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.

AuthorStefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]
Date of publication2015-04-10 01:10:56
MaintainerStefan Roediger <stefan.roediger@hs-lausitz.de>
LicenseGPL-3
Version0.0.8-10
https://github.com/michbur/chipPCR

View on CRAN

Man pages

AmpSim: Amplification curve simulator

AmpSim.gui: Amplification Curve Simulation Graphical User Interface

amptest-class: Class '"amptest"'

amptester: Amplification test

amptester.gui: Amplification Test Graphical User Interface

bg-class: Class '"bg"'

bg.max: Simple function to detect and correct the background range

C126EG595: qPCR Experiment for the Amplification of HPRT1 Using the...

C126EG685: qPCR Experiment for the Amplification of HPRT1 Using the...

C127EGHP: qPCR Experiment for the Amplification of MLC-2v Using the...

C17: Helicase Dependent Amplification of HPRT1 at Different...

C316.amp: qPCR Experiment for the Amplification of adk Using the...

C316.melt.hr: Melting Curves (resolution: 0.2 degrees Celsius / step) for...

C316.melt.lr: Melting Curves (resolution: 0.5 degrees Celsius / step) for...

C317.amp: qPCR Experiment for the Amplification of adk Using the...

C317.melt.hr: Melting Curves (resolution: 0.1 degrees Celsius / step) for...

C317.melt.lr: Melting Curves (resolution: 0.5 degrees Celsius / step) for...

C54: qPCR Experiment for the amplification of MLC-2v using the...

C60.amp: qPCR Experiment for the Amplification of MLC-2v and Vimentin...

C60.melt: Melt Curves MLC-2v and Vimentin for the qPCR Experiment...

C67: Helicase Dependent Amplification of HPRT1 with different...

C81: Helicase Dependent Amplification of pCNG1 using the VideoScan...

C85: Helicase Dependent Amplification of Vimentin using the...

capillaryPCR: capillary convective PCR

CD74: Quantitative PCR with a hydrolysis probe and DNA binding dye

CD75: Helicase Dependent Amplification in the VideoScan HCU

chipPCR.datasets: Overview for data sets of the 'chipPCR' package

chipPCR-package: Toolkit of functions to pre-process amplification data

CPP: Curve Pre-processor

der-class: Class '"der"'

Eff1000: Highly Replicate Number Amplification Curves

Eff625: Highly Replicate Number Amplification Curves

Eff750: Highly Replicate Number Amplification Curves

Eff875: Highly Replicate Number Amplification Curves

effcalc: Analysis of the amplification efficiency

eff-class: Class '"eff"'

fixNA: Impute missing values into a column of amplification data

humanrater: humanrater, a graphical interface to rate curves

inder: Interpolate derivatives

LAMP: real-time loop-mediated isothermal amplification (LAMP) by...

lm.coefs: Compute linear model coefficients

MFIaggr: Multiple comparison of the cycle dependent variance of the...

MFIaggr.gui: Multiple Comparison of the Cycle Dependent Variance -...

normalizer: Normalize data

plot-bg: Plot 'bg' objects

plotCurves: Plot Curves in an Orthogonal Matrix

plot-der: Plot 'der' objects

plot-eff: Plot 'eff' objects

plot-refMFI: Plot 'refMFI' objects

refMFI-class: Class '"refMFI"'

rounder: Round der objects

RPA: Recombinase polymerase amplification (RPA) by Lutz et...

