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The chipPCR package is a toolkit of functions to preprocess amplification curve data. Amplification data can be obtained from conventional PCR reactions or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, a routine to detect the start of an amplification reaction, several smoothers for amplification data, a function to distinguish positive and negative amplification reactions and a function to determine the amplification efficiency. The smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay and others.

In addition the first approximate approximate derivative maximum (FDM) and second approximate derivative maximum (SDM) can be calculated by a 5-point-stencil as quantification points from real-time amplification curves. chipPCR contains data sets of experimental nucleic acid amplification systems including the VideoScan HCU and a capillary convective PCR (ccPCR) system. The amplification data were generated by helicase dependent amplification (HDA) or polymerase chain reaction (PCR) under various temperature conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

Installation

chipPCR is available on CRAN, so installation is as simple as:

install.packages("chipPCR")

You can install the latest development version of the code directly from GitHub:

source("https://install-github.me/michbur/chipPCR")

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Install

install.packages('chipPCR')

Monthly Downloads

942

Version

1.0-2

License

GPL-3

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Last Published

March 5th, 2021

Functions in chipPCR (1.0-2)

C81

Helicase Dependent Amplification of pCNG1 using the 'VideoScan' Platform
Eff750

Highly Replicate Number Amplification Curves
C54

qPCR Experiment for the amplification of MLC-2v using the 'VideoScan' heating/cooling-unit
C60.amp

qPCR Experiment for the Amplification of MLC-2v and Vimentin (as decadic dilutions) Using the Roche Light Cycler 1.5
Eff625

Highly Replicate Number Amplification Curves
AmpSim.gui

Amplification Curve Simulation Graphical User Interface
AmpSim

Amplification curve simulator
C60.melt

Melt Curves MLC-2v and Vimentin for the qPCR Experiment C60.amp Using the Roche Light Cycler 1.5
C67

Helicase Dependent Amplification of HPRT1 with different input DNA quantities using the Bio-Rad iQ5 thermo cycler
Eff1000

Highly Replicate Number Amplification Curves
CPP

Curve Pre-processor
C85

Helicase Dependent Amplification of Vimentin using the 'VideoScan' Platform
bg

Class "bg"
C317.amp

qPCR Experiment for the Amplification of adk Using the Bio-Rad CFX96 thermo cycler
C316.melt.lr

Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
C317.melt.hr

Melting Curves (resolution: 0.1 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
MFIaggr

Multiple comparison of the cycle dependent variance of the fluorescence
eff

Class "eff"
MFIaggr.gui

Multiple Comparison of the Cycle Dependent Variance - Graphical User Interface
bg.max

Simple function to detect and correct the background range
VIMiQ5_melt

Melting Curve Measured with the Bio-Rad iQ5
Eff875

Highly Replicate Number Amplification Curves
C317.melt.lr

Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
C127EGHP

qPCR Experiment for the Amplification of MLC-2v Using the Roche Light Cycler 1.5
LAMP

real-time loop-mediated isothermal amplification (LAMP) by Tanner et al. (2012)
amptest

Class "amptest"
effcalc

Analysis of the amplification efficiency
capillaryPCR

capillary convective PCR
C17

Helicase Dependent Amplification of HPRT1 at Different Temperatures using the 'VideoScan' Platform 2.0
amptester

Amplification test
chipPCR-package

Toolkit of functions to pre-process amplification data
inder

Interpolate derivatives
lm.coefs

Compute linear model coefficients
amptester.gui

Amplification Test Graphical User Interface
CD75

Helicase Dependent Amplification in the 'VideoScan' 'HCU'
normalizer

Normalize data
plot.bg

Plot bg objects
humanrater

humanrater, a graphical interface to rate curves
fixNA

Impute missing values into a column of amplification data
CD74

Quantitative PCR with a hydrolysis probe and DNA binding dye
summary-bg

Summary bg objects
VIMiQ5_595

Amplification Reaction Using the Bio-Rad iQ5
smoother

Wrapper for Several Smoothers of Amplification Data
RPA

Recombinase polymerase amplification (RPA) by Lutz et al.(2009)
der

Class "der"
plot.refMFI

Plot refMFI objects
VIMiQ5_685

Amplification Reaction Using the Bio-Rad iQ5
VIMCFX96_60

Amplification Reaction Using the Bio-Rad CFX96
chipPCR.datasets

Overview for data sets of the chipPCR package
plot.der

Plot der objects
summary-der

Summary der objects
plot.eff

Plot eff objects
plotCurves

Plot Curves in an Orthogonal Matrix
th

Class "th"
summary-refMFI

Summary refMFI objects
th.cyc

Threshold Cycle
refMFI

Class "refMFI"
VIMCFX96_meltcurve

Melting Curve Measured with the Bio-Rad CFX96
VIMCFX96_69

Amplification Reaction Using the Bio-Rad CFX96
rounder

Round der objects
C316.amp

qPCR Experiment for the Amplification of adk Using the Bio-Rad iQ5 thermo cycler
C126EG595

qPCR Experiment for the Amplification of HPRT1 Using the Bio-Rad iQ5 thermo cycler
C316.melt.hr

Melting Curves (resolution: 0.2 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
C126EG685

qPCR Experiment for the Amplification of HPRT1 Using the Roche Light Cycler 1.5