Evidence map›Paper›PMID 34602053›Full record

ArticleBMC bioinformatics2021

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

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

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.6field-weighted citation impact, top 33% of its field
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

3 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
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

7 authors at 1 institution in 1 country.

S Olaechea-LázaroDepartment 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.
I García-SantistebanDepartment 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.
J R PinedaAchucarro Basque Center for Neuroscience, Barrio Sarriena s/n, 48940, Leioa, Spain.
I BadiolaDepartment of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain.
S AlonsoDepartment 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.
Jose Ramon Bilbao *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. joseramon.bilbao@ehu.eus.
Nora Fernandez-Jimenez *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. nora.fernandez@ehu.eus.ORCID http://orcid.org/0000-0001-6307-0880
University of the Basque Country · ES

Funding

Euskal Herriko Unibertsitatea Acción Especial "Desarrollo e implementación del test de diagnóstico para COVID-19
6 · The paper itself

Abstract

backgroundQuantitative, 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.

resultsHere 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.

conclusionsshinyCurves 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.

Indexed as

COVID-19Data AnalysisHumansPandemicsReal-Time Polymerase Chain ReactionSARS-CoV-2COVID-19Data analysisDiagnosisMedical informaticsMelting and amplification curvesqRT-PCRShiny applicationVirology

Identifiers

PMID34602053
PMCPMC8487674
OpenAlexW3204547130

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.