Interactive tool for Phosphoproteomics

Aaron J. Storey , Kevin Naceanceno , Renny Lan , Charity L. Washam, Lisa M. Orr , Samuel G. Mackintosh, Alan J. Tackett, Rick D. Edmondson, Zhengyu Wang, Hong-yu, Brendan Frett, Samantha Kendrick, Stephanie D. Byrum*. (2020) ProteoViz: A tool for the analysis and interactive visualization of phosphoproteomics data. Molecular Omics. DOI: 10.1039/c9mo00149b

Set of R scripts for the analysis and visualization of Phosphoproteomics data sets.

Script 1: Creates metadata that links with the MaxQuant database search results
Script 2: Normalizes and runs limma differential expression on the protein lysate samples
Script 3: Normalizes phosphosites to the protein expression and runs limma differential expression
Script 4: Creates the input data file needed to run PTMsig analysis
Script 5: Runs PTMsig/ssGSEA
Script 6: Runs EGSEA gene set enrichment analysis
Script 7A-7C: Creates the interactive Shiny dashboard for visualization

MaxQuant txt files are saved in the txt folder
Scripts are in the src folder
Create a Sample_metadata.tsv and contrast_matrix.tsv file associated with your experiment to run the code

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3. M. Alhamdoosh, C. W. Law, L. Tian, J. M. Sheridan, M. Ng and M. E. Ritchie, F1000Res, 2017, 6, 2010. https://f1000research.com/articles/6-2010