Microbial lag calculator: A shiny‐based application and an R package for calculating the duration of microbial lag phase
Bogna J. Smug, Monika Opalek, Maks Necki, Dominika Wloch‐Salamon
Abstract
Abstract The duration of lag phase can be used as an organismal fitness marker; however, it is often underreported as its estimation may be challenging and method and parameters dependent. Moreover, there are no publicly available tools to calculate lag duration by different methods. We developed a shiny‐based web application ( https://microbialgrowth.shinyapps.io/lag_calulator/ ) where the lag duration can be calculated based on the user‐specified growth curve data, and for various explicitly specified methods, parameters and data preprocessing techniques. Additionally, we release an R package ‘miLAG’ that can be further customised and developed. We also describe in short the assumptions, advantages and disadvantages of the most popular lag calculation methods and propose a decision tree to choose a method most suited to one's data. Finally, we show some working examples of how to calculate lag duration using our shiny server.