smoother: Wrapper for Several Smoothers of Amplification Data

summary-bg: Summary 'bg' objects

summary-der: Summary 'der' objects

summary-refMFI: Summary 'refMFI' objects

th-class: Class '"th"'

th.cyc: Threshold Cycle

VIMCFX96_60: Amplification Reaction Using the Bio-Rad CFX96

VIMCFX96_69: Amplification Reaction Using the Bio-Rad CFX96

VIMCFX96_meltcurve: Melting Curve Measured with the Bio-Rad CFX96

VIMiQ5_595: Amplification Reaction Using the Bio-Rad iQ5

VIMiQ5_685: Amplification Reaction Using the Bio-Rad iQ5

VIMiQ5_melt: Melting Curve Measured with the Bio-Rad iQ5

Functions

AmpSim Man page
AmpSim.gui Man page
amptest Man page
amptest-class Man page
amptester Man page
amptester.gui Man page
bg Man page
bg-class Man page
bg.max Man page
bg.max.data.frame Man page
bg.max,data.frame,missing-method Man page
bg.max.matrix Man page
bg.max,matrix,missing-method Man page
bg.max.numeric Man page
bg.max,numeric,numeric-method Man page
C126EG595 Man page
C126EG685 Man page
C127EGHP Man page
C17 Man page
C316.amp Man page
C316.melt.hr Man page
C316.melt.lr Man page
C317.amp Man page
C317.melt.hr Man page
C317.melt.lr Man page
C54 Man page
C60.amp Man page
C60.melt Man page
C67 Man page
C81 Man page
C85 Man page
capillaryPCR Man page
CD74 Man page
CD75 Man page
chipPCR Man page
chipPCR.datasets Man page
chipPCR-package Man page
CPP Man page
CPP.data.frame Man page
CPP,data.frame,missing-method Man page
CPP.matrix Man page
CPP,matrix,missing-method Man page
CPP.numeric Man page
CPP,numeric,numeric-method Man page
der Man page
der-class Man page
eff Man page
Eff1000 Man page
Eff625 Man page
Eff750 Man page
Eff875 Man page
effcalc Man page
effcalc.data.frame Man page
effcalc,data.frame,missing-method Man page
effcalc.matrix Man page
effcalc,matrix,missing-method Man page
effcalc.numeric Man page
effcalc,numeric,numeric-method Man page
eff-class Man page
fixNA Man page
fixNA.data.frame Man page
fixNA,data.frame,missing-method Man page
fixNA.matrix Man page
fixNA,matrix,missing-method Man page
fixNA.numeric Man page
fixNA,numeric,numeric-method Man page
humanrater Man page
inder Man page
inder.data.frame Man page
inder,data.frame,missing-method Man page
inder.matrix Man page
inder,matrix,missing-method Man page
inder.numeric Man page
inder,numeric,numeric-method Man page
LAMP Man page
lm.coefs Man page
MFIaggr Man page
MFIaggr.data.frame Man page
MFIaggr,data.frame,missing-method Man page
MFIaggr.gui Man page
MFIaggr.matrix Man page
MFIaggr,matrix,missing-method Man page
MFIaggr.numeric Man page
MFIaggr,numeric,numeric-method Man page
normalizer Man page
plot.amptest Man page
plot,amptest,ANY-method Man page
plot,amptest-method Man page
plot.bg Man page
plot,bg,ANY-method Man page
plot,bg-method Man page
plotCurves Man page
plot.der Man page
plot,der,ANY-method Man page
plot,der-method Man page
plot.eff Man page
plot,eff,ANY-method Man page
plot,eff-method Man page
plot.refMFI Man page
plot,refMFI,ANY-method Man page
plot,refMFI-method Man page
plot,refMFI,refMFI-method Man page
qqline,refMFI-method Man page
qqnorm,refMFI-method Man page
refMFI Man page
refMFI-class Man page
rounder Man page
RPA Man page
show.amptest Man page
show,amptest-method Man page
show.bg Man page
show,bg-method Man page
show.der Man page
show,der-method Man page
show.eff Man page
show,eff-method Man page
show,refMFI-method Man page
show,refMFI-method Man page
show.th Man page
show,th-method Man page
smoother Man page
smoother.data.frame Man page
smoother,data.frame,missing-method Man page
smoother.matrix Man page
smoother,matrix,missing-method Man page
smoother.numeric Man page
smoother,numeric,numeric-method Man page
summary.amptest Man page
summary,amptest-method Man page
summary.bg Man page
summary,bg-method Man page
summary-der Man page
summary.der Man page
summary,der-method Man page
summary.eff Man page
summary,eff-method Man page
summary.refMFI Man page
summary,refMFI-method Man page
summary.th Man page
summary,th-method Man page
th Man page
th-class Man page
th.cyc Man page
VIMCFX96_60 Man page
VIMCFX96_69 Man page
VIMCFX96_meltcurve Man page
VIMiQ5_595 Man page
VIMiQ5_685 Man page
VIMiQ5_melt Man page

