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.
|Author||Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]|
|Date of publication||2015-04-10 01:10:56|
|Maintainer||Stefan Roediger <email@example.com>|
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