POMAShiny is a web-based tool that provides a structured, flexible and user-friendly workflow for pre-processing, exploratory data analysis (EDA) and statistical analysis of metabolomics and proteomics data. This tool is based on the POMA R/Bioconductor package, which increases the reproducibility and flexibility of the analysis outside the web environment. POMAShiny’s workflow is structured in four sequential and well-defined panels: 1) data upload, 2) pre-processing, 3) EDA and 4) statistical analysis panels. POMAShiny is hosted at https://webapps.nutrimetabolomics.com/POMAShiny.
Open the terminal and run:
git clone "https://github.com/pcastellanoescuder/POMAShiny.git"
Open the POMAShiny.Rproj
with RStudio and run:
# CRAN packages
installifnot <- function(pckgName){
if (!(require(pckgName, character.only = TRUE))) {
install.packages(pckgName, dep = TRUE)
require(pckgName, character.only = TRUE)
}
}
pk1 <- c('shiny', 'DT', 'devtools', 'reshape2', 'plotly', 'fresh', 'shinyhelper', 'ggraph',
'rmarkdown', 'shinyWidgets', 'tidyverse', 'knitr', 'patchwork', 'BiocManager')
for (i in 1:length(pk1)){
installifnot(pk1[i])
}
# Install the old version of 'bs4Dash'
devtools::install_version("bs4Dash", version = "0.5.0", repos = "http://cran.us.r-project.org")
# Bioconductor packages
installBiocifnot <- function(pckgName){
if (!(require(pckgName, character.only = TRUE))) {
BiocManager::install(pckgName)
require(pckgName, character.only = TRUE)
}
}
pk2 <- c('Biobase', 'POMA', 'MSnbase')
for (i in 1:length(pk2)){
installBiocifnot(pk2[i])
}
NOTE: POMAShiny was built with bs4Dash
version 0.5.0 and is not
compatible with newer versions of bs4Dash
due to substantial breaking
changes in the API. We keep the old version as indicated by the
bs4Dash
developers.
Once all dependencies have been installed run the following command and enjoy the analysis!
shiny::runApp(appDir = "app")
Pull the POMAShiny Docker container image hosted at Docker Hub by running the following command in the terminal.
docker pull pcastellanoescuder/pomashiny:v.1.1.14
Run the container on your terminal once it has been pulled.
docker run -d --rm -p 3838:3838 pomashiny
Open your browser and paste http://0.0.0.0:3838
. Then, enjoy the
analysis!
Please note that the POMAShiny project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.