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 [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb], Andrej-Nikolai Spiess [ctb]
Maintainer:	Stefan Roediger <stefan.roediger at b-tu.de>
BugReports:	https://github.com/PCRuniversum/chipPCR/issues
License:	GPL-3
URL:	https://github.com/PCRuniversum/chipPCR
NeedsCompilation:	no
Language:	en-US
Citation:	chipPCR citation info
Materials:	README, NEWS, ChangeLog
CRAN checks:	chipPCR results

Documentation:

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

Downloads:

Package source:	chipPCR_1.0-2.tar.gz
Windows binaries:	r-devel: chipPCR_1.0-2.zip, r-release: chipPCR_1.0-2.zip, r-oldrel: chipPCR_1.0-2.zip
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:	dpcR, MBmca, PCRedux
Reverse suggests:	RDML

Linking:

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