Files

chipPCR
chipPCR/inst
chipPCR/inst/AmpSim.gui
chipPCR/inst/AmpSim.gui/ui.R
chipPCR/inst/AmpSim.gui/server.R
chipPCR/inst/AmpSim.gui/readme.md
chipPCR/inst/AmpSim.gui/DESCRIPTION
chipPCR/inst/CITATION
chipPCR/inst/amptester.gui
chipPCR/inst/amptester.gui/ui.R
chipPCR/inst/amptester.gui/server.R
chipPCR/inst/amptester.gui/amptester_report.Rmd
chipPCR/inst/amptester.gui/DESCRIPTION
chipPCR/inst/MFIaggr.gui
chipPCR/inst/MFIaggr.gui/ui.R
chipPCR/inst/MFIaggr.gui/server.R
chipPCR/inst/MFIaggr.gui/readme.md
chipPCR/inst/MFIaggr.gui/refMFI_report.Rmd
chipPCR/inst/MFIaggr.gui/DESCRIPTION
chipPCR/inst/doc
chipPCR/inst/doc/chipPCR.pdf
chipPCR/inst/doc/chipPCR.Rnw
chipPCR/inst/doc/chipPCR.R
chipPCR/NAMESPACE
chipPCR/CHANGELOG
chipPCR/data
chipPCR/data/VIMiQ5_685.rda
chipPCR/data/C126EG685.rda
chipPCR/data/C81.rda
chipPCR/data/VIMCFX96_60.rda
chipPCR/data/C316.melt.hr.rda
chipPCR/data/C126EG595.rda
chipPCR/data/Eff1000.rda
chipPCR/data/CD74.rda
chipPCR/data/C127EGHP.rda
chipPCR/data/RPA.rda
chipPCR/data/C317.melt.lr.rda
chipPCR/data/C67.rda
chipPCR/data/C60.amp.rda
chipPCR/data/C316.amp.rda
chipPCR/data/C316.melt.lr.rda
chipPCR/data/VIMCFX96_69.rda
chipPCR/data/C60.melt.rda
chipPCR/data/VIMCFX96_meltcurve.rda
chipPCR/data/C85.rda
chipPCR/data/Eff625.rda
chipPCR/data/datalist
chipPCR/data/capillaryPCR.rda
chipPCR/data/VIMiQ5_595.rda
chipPCR/data/C17.rda
chipPCR/data/LAMP.rda
chipPCR/data/Eff750.rda
chipPCR/data/C317.amp.rda
chipPCR/data/CD75.rda
chipPCR/data/C54.rda
chipPCR/data/C317.melt.hr.rda
chipPCR/data/VIMiQ5_melt.rda
chipPCR/data/Eff875.rda
chipPCR/R
chipPCR/R/classes.R chipPCR/R/smoother.R chipPCR/R/rounder.R chipPCR/R/CPP.R chipPCR/R/amptester.R chipPCR/R/humanrater.R chipPCR/R/AmpSim.gui.R chipPCR/R/lm.coefs.R chipPCR/R/bg.max.R chipPCR/R/amptester.gui.R chipPCR/R/normalizer.R chipPCR/R/MFIaggr.R chipPCR/R/testxy.R chipPCR/R/MFIaggr.gui.R chipPCR/R/inder.R chipPCR/R/linreg.R chipPCR/R/effcalc.R chipPCR/R/AmpSim.R chipPCR/R/check.method.R chipPCR/R/fixNA.R chipPCR/R/th.cyc.R chipPCR/R/plotCurves.R
chipPCR/vignettes
chipPCR/vignettes/MFIaggr_gui.png
