Introduction

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.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.http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR.stefan.roediger@b-tu.deSupplementary data are available at Bioinformatics online.

Publications

  1. chipPCR: an R package to pre-process raw data of amplification curves.
    Cite this
    Rödiger S, Burdukiewicz M, Schierack P, 2015-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Stefan Rödiger
    Developer

    Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg

  2. Michał Burdukiewicz
    Developer

    Department of Genomics, Faculty of Biotechnology, Poland

  3. Peter Schierack
    Investigator

    Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg

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Summary
AccessionBT000294
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByPeter Schierack