Toolkit of Helper Functions to Pre-Process Amplification Data
Amplification Curve Simulation Graphical User Interface
Amplification curve simulator
Class "amptest"
Amplification Test Graphical User Interface
Amplification test
Class "bg"
Simple function to detect and correct the background range
Toolkit of functions to pre-process amplification data
Overview for data sets of the chipPCR package
Curve Pre-processor
Class "der"
Class "eff"
Analysis of the amplification efficiency
Impute missing values into a column of amplification data
humanrater, a graphical interface to rate curves
Interpolate derivatives
Compute linear model coefficients
Multiple Comparison of the Cycle Dependent Variance - Graphical User I...
Multiple comparison of the cycle dependent variance of the fluorescenc...
Normalize data
Plot bg objects
Plot der objects
Plot eff objects
Plot refMFI objects
Plot Curves in an Orthogonal Matrix
Class "refMFI"
Round der objects
Wrapper for Several Smoothers of Amplification Data
Summary bg objects
Summary der objects
Summary refMFI objects
Class "th"
Threshold Cycle
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>.