QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data.

Manci Li, Damani N Bryant, Sarah Gresch, Marissa S Milstein, Peter R Christenson, Stuart S Lichtenberg, Peter A Larsen, Sang-Hyun Oh
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Abstract

Motivation: Fluorophore-assisted seed amplification assays (F-SAAs), such as real-time quaking-induced conversion (RT-QuIC) and fluorophore-assisted protein misfolding cyclic amplification (F-PMCA), have become indispensable tools for studying protein misfolding in neurodegenerative diseases. However, analyzing data generated by these techniques often requires complex and time-consuming manual processes. In addition, the lack of standardization in F-SAA data analysis presents a significant challenge to the interpretation and reproducibility of F-SAA results across different laboratories and studies. There is a need for automated, standardized analysis tools that can efficiently process F-SAA data while ensuring consistency and reliability across different research settings.

Results: Here, we present QuICSeedR (pronounced as "quick seeder"), an R package that addresses these challenges by providing a comprehensive toolkit for the automated processing, analysis, and visualization of F-SAA data. Importantly, QuICSeedR also establishes the foundation for building an F-SAA data management and analysis framework, enabling more consistent and comparable results across different research groups.

Availability and implementation: QuICSeedR is freely available at: https://CRAN.R-project.org/package=QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials.

QuICSeedR:用于分析荧光团辅助种子扩增分析数据的R包。
动机:荧光团辅助种子扩增试验(F-SAAs),如实时振动诱导转化(RT-QuIC)和荧光团辅助蛋白质错误折叠循环扩增(F-PMCA),已成为研究神经退行性疾病中蛋白质错误折叠不可或缺的工具。然而,分析由这些技术生成的数据通常需要复杂且耗时的手动过程。此外,F-SAA数据分析缺乏标准化,对不同实验室和研究中F-SAA结果的解释和可重复性提出了重大挑战。需要自动化、标准化的分析工具来有效地处理F-SAA数据,同时确保不同研究设置的一致性和可靠性。结果:在这里,我们提出了QuICSeedR(发音为“quick seed”),这是一个R软件包,通过提供一个全面的工具包来自动处理、分析和可视化F-SAA数据,解决了这些挑战。重要的是,QuICSeedR还为构建F-SAA数据管理和分析框架奠定了基础,使不同研究小组的结果更加一致和可比。可用性:QuICSeedR免费提供:https://CRAN.R-project.org/package=QuICSeedR。本文中使用的数据和代码在补充材料中提供。补充信息:补充数据可在生物信息学在线获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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