Rejoice! Increased user-friendliness and new analysis modes can be at your fingertips in a mere couple of clicks!
Whereas in previous versions a single channel of a single reaction had to used as input, these version will take the entire read.QX output object as input. A separate input variable 'well' allows for selection of which well(s) to analyse. Choice of the channel is done via the 'method' input variable. Under method, we now support analysis of either fluorescence channel, full duplex analysis (simultaneous analysis for both channels), and an evagreen-specific approach that corrects for channel cross-talk.
Another new feature of the V3 series is the option to choose different threshold setting approaches. Net to the standard 'cloudy' analysis, I have implemented the Generalized Extreme Value (GEV) approach of Trypsteen et al. on a single reaction basis (see the readme for some details on the implementation and link to their publication). Another threshold option available is 'mixed' where 'cloudy' and 'gev' are run sequential and the respective thresholds are averaged. As 'gev' tends to fail in reactions that are close to saturation, 'cloudy' is always used as back-up mechanism, ensuring valid output.
I now also offer a Shiny-app script that you can run locally to have a graphical user interface to analyze reactions with the 'cloudy' algorithm. In addition, a few plotting functions are available that should make inspecting reactions more straightforward.