easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
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DOI：
10.1371/journal.pone.0252000
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Andersen EC
中科院分区：
文献类型：
--
作者：
Nyaanga J;Crombie TA;Widmayer SJ;Andersen EC
高通量成像技术已经广泛应用于生物学的许多领域。这些强大的平台生成大量数据，使用现有工具很难有效地处理和可视化。我们开发了easyXpress来处理和审查C。在R环境中的线虫高通量显微镜数据。该软件包提供了一个逻辑工作流程，用于阅读、分析和可视化使用CellProfiler的Wormplane生成的数据。我们为easyXpress配备了强大的功能，可以自定义数据中噪声的过滤，特别是通过识别和删除偏离预期动物测量的对象。这种数据过滤的灵活性允许用户优化其分析管道以满足其需求。此外，easyXpress还包括用于生成详细可视化的工具，允许用户轻松地交互式比较威尔斯和平板之间的汇总统计数据。研究人员对C. elegans受益于这个精简和可扩展的软件包，因为它是CellProfiler的补充，并利用R环境快速处理和分析大型高通量成像数据集。
High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.
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