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).
if (!require("devtools")) {
install.packages("devtools")
}::install_github("li081766/shinyWGD", dependencies = TRUE, build_vignettes = TRUE) devtools
To ensure the successfully loading of Gallery
and
Help
pages in shinyWGD
, please set
build_vignettes
to TRUE
when installing the
package.
Please refer to the shinyWGD
server or the vignettes of shinyWGD
to see the detailed
usage.
library(shinyWGD)
runshinyWGD()
help(package="shinyWGD")
shinyWGD
{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}