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chipPCR
View on CRAN: Click
here
Download and install chipPCR package within the R console
Install from CRAN:
install.packages("chipPCR")
Install from Github:
library("remotes")
install_github("cran/chipPCR")
Install by package version:
library("remotes")
install_version("chipPCR", "1.0-2")
Attach the package and use:
library("chipPCR")
Maintained by
Stefan Roediger
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-12-12
Latest Update: 2021-03-05
Description:
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) .
How to cite:
Stefan Roediger (2013). chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data. R package version 1.0-2, https://cran.r-project.org/web/packages/chipPCR. Accessed 29 Jan. 2025.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for chipPCR
Functions, R codes and Examples using
the chipPCR R package
Some associated functions: AmpSim.gui . AmpSim . C126EG595 . C126EG685 . C127EGHP . C17 . C316.amp . C316.melt.hr . C316.melt.lr . C317.amp . C317.melt.hr . C317.melt.lr . C54 . C60.amp . C60.melt . C67 . C81 . C85 . CD74 . CD75 . CPP . Eff1000 . Eff625 . Eff750 . Eff875 . LAMP . MFIaggr.gui . MFIaggr . RPA . VIMCFX96_60 . VIMCFX96_69 . VIMCFX96_meltcurve . VIMiQ5_595 . VIMiQ5_685 . VIMiQ5_melt . amptest-class . amptester.gui . amptester . bg-class . bg.max . capillaryPCR . chipPCR-package . chipPCR.datasets . der-class . eff-class . effcalc . fixNA . humanrater . inder . lm.coefs . normalizer . plot-bg . plot-der . plot-eff . plot-refMFI . plotCurves . refMFI-class . rounder . smoother . summary-bg . summary-der . summary-refMFI . th-class . th.cyc .
Some associated R codes: AmpSim.R . AmpSim.gui.R . CPP.R . MFIaggr.R . MFIaggr.gui.R . amptester.R . amptester.gui.R . bg.max.R . check.method.R . classes.R . effcalc.R . fixNA.R . humanrater.R . inder.R . lm.coefs.R . normalizer.R . plotCurves.R . rounder.R . smoother.R . testxy.R . th.cyc.R . Full chipPCR package functions and examples
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