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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 |
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: 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 imports: | MBmca |
Reverse suggests: | RDML, shinyMolBio |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.