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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.
  • Olaechea-Lázaro S; Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
  • García-Santisteban I; Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
  • Pineda JR; Biocruces-Bizkaia Health Research Institute, Plaza de Cruces, 48903, Barakaldo, Spain.
  • Badiola I; Achucarro Basque Center for Neuroscience, Barrio Sarriena s/n, 48940, Leioa, Spain.
  • Alonso S; Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
  • Bilbao JR; Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
  • Fernandez-Jimenez N; Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
BMC Bioinformatics ; 22(1): 476, 2021 Oct 03.
Article in English | MEDLINE | ID: covidwho-1448207
ABSTRACT

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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Case report / Experimental Studies Limits: Humans Language: English Journal: BMC Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: S12859-021-04392-1

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Case report / Experimental Studies Limits: Humans Language: English Journal: BMC Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: S12859-021-04392-1