twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.
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twoddpcr An RBioconductor package ...
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Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, Manchester, M20 4BXIssue Date
2017-05-05
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Droplet Digital PCR (ddPCR) is a sensitive platform used to quantify specific nucleic acid molecules amplified by polymerase chain reactions. Its sensitivity makes it particularly useful for the detection of rare mutant molecules, such as those present in a sample of circulating free tumour DNA obtained from cancer patients. ddPCR works by partitioning a sample into individual droplets for which the majority contain only zero or one target molecule. Each droplet then becomes a reaction chamber for PCR, which through the use of fluorochrome labelled probes allows the target molecules to be detected by measuring the fluorescence intensity of each droplet. The technology supports two channels, allowing, for example, mutant and wild type molecules to be detected simultaneously in the same sample. As yet, no open source software is available for the automatic gating of two channel ddPCR experiments in the case where the droplets can be grouped into four clusters. Here, we present an open source R package 'twoddpcr', which uses Poisson statistics to estimate the number of molecules in such two channel ddPCR data. Using the Shiny framework, an accompanying graphical user interface (GUI) is also included for the package, allowing users to adjust parameters and see the results in real-time.Citation
twoddpcr: An R/Bioconductor package and Shiny app for Droplet Digital PCR analysis. 2017 BioinformaticsJournal
BioinformaticsDOI
10.1093/bioinformatics/btx308PubMed ID
28475662Type
ArticleLanguage
enISSN
1367-4811ae974a485f413a2113503eed53cd6c53
10.1093/bioinformatics/btx308
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