A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

Maintainer: Stefan Roediger <stefan.roediger at hs-lausitz.de>

Author(s): Stefan Roediger*, Michal Burdukiewicz*, Konstantin A. Blagodatskikh*

Install package and any missing dependencies by running this line in your R console:

install.packages("chipPCR")

Depends R (>= 3.0.0), methods
Imports lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase, shiny, signal
Suggests drc, knitr, markdown, MBmca(>=0.0.3-4), qpcR, RDML, xtable
Enhances
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MBmca
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dpcR
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RDML
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Package chipPCR
Materials
URL https://github.com/michbur/chipPCR
Task Views
Version 0.0.8-10
Published 2015-04-10
License GPL-3
BugReports https://github.com/michbur/chipPCR/issues
SystemRequirements
NeedsCompilation no
Citation
CRAN checks chipPCR check results
Package source chipPCR_0.0.8-10.tar.gz