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G3 (Bethesda). 2020 Mar 5;10(3):933-943. doi: 10.1534/g3.119.400898.

Interactively AUDIT Your Growth Curves with a Suite of R Packages.

Author information

1
Department of Biochemistry and Molecular Biology, Faculty of Medicine, and.
2
Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, B.C., Canada, V6T 1Z3.
3
Department of Biochemistry and Molecular Biology, Faculty of Medicine, and corey.nislow@ubc.ca.

Abstract

Bottlenecks often occur during data analysis when studying microbial growth in liquid culture at large scale. A researcher can collect thousands of growth curves, repeated measures of a microbial liquid culture, at once in multiple micro titer plates by purpose-built robotic instruments. However, it can be difficult and time-consuming to inspect and analyze these data. This is especially true for researchers without programming experience. To enable this researcher, we created and describe an interactive application: Automated Usher for Data Inspection and Tidying (AUDIT). It allows the user to analyze growth curve data generated from one or more runs each with one or more micro titer plates alongside their experimental design. AUDIT covers input, pre-processing, summarizing, visual exploration and output. Compared to previously available tools AUDIT handles more data, provides live previews and is built from individually re-usable pieces distributed as R packages.

KEYWORDS:

chemical genetics; fitness; growth curve; yeast

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