Analyze Data for Fluorophore-Assisted Seed Amplification Assays

A toolkit for analysis and visualization of data from fluorophore-assisted seed amplification assays, such as Real-Time Quaking-Induced Conversion (RT-QuIC) and Fluorophore-Assisted Protein Misfolding Cyclic Amplification (PMCA). 'QuICSeedR' addresses limitations in existing software by automating data processing, supporting large-scale analysis, and enabling comparative studies of analysis methods. It incorporates methods described in Henderson et al. (2015) , Li et al. (2020) , Rowden et al. (2023) , Haley et al. (2013) , and Mair and Wilcox (2020) . Please refer to the original publications for details.

QuICSeedR

Overview

QuICSeedR is a comprehensive R package for analyzing and visualizing data from fluorophore-assisted seed amplification assays, such as Real-Time Quaking-Induced Conversion (RT-QuIC) and fluorophore-assisted Protein Misfolding Cyclic Amplification (PMCA). This toolkit addresses limitations in existing software by automating data processing, supporting large-scale analysis, and enabling comparative studies of analysis methods.

Features

• Automated data processing for RT-QuIC and PMCA assays
• Support for large-scale data analysis
• Comparative analysis of different methodologies
• Visualization tools for assay results
• Statistical analysis functions tailored for seed amplification data

Installation

You can install the development version of QuICSeedR from GitHub with:

# install.packages("devtools")
devtools::install_github("mancili/QuICSeedR")

Usage

For more detailed examples and function documentation, please refer to the function help pages. The manuscript link will be added here once it becomes available.

Requirements

• R (>= 4.1.0)

License

This R package for analyzing seed amplification assay data is available under a dual licensing model: it is freely available under the GNU General Public License v3.0 (GPL-3) for open-source use, and a separate commercial LICENSE is offered for use cases that require additional rights or support beyond the scope of GPL-3.

Author

Manci Li, PhD

ORCID: 0000-0003-3930-7117

Citation

If you use QuICSeedR in your research, please cite it as follows:

Li, M. (2024). QuICSeedR: Data analysis for fluorophore-assisted seed amplification assays. R package version 0.1.2. https://github.com/mancili/QuICSeedR

Contact

For questions and feedback, please contact Dr. Manci Li at [email protected].