chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

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. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Version: 1.0-2
Depends: R (≥ 3.0.0), methods
Imports: lmtest, MASS, outliers, ptw, quantreg, Rfit, robustbase, shiny, signal
Suggests: drc, knitr, markdown, qpcR, RDML, rmarkdown, spelling, testthat, tinytex, xtable
Published: 2021-03-05
DOI: 10.32614/CRAN.package.chipPCR
Author: Stefan Roediger ORCID iD [cre, aut], Michal Burdukiewicz ORCID iD [aut], Konstantin A. Blagodatskikh [ctb], Andrej-Nikolai Spiess ORCID iD [ctb]
Maintainer: Stefan Roediger <stefan.roediger at>
License: GPL-3
NeedsCompilation: no
Language: en-US
Citation: chipPCR citation info
Materials: README NEWS ChangeLog
CRAN checks: chipPCR results


Reference manual: chipPCR.pdf
Vignettes: Supplement to: chipPCR: an R Package to Pre-Process Raw Data of Amplification Curves


Package source: chipPCR_1.0-2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): chipPCR_1.0-2.tgz, r-oldrel (arm64): chipPCR_1.0-2.tgz, r-release (x86_64): chipPCR_1.0-2.tgz, r-oldrel (x86_64): chipPCR_1.0-2.tgz
Old sources: chipPCR archive

Reverse dependencies:

Reverse imports: MBmca
Reverse suggests: RDML, shinyMolBio


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