protein-protein interaction network. The "distance-based" method scores each drug based on these scores and distances between drugs and genes to rank given drugs. The "RWR" method propagates these scores via a random-walk with restart framework to rank the drugs. The methods are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2023. PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology. Bioinformatics <doi:10.1093/bioinformatics/btad022>.
Authors:
PANACEA_1.0.1.9000.tar.gz
PANACEA_1.0.1.9000.zip(r-4.5)PANACEA_1.0.1.9000.zip(r-4.4)PANACEA_1.0.1.9000.zip(r-4.3)
PANACEA_1.0.1.9000.tgz(r-4.4-x86_64)PANACEA_1.0.1.9000.tgz(r-4.4-arm64)PANACEA_1.0.1.9000.tgz(r-4.3-x86_64)PANACEA_1.0.1.9000.tgz(r-4.3-arm64)
PANACEA_1.0.1.9000.tar.gz(r-4.5-noble)PANACEA_1.0.1.9000.tar.gz(r-4.4-noble)
PANACEA_1.0.1.9000.tgz(r-4.4-emscripten)PANACEA_1.0.1.9000.tgz(r-4.3-emscripten)
PANACEA.pdf |PANACEA.html✨
PANACEA/json (API)
NEWS
| # Install 'PANACEA' in R: |
| install.packages('PANACEA', repos = c('https://egeulgen.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/egeulgen/panacea/issues
- DGIdb_interactions_df - DGIdb Interactions Expert-curated Sources
- STRING_adj_df - Adjacency List for STRING v11.5 - High Confidence Interactions
- example_driveR_res - Example driveR Result
- example_scores_RWR - Example PANACEA "RWR" Method Result
- example_scores_dist - Example PANACEA "distance-based" Method Result
- toy_W_mat - Toy Adjacency Matrix
drugnetwork-analysisoncologypersonalized-medicine
Last updated 1 years agofrom:d63e8df3bb. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 03 2024 |
| R-4.5-win-x86_64 | OK | Sep 03 2024 |
| R-4.5-linux-x86_64 | OK | Sep 03 2024 |
| R-4.4-win-x86_64 | OK | Sep 03 2024 |
| R-4.4-mac-x86_64 | OK | Sep 03 2024 |
| R-4.4-mac-aarch64 | OK | Sep 03 2024 |
| R-4.3-win-x86_64 | OK | Sep 03 2024 |
| R-4.3-mac-x86_64 | OK | Sep 03 2024 |
| R-4.3-mac-aarch64 | OK | Sep 03 2024 |
Exports:Laplacian.normscore_drugsscore_drugs_distance_basedscore_drugs_RWR_based
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluehttrigraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrplyrpngR6Rcppreshape2rlangRSQLiteS4VectorsstringistringrsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Drugs as Nodes | add_drugs_as_nodes |
| Turn Adjacency List into Adjacency Matrix | adj_list2mat |
| Convert Input Gene Symbols to Alias | convert2alias |
| DGIdb Interactions Expert-curated Sources | DGIdb_interactions_df |
| Example driveR Result | example_driveR_res |
| Example PANACEA "distance-based" Method Result | example_scores_dist |
| Example PANACEA "RWR" Method Result | example_scores_RWR |
| Graph Laplacian Normalization | Laplacian.norm |
| Network Propagation (Random-walk with Restart) | network_propagation |
| PANACEA: Personalized Network-based Anti-Cancer Therapy Evaluation | PANACEA-package PANACEA |
| Process Drug-Target Interactions | process_drug_target_interactions |
| Scoring of Drugs via Network-based Methods | score_drugs |
| Distance-based Scoring of Drugs | score_drugs_distance_based |
| RWR-based Scoring of Drugs | score_drugs_RWR_based |
| Adjacency List for STRING v11.5 - High Confidence Interactions | STRING_adj_df |
| Toy Adjacency Matrix (for examples) | toy_W_mat |
