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qpcR (version 1.0-6)

Modelling and analysis of real-time PCR data

Description

Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

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Version

Install

install.packages('qpcR')

Monthly Downloads

239

Version

1.0-6

License

GNU GPL (version 2 or any later version)

Maintainer

Andrej-Nikolai Spiess

Last Published

June 10th, 2025

Functions in qpcR (1.0-6)

qpcR

Modelling and analysis of real-time PCR data
rutledge

qPCR dilution experiment with replicates and different runs from Rutledge et al (Biorad Opticon)
efficiency

Calculation of qPCR efficiency and several other important qPCR parameters
pcrplot

Plotting PCR data with fitted curves
expfit2

Calculation of PCR efficiency by fitting of an exponential model after outlier cycle detection
pcrpred

Value prediction from a fitted sigmoidal model
pcrbatch

Batch calculation of qPCR efficiency and several other important qPCR parameters with different methods
S27

PCR data from 15 different testicular biopsies (Roche Lightcycler)
evidence

Evidence ratio for model comparison with AIC or AICc
pcrfit

Simple wrapper function for fast model fitting
pcropt1

Optimization of efficiency and F0 estimation by combinatorial cycle elimination of plateau and ground phase cycles
reps

qPCR dilution experiment with replicates (Roche Lightcycler)
Rsq

R-square of a sigmoidal fit
modlist

Create sigmoidal models from a dataframe and coerce them into a list
AICc

Akaike's second-order Information Criterion for small sample numbers
expcomp

Comparison of several sigmodal models by RMSE within the exponential region
reps3

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)
pcrimport

Simple qPCR data import function (i.e. from text files or clipboard).
resVar

Residual variance of a sigmoidal fit
RMSE

Root-mean-squared-error of a sigmoidal fit
calib

Calculation of qPCR efficiency by dilution curve analysis
repform

Formatting of PCR data with or without replicates for analysis
expfit

Calculation of PCR efficiency by fitting of an exponential model and minimization of residual variance
reps2

Another qPCR dilution experiment with replicates (Roche Lightcycler)
confband

Confidence bands for a sigmoidal fit
eff

The amplification efficiency curve of a fitted object
pcrGOF

Summarize measures for the goodness-of-fit
mchoice

Selection of the best model by nested F-tests
sliwin

Calculation of PCR efficiency by the window-of-linearity method