chipPCR: an R package to pre-process raw data of amplification curves.
BACKGROUND
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.


METHODS
http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR.


BACKGROUND
stefan.roediger@b-tu.de


BACKGROUND
Supplementary data are available at Bioinformatics online.
Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany and.
Stefan
S
Rödiger
Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
Michał
M
Burdukiewicz
Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany and.
Peter
P
Schierack
D000465:Algorithms; D020869:Gene Expression Profiling; D006801:Humans; D008962:Models, Theoretical; D011381:Programming Languages; D012313:RNA / Q000032:analysis* / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012984:Software
D012313:RNA