[](https://anaconda.org/bioconda/polystest) **Welcome to the repository of PolySTest** developed at the [Protein Research Group](http://www.sdu.dk/en/Om_SDU/Institutter_centre/Bmb_biokemi_og_molekylaer_biologi/Forskning/Forskningsgrupper/Protein.aspx) Department of Biochemistry and Molecular Biology [University of Southern Denmark](http://www.sdu.dk) ## Citation 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). ## Shiny app ### Web service 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. ### Implementation on own computer The easiest option is to use the docker image or as bioconda package. #### Docker `docker pull veitveit/polystest` `docker run -t -i -p 3838:3838 veitveit/polystest` and access the shiny app through http://localhost:3838 #### Bioconda Install the package `conda install -c bioconda polystest` `run_app.sh` and access the shiny app through http://localhost:3838 ### Installation 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](http://rstudio.com) or run the app on a [shiny-server](https://www.rstudio.com/products/shiny/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* ### Build and use Docker image 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 ## Command-line version 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 ### Installation The command-line version comes with all version of PolySTest. ## Contact For software issues and general questions, please submit an issue. ## License GPL-2 or higher