Introduction | Installation | Run the shiny application | Interactive Web Interface | Tree structure exploration panel | Sample date panel | Temporal signal panel | Phylogenetic signal panel
Package: shinyTempSignal 0.0.8
Guangchuang Yu
shinyTempSignal: Explore Temporal and Other Phylogenetic Signals
Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
Authors:
shinyTempSignal_0.0.8.tar.gz
shinyTempSignal_0.0.8.zip(r-4.7)shinyTempSignal_0.0.8.zip(r-4.6)shinyTempSignal_0.0.8.zip(r-4.5)
shinyTempSignal_0.0.8.tgz(r-4.6-any)shinyTempSignal_0.0.8.tgz(r-4.5-any)
shinyTempSignal_0.0.8.tar.gz(r-4.7-any)shinyTempSignal_0.0.8.tar.gz(r-4.6-any)
shinyTempSignal_0.0.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
shinyTempSignal/json (API)
| # Install 'shinyTempSignal' in R: |
| install.packages('shinyTempSignal', repos = c('https://yulab-smu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/shinytempsignal/issues
molecular-clockphylogeneticsshiny-app
Last updated from:59da65406a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 210 | ||
| source / vignettes | OK | 225 | ||
| linux-release-x86_64 | OK | 205 | ||
| macos-release-arm64 | OK | 359 | ||
| macos-oldrel-arm64 | OK | 127 | ||
| windows-devel | OK | 189 | ||
| windows-release | OK | 138 | ||
| windows-oldrel | OK | 141 | ||
| wasm-release | OK | 149 |
Exports:dateNumericrun_shinyTempSignalshinyTempSignal_set_theme
Dependencies:apeaplotattemptbase64encbitopsbootbslibcachemcaToolsclicolorspacecommonmarkconfigconfintrcpp11digestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastfracdifffsgdtoolsgenericsggfunggiraphggplot2ggplotifyggpmiscggppggprismggtreegluegolemgridExtragridGraphicsgtableherehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelmtestlubridatemagrittrMASSMatrixMatrixModelsmemoisemimenlmennetotelpatchworkpillarpkgconfigplyrpolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownrprojrootS7sassscalesshinyshinydashboardshinyjsshinyWidgetssourcetoolsSparseMsplus2RstringistringrsurvivalsystemfontstibbletidyrtidyselecttidytreetimechangetimeDatetinytextreeiourcautf8vctrsviridisLitewithrxfunxtablextsyamlyulab.utilszoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The application server-side | app_server |
| The application User-Interface | app_ui |
| Convert dates according to date format | dateNumeric |
| Example data: a tree of 76 H3 hemagglutinin gene sequences of a lineage containing swine and human influenza A viruses | MCC_FluA_H3_tree |
| Run the Shiny Application | run_shinyTempSignal |
| shinyTempSignal_set_theme | shinyTempSignal_set_theme |
