Introduction | Example 1: Calculate the enrichment scores of drugs. | Example 2. Get the influence of the specific disease in the PPI network | Example 3. Calculate the consistency of the prediction | Multicore capability | Supplementary data files | Known bugs
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-4.7)DTSEA_0.0.3.zip(r-4.6)DTSEA_0.0.3.zip(r-4.5)
DTSEA_0.0.3.tgz(r-4.6-any)DTSEA_0.0.3.tgz(r-4.5-any)
DTSEA_0.0.3.tar.gz(r-4.7-any)DTSEA_0.0.3.tar.gz(r-4.6-any)
DTSEA_0.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DTSEA/json (API)
| # 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
Datasets:
- 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 from:5a6e47743c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 183 | ||
| source / vignettes | OK | 210 | ||
| linux-release-x86_64 | OK | 185 | ||
| macos-release-arm64 | OK | 104 | ||
| macos-oldrel-arm64 | OK | 117 | ||
| windows-devel | OK | 127 | ||
| windows-release | OK | 135 | ||
| windows-oldrel | OK | 134 | ||
| wasm-release | OK | 168 |
Exports:calculate_p0cronbach.alphaDTSEAget_datakendall.wrandom.walkseparation
Dependencies:BHBiocParallelclicodetoolscowplotcpp11data.tabledplyrfarverfastmatchfgseaformatRfutile.loggerfutile.optionsgenericsggplot2gluegtableigraphisobandlabelinglambda.rlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RColorBrewerRcpprlangS7scalessnowstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
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 |
