Package: DTSEA 0.0.3
DTSEA: Drug Target Set Enrichment Analysis
It is a novel tool used to identify the candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. (See Gómez-Carballa et al. (2022) <doi:10.1016/j.envres.2022.112890> and Feng et al. (2022) <doi:10.7150/ijms.67815> for disease expression profiles; see Wishart et al. (2018) <doi:10.1093/nar/gkx1037> and Gaulton et al. (2017) <doi:10.1093/nar/gkw1074> for drug target information; see Kanehisa et al. (2021) <doi:10.1093/nar/gkaa970> for the details of KEGG database.)
Authors:
DTSEA_0.0.3.tar.gz
DTSEA_0.0.3.zip(r-4.5)DTSEA_0.0.3.zip(r-4.4)DTSEA_0.0.3.zip(r-4.3)
DTSEA_0.0.3.tgz(r-4.4-any)DTSEA_0.0.3.tgz(r-4.3-any)
DTSEA_0.0.3.tar.gz(r-4.5-noble)DTSEA_0.0.3.tar.gz(r-4.4-noble)
DTSEA_0.0.3.tgz(r-4.4-emscripten)DTSEA_0.0.3.tgz(r-4.3-emscripten)
DTSEA.pdf |DTSEA.html✨
DTSEA/json (API)
NEWS
| # Install 'DTSEA' in R: |
| install.packages('DTSEA', repos = c('https://hanjunwei-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hanjunwei-lab/dtsea/issues
- example_disease_list - An example vector of disease nodes
- example_drug_target_list - An example data frame of drug target lists
- example_ppi - An example human gene functional interaction network object
- random_graph - A random graph for the computation of the separation measure
Last updated 2 years agofrom:5a6e47743c. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | OK | Nov 22 2024 |
| R-4.5-linux | OK | Nov 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:calculate_p0cronbach.alphaDTSEAget_datakendall.wrandom.walkseparation
Dependencies:BHBiocParallelclicodetoolscolorspacecowplotcpp11data.tabledplyrfansifarverfastmatchfgseaformatRfutile.loggerfutile.optionsgenericsggplot2gluegtableigraphisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalessnowstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The Drug target set enrichment analysis (DTSEA) | DTSEA-package |
| Function to calculate the p0 vector used in Random Walk with Restart (RwR) | calculate_p0 |
| Cronbach's alpha | cronbach.alpha |
| Main function of drug target set enrichment analysis (DTSEA) | DTSEA |
| An example vector of disease nodes | example_disease_list |
| An example data frame of drug target lists | example_drug_target_list |
| An example human gene functional interaction network object | example_ppi |
| Kendall's coefficient of concordance W | kendall.w |
| A random graph for the computation of the separation measure | random_graph |
| Function to implement Random Walk with Restart (RwR) algorithm on the input graph | random.walk |
| A measure of network separation | separation |
