PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from pre-processing to deep and comprehensive analysis

Abstract

Abstract Summary PICAFlow is a R-written integrative workflow dedicated to flow/mass cytometry data handling, from pre-processing to deep and comprehensive analysis. It is designed as a powerful all-in-one tool which contains all the necessary functions and packages presented in a user-friendly and ease-to-use fashion. PICAFlow also includes important features that are very frequently lacking in other close software, such as interactive R Shiny applications for real-time data transformation and compensation as well as normalization methods aiming to remove batch effects and unwanted inter- and intra-group heterogeneity. It also allows to perform dimensionality reduction, cell clustering (using different available approaches), as well as complementary statistical analyses and export different support for data interpretation and visualization. Availability PICAFlow is available as a R-written package hosted at the following GitHub repository: https://github.com/PaulRegnier/PICAFlow and is complemented by a fully detailed tutorial available at the following URL: https://paul-regnier.fr/tutoriel-picaflow/.