School of Biological and Behavioural Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6DD, UK.
BMC Bioinformatics. 2022 Feb 5;23(1):60. doi: 10.1186/s12859-022-04586-1.
Colony growth on solid media is a simple and effective measure for high-throughput genomic experiments such as yeast two-hybrid, synthetic dosage lethality and Synthetic Physical Interaction screens. The development of robotic pinning tools has facilitated the experimental design of these assays, and different imaging software can be used to automatically measure colony sizes on plates. However, comparison to control plates and statistical data analysis is often laborious and pinning issues or plate specific growth effects can lead to the detection of false-positive growth defects.
We have developed ScreenGarden, a shinyR application, to enable easy, quick and robust data analysis of plate-based high throughput assays. The code allows comparisons of different formats of data and different sized arrays of colonies. A comparison of ScreenGarden with previous analysis tools shows that it performs, at least, equivalently. The software can be run either via a website or offline via the RStudio program; the code is available and can be modified by expert uses to customise the analysis.
ScreenGarden provides a simple, fast and effective tool to analyse colony growth data from genomic experiments.
在固体培养基上进行菌落生长是高通量基因组实验（如酵母双杂交、合成剂量致死和合成物理相互作用筛选）的一种简单而有效的方法。机器人点样工具的发展促进了这些测定的实验设计，并且可以使用不同的成像软件来自动测量平板上的菌落大小。然而，与对照平板的比较和统计数据分析通常很繁琐，点样问题或特定于平板的生长效应可能导致假阳性生长缺陷的检测。
我们开发了 ScreenGarden，一个 shinyR 应用程序，用于轻松、快速和稳健地分析基于平板的高通量测定。该代码允许比较不同格式的数据和不同大小的菌落阵列。ScreenGarden 与以前的分析工具的比较表明，它的性能至少相当。该软件可以通过网站或 RStudio 程序离线运行；代码是可用的，并且可以由专家用户修改以定制分析。
ScreenGarden 提供了一种简单、快速和有效的工具，用于分析基因组实验中的菌落生长数据。
