The bioinformatics tools for flow cytometry (FCM) were many years behind comparing to other platforms in genomics and proteomics. The objective of this project was to create new tools able to take advantage of the high dimensionality of high throughput flow cytometry (HT-FCM) data and to combine the result with genomics and proteomics. Based on the widely adopted research and clinical tool called GenePattern (GP), this project developed 45 modules covering FCM methods from basic processing to advanced automated identification, as well as high throughput data processing. This project also generated an R library called Dr. DOBUS (FlOWHTR) for executing analysis pipelines, 5 applicable visualization modules for whole study analysis. These resources largely increased the efficiency of GP and were under unrestricted use by academic community. The potentially profound impact could be realized through significantly reduced cost and analysis time (from weeks to hours), vastly improved scientific reporting and reproducibility of FCM studies, and the global recognition of international FCM community.