shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study

• Main Authors: Alonso, S. (Author), Badiola, I. (Author), Bilbao, J.R (Author), Fernandez-Jimenez, N. (Author), García-Santisteban, I. (Author), Olaechea-Lázaro, S. (Author), Pineda, J.R (Author)
• Format: Article
• Language: English
• Published: BioMed Central Ltd 2021
• Subjects: Amplification curves; Case-studies; COVID-19; data analysis; Data analysis; Data Analysis; Data handling; Diagnosis; Diseases; human; Humans; Information analysis; Medical informatics; Melting; Melting and amplification curves; Melting curves; Multi-Sources; pandemic; Pandemics; Polymerase chain reaction; qRT-PCR; Quantitative, reverse transcription PCR; real time polymerase chain reaction; Real-Time Polymerase Chain Reaction; Reverse transcription PCR; SARS-CoV-2; Shiny application; Virology; Viruses; WEB application; Web applications
• Online Access: View Fulltext in Publisher

 Background: Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR plates per day is a relatively simple task, but automated, integrative strategies are needed if a laboratory is dealing with hundreds of plates per day, as is being the case in the COVID-19 pandemic. Results: Here we present shinyCurves, an online shiny-based, free software to analyze qRT-PCR amplification data from multi-plate and multi-platform formats. Our shiny application does not require any programming experience and is able to call samples Positive, Negative or Undetermined for viral infection according to a number of user-defined settings, apart from providing a complete set of melting and amplification curve plots for the visual inspection of results. Conclusions: shinyCurves is a flexible, integrative and user-friendly software that speeds-up the analysis of massive qRT-PCR data from different sources, with the possibility of automatically producing and evaluating melting and amplification curve plots. © 2021, The Author(s).