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shinyWGD

Overview

shinyWGD can prepare the input and command lines for wgd, ksrates, i-ADHoRe, and OrthoFinder.

shinyWGD can also assist users in using Whale to infer reconciled gene trees and parameters of a model of gene family evolution given a known species tree.

After directly uploading the output of wgd, ksrates, i-ADHoRe, or OrthoFinder, shinyWGD can study the whole genome duplication events (WGDs).

Installation

• Install the latest development version from GitHub (requires devtools package):

if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("li081766/shinyWGD", dependencies = TRUE, build_vignettes = TRUE)

To ensure the successfully loading of Gallery and Help pages in shinyWGD, please set build_vignettes to TRUE when installing the package.

Usage

Please refer to the shinyWGD server or the vignettes of shinyWGD to see the detailed usage.

library(shinyWGD)
runshinyWGD()
help(package="shinyWGD")

The structure of shinyWGD

• Home

• Scripts

  • Data Preparation
  • Codes

• Analysis

  • Age Distribution Analysis
  • Synteny Analysis
  • Tree Building
  • Gene Tree – Species Tree Reconciliation Analysis

• Help

Usage

Gallery

Dependencies

• External software

  • wgd
  • ksrates
  • i-ADHoRe
  • Whale
  • OrthoFinder
  • diamond
  • MAFFT
  • trimAl
  • PAML
  • MrBayes
  • ALE

• R packages

  • {shiny}
  • {shinyjs}
  • {shinyFiles}
  • {shinyBS}
  • {shinyWidgets}
  • {shinyalert}
  • {bslib}
  • {bsplus}
  • {htmltools}
  • {tidyverse}
  • {vroom}
  • {english}
  • {data.table}
  • {argparse}
  • {dplyr}
  • {tools}
  • {seqinr}
  • {DT}
  • {stringr}
  • {fs}
  • {tidyr}
  • {ape}
  • {ks}
  • {mclust}

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.