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

Olaechea-Lázaro, S.; García-Santisteban, I.; Pineda, J. R.; Badiola, I.; Alonso, S.; Bilbao, Jose Ramon; Fernandez-Jimenez, Nora

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04392-1.