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}