Download data and directory structure from here.
Unzip.
Open R studio and set folder as Project.
Copy DIA_workflow_1.0.rmd and DIA_report_1.0.rmd to the Project folder (scripts/proteomics folder) and open inside R studio.
Run the DIA_workflow_1.0.rmd file, use the Shiny app to define your experimental design, contrasts and linear model you wish to use.
Proceed chunk by chunk.
Run DIA_report_1.0.rmd and generate a document that will dynamically produce a shareable report for your analysis.
All the results are in the summary_results folder in the project root directory.
Do the science :)
Enjoy!