Welcome to the repository of PolySTest
developed at the Protein Research Group
Department of Biochemistry and Molecular Biology
University of Southern Denmark
When using PolySTest, please cite our paper:
Veit Schwämmle, Christina E Hagensen, Adelina Rogowska-Wrzesinska, and Ole N. Jensen, doi: https://doi.org/10.1074/mcp.RA119.001777
PolySTest can be run as shiny app on our server or using the docker version of the tool to avoid installation issues and computational bottlenecks.
A command-line version is available to run PolySTest as workflow component (see below).
You can use our web server http://computproteomics.bmb.sdu.dk:
http://computproteomics.bmb.sdu.dk/Apps/PolySTest
Be aware that the tool does allow only one user to run the background R calculations at a time. Therefore the app might become temporarily irresponsive. However, multiple sessions are separated and your data won't be shared between sessions or overwritten.
The easiest option is to use the docker image or as bioconda package.
docker pull veitveit/polystest
docker run -t -i -p 3838:3838 veitveit/polystest
and access the shiny app through http://localhost:3838
Install the package
conda install -c bioconda polystest
run_app.sh
and access the shiny app through http://localhost:3838
Download the files from this repository
Install the following R libraries in R:
library(BiocManager) BiocManager::install(c('matrixStats','fdrtool','parallel','qvalue','circlize','DT','UpSetR','heatmaply','gplots','shinyBS','shinydashboard','limma'),ask=F)
You can run the shiny app from the server.R or ui.R files using Rstudio or run the app on a shiny-server
Alternatively, just (in Linux) call the script run_app.sh
and access the app through http://localhost:3838
Be aware that you need to have all files and all necessary R libraries described in the Installation
A Dockerfile has been created on the basis of an OpenSuse distribution. Copy the repository to a folder and carry out the following command to build the images (takes a while)
docker build -t veitveit/polystest .
You can run the image by
docker run -t -i -p 3838:3838 veitveit/polystest
and access the server through http://localhost:3838
You can run PolySTest via the file runPolySTestCLI.R. You need to specify a parameter file (yaml) to set parameters and the input file. See polystest.yml for an example and extensive description of the parameters
The command-line version comes with all version of PolySTest.
For software issues and general questions, please submit an issue.
GPL-2 or higher