CytoPipeline & CytoPipelineGUI: An R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data

With the increase of the dimensionality in conventional flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps : margin events removal, signal compensation, scale transformations, debris and dead cells removal, batch effect correction, etc. However, when designing automated flow cytometry data analysis pipelines, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, non standardized diagnostic and visualizations, making objective comparison difficult for the end user. Here, we present CytoPipeline and CytoPipelineGUI, two R packages to build, compare and assess pre-processing pipelines for flow cytometry data. To exemplify these new tools, we present the steps involved in designing a pre-processing pipeline on a real life dataset and demonstrate the visualization utilities. We show that these two packages can help increasing the productivity during pipeline development and testing and how they can complement benchmarking tools, by providing user intuitive insight into benchmarking results. ### Competing Interest Statement - B.B., S.D., M.H., M.T., S.T., and D.L. are employees of the GSK group of Companies. - B.B., S.D., M.T., S.T., and D.L. report ownership of GSK shares. - B.B., M.T., and S.T. are listed as inventors on patent(s) owned by the GSK group of companies. - P.H. is a student at the de Duve Institute (UCLouvain) and participates in a post graduate studentship program at GSK.