Description
'Shiny' Application for Whole Genome Duplication Analysis.
Description
Provides a comprehensive 'Shiny' application for analyzing Whole Genome Duplication ('WGD') events. This package provides a user-friendly 'Shiny' web application for non-experienced researchers to prepare input data and execute command lines for several well-known 'WGD' analysis tools, including 'wgd', 'ksrates', 'i-ADHoRe', 'OrthoFinder', and 'Whale'. This package also provides the source code for experienced researchers to adjust and install the package to their own server. Key Features 1) Input Data Preparation This package allows users to conveniently upload and format their data, making it compatible with various 'WGD' analysis tools. 2) Command Line Generation This package automatically generates the necessary command lines for selected 'WGD' analysis tools, reducing manual errors and saving time. 3) Visualization This package offers interactive visualizations to explore and interpret 'WGD' results, facilitating in-depth 'WGD' analysis. 4) Comparative Genomics Users can study and compare 'WGD' events across different species, aiding in evolutionary and comparative genomics studies. 5) User-Friendly Interface This 'Shiny' web application provides an intuitive and accessible interface, making 'WGD' analysis accessible to researchers and 'bioinformaticians' of all levels.
README.md
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