Stefan Rödiger1, Michał Burdukiewicz2, Peter Schierack1. 1. Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany and. 2. Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
Abstract
MOTIVATION: Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. RESULTS: chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. AVAILABILITY AND IMPLEMENTATION: http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. CONTACT: stefan.roediger@b-tu.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. RESULTS: chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. AVAILABILITY AND IMPLEMENTATION: http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. CONTACT: stefan.roediger@b-tu.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Michał Burdukiewicz; Stefan Rödiger; Piotr Sobczyk; Mario Menschikowski; Peter Schierack; Paweł Mackiewicz Journal: Biomol Detect Quantif Date: 2016-08-10
Authors: Matthew N McCall; Alexander S Baras; Alexander Crits-Christoph; Roxann Ingersoll; Melissa A McAlexander; Kenneth W Witwer; Marc K Halushka Journal: BMC Bioinformatics Date: 2016-03-22 Impact factor: 3.169
Authors: Andrej-Nikolai Spiess; Stefan Rödiger; Michał Burdukiewicz; Thomas Volksdorf; Joel Tellinghuisen Journal: Sci Rep Date: 2016-12-13 Impact factor: 4.379