exploreDEG Interactive Shiny App

An interactive shiny app to enable users to create custom figures based on their differential expression (DE) analysis results, and aid their investigation and interpretation of their results. Supports both RNA seq and proteomics data, in the SummarizedExperiment R data format. 

DE and pathway analysis results are generated by the user in either the SUSHI platform (Hatakeyama et al., 2016) or in Prolfqua (Wolski et al., 2023) and then loaded into this app. Almost no further analyses are performed within the shiny app, merely the modification of figures and selection of particular features and pathways. Many of the figures are derived directly from the DE and pathway results, while others are derived from the feature counts and are independent of the DE results. Features include:

1. Generation and modification of a wide range of figures including:

• Table of results
• Volcano plots, including highlighting features of interest.
• PCA plots (here, users can include/exclude groups, and the PCA will be recalculated, the only instance of results generation in the app, though it is not directly linked to the DE results).
• Heatmaps, boxplots, and barplots of feature expression.
• KEGG pathway plots for RNA seq.
• Pathway analysis results (network plots, heatmaps, etc.) for RNA seq.

2. The ability to export figures as PDFs, and relevant results tables as Excel files.