Growthcurver：一个用于从微生物生长曲线获取可解释指标的R软件包。
Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.
作者信息
Sprouffske Kathleen, Wagner Andreas
机构信息
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, Lausanne, 1015, Switzerland.
出版信息
BMC Bioinformatics. 2016 Apr 19;17:172. doi: 10.1186/s12859-016-1016-7.
BACKGROUND
Plate 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.
RESULTS
Growthcurver 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.
CONCLUSIONS
Growthcurver 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).
背景
酶标仪能够以高通量方式测量多种微生物菌株的生长曲线。针对数百个样本同时收集的数百个吸光度读数给数据分析带来了技术障碍。
结果
Growthcurver总结了在酶标仪中进行的微生物生长曲线实验的生长特征。数据被拟合到逻辑方程的标准形式，并且这些参数对群体水平特征具有清晰的解释，如倍增时间、承载能力和生长速率。
结论
Growthcurver是一个易于使用的R包，可从综合R存档网络（CRAN）进行安装。源代码在GNU通用公共许可证下可用，可从Github获取（Sprouffske K，Growthcurver源代码，2016）。
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