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bioRxiv · 10.1101/2024.08.27.609919

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

Li, M.·Bryant, D. N.·Gresch, S.·Milstein, M.·Christenson, P. R.·Lichtenberg, S. S.·Larsen, P. A.·Oh, S.-H.
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Abstract

SummaryFluorophore-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. Additionally, 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. 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 sets up the foundation for building an F-SAA data management and analysis framework, enabling more consistent and comparable results across different research groups. Availability and implementationQuICSeedR source code is freely available at: https://github.com/mancili/QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials. Supplementary informationSupplementary Materials are available with the manuscript.

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Li, M., Bryant, D. N., Gresch, S., Milstein, M., Christenson, P. R., Lichtenberg, S. S., Larsen, P. A., Oh, S.-H.. 2024-08-27. QuICSeedR: An R package for analyzing fluorophore-assisted seed amplification assay data. https://doi.org/10.1101/2024.08.27.609919

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