README.md

In shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis

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}

shinyWGD documentation built on April 4, 2025, 2:28 a.m.