scpGUI and QFeaturesGUI: Graphical Interfaces for Single-Cell and Bulk Proteomics

Author(s): Léopold Guyot,Christophe Vanderaa,Laurent Gatto

Affiliation(s): Computational Biology and Bioinformatics, de Duve Institute, Belgium



In recent years, significant advancements have been made in the field of proteomics data analysis. However, the complexity of workflows involving programming languages such as R and Python can pose challenges for practitioners without any coding backgrounds. To address this issue, we introduce two user-friendly packages: *scpGUI* and *QFeaturesGUI*. *scpGUI* is tailored for downstream visual analysis in single-cell proteomics, using the outcomes of the popular package *scp*. Developed using *Shiny* and built upon the elegant and efficient *iSEE* suite, *scpGUI* offers interactive data visualisations specifically crafted for single-cell proteomics downstream analysis. The app's interactivity helps users in comprehending their results through various visualisations. Similarly, *QFeaturesGUI* is designed for single-cell and bulk proteomics analysis, capitalising on the strengths of the *QFeatures* package. Providing a suite of *Shiny* apps, *QFeaturesGUI* offers comprehensive tools for data import and basic processing steps, simplifying pre-treatment of quantitative proteomics data. Its modular design ensures flexibility and adaptability to specific requirements. These apps also enhance transparency and facilitate replication by generating reproducible R code. Together, *scpGUI* and *QFeaturesGUI* offer valuable support for proteomics data analysis. By combining user-friendly graphical interfaces with powerful back-end tools, they make advanced analysis techniques more accessible to the wider proteomics community.