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

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.