ArticleBMC bioinformatics2021
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data.
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 84 papers.
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Who cites it
84 citing papers in PubMed.
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- Efficiency-Corrected Relative Quantification of qPCR Data Using LinRegPCR and a Spreadsheet-Based Workflow.Bio-protocol · 2026Article
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- Metabolic host-microbe crosstalk in stabilization of epithelial HIF.Microbiome · 2026Article
- Effects of RNA Interference-Mediated Silencing of the Insulin-Like Androgenic Gland Hormone Gene on Growth and Gonad Development in the Swimming Crab (Animals : an open access journal from MDPI · 2026Article
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- Impact of organic pollutants on phenotype and gene expression in human breast cancer cells.Journal of applied toxicology : JAT · 2026Article
- Implementation and Validation of a Limiting Component Quantification Method for qPCR.International journal of molecular sciences · 2026Article
- Canonical WNT signalling governs Echinococcus metacestode development.PLoS pathogens · 2026Article
- Acetate Metabolism in Thyroid Cancer Progression.International journal of molecular sciences · 2026Article
- Information storage across a microbial community using universal RNA barcoding.Nature biotechnology · 2026Article
- A Multimodal Approach to Identify Metallothionein Metal Inducers in Nile Tilapia: Insights From Molecular Docking and Hepatocyte Exposure.Journal of applied toxicology : JAT · 2026Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable and reproducible quantitative results. IMPLEMENTATION: The main steps in the amplification curve analysis are (1) a unique baseline subtraction, not using the ground phase cycles, (2) PCR efficiency determination from the exponential phase of the individual reactions, (3) setting a common quantification threshold and (4) calculation of the efficiency-corrected target quantity with the common threshold, efficiency per assay and C
resultsThe LinRegPCR web application provides visualization and analysis of a single qPCR run. The user interface displays the analysis results on the amplification curve analysis and melting curve analysis in tables and graphs in which deviant reactions are highlighted. The annotated results in the tables can be exported for calculation of gene-expression ratios, fold-change between experimental conditions and further statistical analysis. Web-based LinRegPCR addresses two types of users, wet-lab scientists analyzing the amplification and melting curves of their own qPCR experiments and bioinformaticians creating pipelines for analysis of series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization, analysis and interactive access. The use of the RDML data standard enables machine independent storage and exchange of qPCR data and the RDML-Tools assist with the import of qPCR data from the files exported by the qPCR instrument.
conclusionsThe combined implementation of these analyses in the newly developed web-based LinRegPCR ( https://www.gear-genomics.com/rdml-tools/ ) is platform independent and much faster than the original Windows-based versions of the LinRegPCR program. Moreover, web-based LinRegPCR includes a novel statistical outlier detection and the combination of amplification and melting curve analyses allows direct validation of the amplification product and reporting of reactions that amplify artefacts.
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