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qpcR (version 1.1-7)

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

1,483

Version

1.1-7

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

June 10th, 2025

Functions in qpcR (1.1-7)

Building a model which averages a batch of qPCR curves

PCR data from 15 different testicular biopsies (Roche Lightcycler)

The amplification efficiency curve of a fitted object

Calculation of PCR efficiency by fitting an exponential model

Akaike's second-order corrected Information Criterion for small sample sizes

Calculation of Akaike weights/relative likelihoods/delta-AICs

Create nonlinear models from a dataframe and coerce them into a list

Calculation of qPCR efficiency and several other important qPCR parameters

Calculation of ratios/propagated errors/t-statistics for all permutations/combinations of qPCR runs with or without reference data

Comparison of several sigmodal models by RMSE within the exponential region

Residual variance of a fitted model

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

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

Allen's PRESS (Prediction Sum-Of-Squares) statistic

A qPCR experiment with replicates and simulated inhibition (Lightcycler 480) from Guescini et al

Another qPCR dilution experiment with replicates (Roche Lightcycler)

R-square value of a fitted model

Value prediction from a fitted sigmoidal model

General error propagation function using covariates and Monte Carlo simulations

A residuals bar-plot with colour-coded bars

Summarize measures for the goodness-of-fit

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

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

Cy0 alternative to crossing points/threshold cycles as in Guescini et al

Calculation of qPCR efficiency by dilution curve analysis

Formatting of PCR data with or without replicates for analysis

Calculation of likelihood ratios for nested models

Combinatorial elimination of plateau and ground phase cycles

Plotting PCR data with fitted curves

Evidence ratio for model comparison with AIC or AICc

Simple wrapper function for fast model fitting

Modelling and analysis of real-time PCR data

Selection of the best model by nested F-tests/likelihood ratios/Akaike weights

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)

Confidence bands for a sigmoidal fit

Residual sum-of-squares of a fitted model

Root-mean-squared-error of a fitted model

The maxRatio method as in Shain et al

qPCR dilution experiment with replicates (Roche Lightcycler)

A qPCR dilution experiment with replicates (Lightcycler 480) from Guescini et al

Plot method for data of class 'ratiocalc' which displays barplots of ratios with error bars