The chipPCR package is a toolkit of functions to preprocessamplification curve data. Amplification data can be obtained fromconventional PCR reactions or isothermal amplification reactions. Thepackage contains functions to normalize and baseline amplificationcurves, a routine to detect the start of an amplification reaction,several smoothers for amplification data, a function to distinguishpositive and negative amplification reactions and a function todetermine the amplification efficiency. The smoothers are based onLOWESS, moving average, cubic splines, Savitzky-Golay and others.
In addition the first approximate approximate derivative maximum(FDM) and second approximate derivative maximum (SDM) can be calculatedby a 5-point-stencil as quantification points from real-timeamplification curves. chipPCR contains data sets of experimental nucleicacid amplification systems including the VideoScan HCU and a capillaryconvective PCR (ccPCR) system. The amplification data were generated byhelicase dependent amplification (HDA) or polymerase chain reaction(PCR) under various temperature conditions. As detection systemintercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan)were used.
chipPCR is availableon CRAN, soinstallation is as simple as:
install.packages("chipPCR")You can install the latest development version of the code directlyfrom GitHub:
source("https://install-github.me/michbur/chipPCR")