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qpcR (version 1.3-0)

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

1.3-0

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

August 16th, 2010

Functions in qpcR (1.3-0)

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

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

Calculation of qPCR efficiency and several other important qPCR parameters

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

PCR data from 15 different testicular biopsies (Roche Lightcycler)

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

Comparison of all available sigmodal models by RMSE within the exponential region

Evidence ratio for model comparison with AIC or AICc

Another qPCR dilution experiment with replicates (Roche Lightcycler)

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

qPCR dilution experiment with replicates (Roche Lightcycler)

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

Residual variance of a fitted model

Combinatorial elimination of plateau and ground phase cycles

R-square value of a fitted model

The amplification efficiency curve of a fitted object

A residuals bar-plot with colour-coded bars

Building a model which averages a batch of qPCR curves

General error analysis function using Monte-Carlo simulation/permutation/(first-order) error propagation

Residual sum-of-squares of a fitted model

Plotting qPCR data with fitted curves/confidence bands/error bars

Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-square

Root-mean-squared-error of a fitted model

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

Calculation of Akaike weights/relative likelihoods/delta-AICs

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

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

Summarize measures for the goodness-of-fit

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)

Calculation of PCR efficiency by fitting an exponential model

Calculation of qPCR efficiency by dilution curve analysis with an optional iterative search of the optimal threshold border

Calculation of ratios/propagated errors/confidence intervals/permutation p-values from qPCR runs with/without reference data

Function for qPCR model fitting