Joanna Veazey Brooks, Dorothy Hughes
Flipping the expert: faculty educator sensemaking during transition to an active learning-based curriculum
BMC medical education
increase dimensionality flow cytometry data past years growing need replace complement traditional manual analysis ie iterative 2d gating automated data analysis pipelines crucial part pipelines consists preprocessing applying quality control filtering raw data order use high quality events downstream analyses part turn split number elementary steps signal compensation unmixing scale transformation debris doublets dead cells removal batch effect correction etc however assembling assessing preprocessing part challenging number reasons first involved elementary steps implemented using various methods r packages second order steps impact downstream analysis results finally method typically comes specific non standardized diagnostic visualizations making objective comparison difficult end user present cytopipeline cytopipelinegui two r packages build compare assess preprocessing pipelines flow cytometry data exemplify new tools present steps involved designing preprocessing pipeline real life dataset demonstrate different visual assessment use cases also set benchmarking comparing two preprocessing pipelines differing quality control methods show package visualization utilities provide crucial user insight obtained benchmark metrics cytopipeline cytopipelinegui two bioconductor r packages help building visualizing assessing preprocessing pipelines flow cytometry data increase productivity pipeline development testing complement benchmarking tools providing user intuitive insight benchmarking results