Evidence map›Paper›PMID 39718778›Full record

ArticleBioinformatics (Oxford, England)2024

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Manci LiDepartment of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States.ORCID 0000-0003-3930-7117
Damani N BryantMinnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States.ORCID 0009-0000-3623-8035
Sarah GreschMinnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States.
Marissa S MilsteinMinnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States.
Peter R ChristensonDepartment of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States.
Stuart S LichtenbergMinnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States.ORCID 0000-0002-2445-8927
Peter A LarsenMinnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, United States.
Sang-Hyun OhDepartment of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, United States.ORCID 0000-0002-6992-5007

Funding

Legislative-Citizen Commission on Minnesota ResourcesMinnesota Partnership for Biotechnology and Medical Genomics
6 · The paper itself

Abstract

motivationFluorophore-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.

resultsHere, 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.

Indexed as

Computational BiologyFluorescent DyesSoftwareHumansProtein FoldingFluorescent Dyes

Identifiers

PMID39718778
PMCPMC11742141

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.