Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

BMC Bioinformatics

Software

Kathleen Sprouffske¹  Andreas Wagner² 

[1] Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland;Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015, Lausanne, Switzerland;Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland;Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015, Lausanne, Switzerland;The Santa Fe Institute, 1399 Hyde Park Road, 24105, Santa Fe, New Mexico, USA;

关键词: Growth curve;    Logistic;    Experimental evolution;   

DOI  :  10.1186/s12859-016-1016-7

 received in 2015-11-04, accepted in 2016-04-06,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundPlate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis.ResultsGrowthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate.ConclusionsGrowthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

【 授权许可】

CC BY   
© Sprouffske and Wagner. 2016