chipPCR/vignettes/humanrater.png
chipPCR/vignettes/datdf.RData
chipPCR/vignettes/roediger-burdukiewicz.bib
chipPCR/vignettes/logo.png
chipPCR/vignettes/logo.pdf
chipPCR/vignettes/natbib.bst
chipPCR/vignettes/browser.png
chipPCR/vignettes/chipPCR.Rnw
chipPCR/vignettes/fixNAevaluation.RData
chipPCR/vignettes/fixNA_test1.png
chipPCR/vignettes/natbib.sty
chipPCR/README.md
chipPCR/MD5
chipPCR/build
chipPCR/build/vignette.rds
chipPCR/DESCRIPTION
chipPCR/man
chipPCR/man/AmpSim.Rd chipPCR/man/C17.Rd chipPCR/man/VIMCFX96_60.Rd chipPCR/man/C67.Rd chipPCR/man/VIMiQ5_595.Rd chipPCR/man/C127EGHP.Rd chipPCR/man/plot-der.Rd chipPCR/man/Eff1000.Rd chipPCR/man/C54.Rd chipPCR/man/bg.max.Rd chipPCR/man/amptest-class.Rd chipPCR/man/C317.melt.lr.Rd chipPCR/man/eff-class.Rd chipPCR/man/C317.melt.hr.Rd chipPCR/man/plotCurves.Rd chipPCR/man/MFIaggr.gui.Rd chipPCR/man/summary-refMFI.Rd chipPCR/man/RPA.Rd chipPCR/man/effcalc.Rd chipPCR/man/summary-bg.Rd chipPCR/man/Eff625.Rd chipPCR/man/plot-refMFI.Rd chipPCR/man/C60.melt.Rd chipPCR/man/C316.melt.lr.Rd chipPCR/man/AmpSim.gui.Rd chipPCR/man/LAMP.Rd chipPCR/man/C126EG685.Rd chipPCR/man/bg-class.Rd chipPCR/man/capillaryPCR.Rd chipPCR/man/VIMiQ5_melt.Rd chipPCR/man/chipPCR.datasets.Rd chipPCR/man/C81.Rd chipPCR/man/VIMCFX96_69.Rd chipPCR/man/plot-bg.Rd chipPCR/man/C316.amp.Rd chipPCR/man/CD75.Rd chipPCR/man/amptester.Rd chipPCR/man/VIMCFX96_meltcurve.Rd chipPCR/man/CPP.Rd chipPCR/man/refMFI-class.Rd chipPCR/man/th.cyc.Rd chipPCR/man/th-class.Rd chipPCR/man/amptester.gui.Rd chipPCR/man/summary-der.Rd chipPCR/man/normalizer.Rd chipPCR/man/smoother.Rd chipPCR/man/C317.amp.Rd chipPCR/man/inder.Rd chipPCR/man/der-class.Rd chipPCR/man/C126EG595.Rd chipPCR/man/C85.Rd chipPCR/man/humanrater.Rd chipPCR/man/C316.melt.hr.Rd chipPCR/man/lm.coefs.Rd chipPCR/man/CD74.Rd chipPCR/man/chipPCR-package.Rd chipPCR/man/plot-eff.Rd chipPCR/man/C60.amp.Rd chipPCR/man/MFIaggr.Rd chipPCR/man/VIMiQ5_685.Rd chipPCR/man/fixNA.Rd chipPCR/man/Eff750.Rd chipPCR/man/rounder.Rd chipPCR/man/Eff875.Rd

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