OptiREF

Is an ongoing open source project designed to create a single platform where researchers working on real-time quantitative PCR (qPCR) projects can choose their optimal reference genes. Currently, there are three established methods for choosing reference genes using different algorithms; NormFinder, geNorm and Best Keeper. However, the original software packages utilizing these equations are not in a standard format that would allow for simple comparison across multiple methods. More recently, R scripts and library packages have been created that utilize one or even two of the methods, but not all of them together. There is a free webpage that allows you to upload your data and it will run all of the most common methods, however this resource is quite limited in its abilities and does include the effects of the efficiency values of your qPCR. As such, the results that are displayed by the program are not optimized for a specific assay. For OptiREF, we are creating an open source R library package that will allow anyone to choose or run multiple methods and easily compare the results. We will eventually implement this into an R Shiny app that will allow both programmers and non-programmers alike to use one platform to run the same analysis on their data with minimal effort by the end user.