(The) Operation (formally known as) Warp Speed is a joint venture between pharma and government to bring COVID-19 vaccines to market at unprecedented speed. A key tenet of the program is to generate the data needed to establish correlates of vaccine protection – immune responses that predict the level of protective efficacy of the vaccines. Our team was tasked with designing an analysis plan and the code needed to analyze the data and produce results that answered these key questions. However, lacking full FDA approval of their products, some vaccine manufacturers were highly protective of their data. Thus, our team was faced with the challenge of building an analysis pipeline capable of analyzing data that we have never seen, on servers that we do not have access to, all under the extreme time pressure associated with COVID vaccine development. In this talk, I will describe the R-based set of tools that we used to achieve this goal and some lessons learned along the way.