/PDD-shiny

Processing of DIA-NN Data

Primary LanguageR

PDD-shiny

A shiny app to analyse the report.tsv, extract of results of DIA-NN 1.8 version software (https://github.com/vdemichev/DiaNN)

Requirements

R4.1 or higher RStudio 2021.09.0 Build 351 or higher

Required data

  1. report.tsv from DIA-NN software The format of the name of run must not contain "." or "_", but for the same biological replicat, you must add "_increment" example: you have 3 biologicals replicats for sampleA et sampleB, the name of run must be : sampleA_1,sampleA_2,sampleA_3 and sampleB_1,sampleB_2, sampleB_3

What types of analyses can I do in PDD-shiny?

  • Data

Create a table of proteins for each run, with differents informations extract in report.tsv : number of peptides, MaxLFQ,Protein.Q.Value and the peptide sequence used for the MaxLFQ.

  • Visualization

The plots currently present are essentially centered on the global analysis of proteins by condition. For the Upset plot ((like a Venn diagramm with bar, an app that i recommend just for this plot : https://github.com/hms-dbmi/UpSetR), the intersection data are downloadable.

  • Boxplot
  • Barplot
  • Multiscatterplot
  • Upset plot
  • Violin plot

Installation

You need to install R, RStudio and download the PDD-shiny. In RStudio, you must open the app.R file, click on Run App (top right). Think to check, only for the first time, if you have all packages. You will see at the top of the script. This will open your default browser and run PDD-shiny locally on your computer. All you have to do is download your report.tsv, check that it is correctly read and click on Integration