title: A survey of tools for the analysis of quantitative PCR (qPCR) data.
abstract: Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.
authors.affiliation: Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria.
authors.forename: Stephan
authors.initials: S
authors.lastname: Pabinger
authors.affiliation: Faculty of Natural Sciences, InnoProfile Group "Image-based Assays", Brandenburg University of Technology Cottbus - Senftenberg, Großenhainer Straße 57, 01968 Senftenberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Rödiger
authors.affiliation: Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria.
authors.forename: Albert
authors.initials: A
authors.lastname: Kriegner
authors.affiliation: Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria.
authors.forename: Klemens
authors.initials: K
authors.lastname: Vierlinger
authors.affiliation: Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Weinhäusel
keywords: Data analysis; MIQE; RDML; Software; Tools; qPCR