The CADAA (Computer Aided Detection Agonist Antagonist) is an R-Shiny application designed to predict an unknown substance's agonist/antagonist state concerning GPCRs using graph theory and similarity network. In this approach, at first, the SDF file related to an unknown substance is submitted as the input file and compared with the knowledge-based fingerprints of 400 drugs affecting GPCRs. This knowledge-based database was made by random walk on a similarity network of cognate ligands acting on different GPCRs (starting with each compound as a seed node). A resulting probability vector could indicate how this unknown compound might affect each receptor.
cran_pkgs <- c("igraph", "shiny","shinyjs", "shinyBS", "shinydashboard", "ggplot2", "dnet","ChemmineR","digest")
cran_pkgs.inst <- cran_pkgs[!(cran_pkgs %in% rownames(installed.packages()))]
if(length(cran_pkgs.inst)>0){
print(paste0("Missing ", length(cran_pkgs.inst), " CRAN Packages:"))
for(pkg in cran_pkgs.inst){
print(paste0("Installing Package:'", pkg, "'..."));
install.packages(pkg, repo="http://cran.rstudio.org", dependencies=TRUE);print("Installed!!!")
}
}if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.12")
bioc_pkgs <- c( "supraHex","hexbin")
bioc_pkgs.inst <- bioc_pkgs[!(bioc_pkgs %in% rownames(installed.packages()))];
if(length(bioc_pkgs.inst)>0){
print(paste0("Missing ", length(bioc_pkgs.inst), " Bioconductor Packages:"));
for(pkg in bioc_pkgs.inst){
print(paste0("Installing Package:'", pkg, "'..."));
BiocManager::install(pkg)
print("Installed!!!")
}
}runGitHub("shiny", "hadi-masjedy", subdir="shiny")
## Using the archived file
runUrl("https://github.com/hadi-masjedy/shiny/archive/refs/heads/master.tar.gz", subdir="shiny")
runUrl("https://github.com/hadi-masjedy/shiny/archive/refs/heads/master.zip", subdir="shiny")git clone https://github.com/hadi-masjedy/shiny
## Run by using runApp()
setwd("~/shiny")
shiny::runApp(appDir = getwd(), port = getOption("shiny.port"),
launch.browser = getOption("shiny.launch.browser", interactive()),
host = getOption("shiny.host", "127.0.0.1"), workerId = "",
quiet = FALSE, display.mode = c("auto", "normal", "showcase"),
test.mode = getOption("shiny.testmode", FALSE))
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