Microbial lag calculator: A shiny‐based application and an R package for calculating the duration of microbial lag phase
Methods in Ecology and Evolution, 2024•Wiley Online Library
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 …
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 …
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.
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