c(
person("Stefan", "Roediger",
email = "stefan.roediger@hs-lausitz.de",
role = c("cre", "aut")),
person("Michal", "Burdukiewicz",
email = "michalburdukiewicz@gmail.com", role = "aut"))
The chipPCR package is a toolkit of functions to pre-process
amplification curve data. Amplification data can be obtained from
conventional PCR reactions or isothermal amplification reactions. The
package contains functions to normalize and baseline amplification curves,
a routine to detect the start of an amplification reaction, several
smoothers for amplification data, a function to distinguish positive and
negative amplification reactions and a function to determine the
amplification efficiency. The smoothers are based on LOWESS, 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 calculated by a 5-point-stencil as
quantification points from real-time amplification curves. chipPCR contains
data sets of experimental nucleic acid amplification systems including the
VideoScan HCU and a capillary convective PCR (ccPCR) system. The
amplification data were generated by helicase dependent amplification (HDA)
or polymerase chain reaction (PCR) under various temperature conditions. As
detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis
probes (TaqMan) were used. The latest source code is available via:
https://github.com/michbur/chipPCR
Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut]

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. The package 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.