Package: populationPDXdesign 1.0.3
Maria Luisa Guerriero
populationPDXdesign: Designing Population PDX Studies
Run simulations to assess the impact of various designs features and the underlying biological behaviour on the outcome of a Patient Derived Xenograft (PDX) population study. This project can either be deployed to a server as a 'shiny' app or installed locally as a package and run the app using the command 'populationPDXdesignApp()'.
Authors:
populationPDXdesign_1.0.3.tar.gz
populationPDXdesign_1.0.3.tar.gz(r-4.5-noble)populationPDXdesign_1.0.3.tar.gz(r-4.4-noble)
populationPDXdesign_1.0.3.tgz(r-4.4-emscripten)populationPDXdesign_1.0.3.tgz(r-4.3-emscripten)
populationPDXdesign.pdf |populationPDXdesign.html✨
populationPDXdesign/json (API)
| # Install 'populationPDXdesign' in R: |
| install.packages('populationPDXdesign', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:c0b7e829e8. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-linux | OK | Oct 29 2024 |
Exports:populationPDXdesignApp
Dependencies:askpassbase64encbrewbriobslibcachemcallrclicliprcolorspacecommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifarverfastmapfontawesomefsgertggplot2ghgitcredsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttr2iniisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcpprematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapirversionssassscalessessioninfoshinyshinycssloaderssourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulation of a single population PDX experiment | callsInSingleExperiment |
| Function to return the mode of a vector of values | getMode |
| Function to calculate the number of false calls for a design for a go-no go threshold | noFalseCalls |
| Function to calculate the number of missed calls for a design for a go-no go threshold | noMissedCalls |
| Function to summarise the results for a single simulation representing one experiment | outcomeInSingleExperiment |
| Function to run simulations to mimic population PDX studies for a defined scenario | outcomeMultipleExperiments |
| A function to visualise the false postive rate as a function of PDXn and PDXr | plotFalsepositive |
| A function to visualise the sensitivity as a function of PDXn and PDXr | plotSensitivity |
| Function 'populationPDXdesignApp' | populationPDXdesignApp |
| 'shiny' app server function | server |
| 'shiny' app user interface function | ui |
| Function to run simulations to mimic population PDX studies for variety of experimental and biological scenarios | varyingPDXnPDXrBiolRR |