PhosPiR is an automatic pipeline to analyze phosphoproteomics data. It is fully tested on Windows. To initiate PhosPiR pipeline, drag the run.R file to an R window. R version 4.0.3 for Windows can be downloaded from https://cran.r-project.org/bin/windows/base/old/4.0.3/ To download the pipeline, click the "Code" button on the upper right, and select "Download ZIP" from the drop down menu.

A few things to pay attention to: -Should have good internet connection -When running statistical analysis, try not to click on the running window, sometimes the window will become “non-responding” when clicked, the cutoff selection window, for example, when pops up after statistical analysis will not display property from “non-responding” R windows -Should leave enough space in your storage drive, 1-2G should be enough

Two user support videos could be found at https://youtu.be/8qvEStg28dQ (short setup introduction video), and https://youtu.be/n4EagNoxusI (long pipeline run demonstration and result file introduction video).

Example data from the videos with complementary group setup input file and comparison input file could be found in the Example Data folder.

Text file containing R and R package versions during the development of PhosPiR can be found in Useful Information folder. A STRING interaction color key can also be found in the same folder.