{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:31Z","timestamp":1772138071324,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T00:00:00Z","timestamp":1734998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Minnesota Partnership for Biotechnology and Medical Genomics"},{"DOI":"10.13039\/100013423","name":"Legislative-Citizen Commission on Minnesota Resources","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013423","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present QuICSeedR (pronounced as \u201cquick seeder\u201d), 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>QuICSeedR is freely available at: https:\/\/CRAN.R-project.org\/package=QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae752","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T23:32:21Z","timestamp":1734651141000},"source":"Crossref","is-referenced-by-count":2,"title":["QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3930-7117","authenticated-orcid":false,"given":"Manci","family":"Li","sequence":"first","affiliation":[{"name":"Department of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota , Minneapolis, MN 55455,","place":["United States"]},{"name":"Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota , St. Paul, MN 55108,","place":["United 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States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marissa S","family":"Milstein","sequence":"additional","affiliation":[{"name":"Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota , St. Paul, MN 55108,","place":["United States"]},{"name":"Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota , St. Paul, MN 55108,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter R","family":"Christenson","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota , Minneapolis, MN 55455,","place":["United States"]},{"name":"Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota , St. Paul, MN 55108,","place":["United 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