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qpcR (version 1.3-2)

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

1.3-2

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

September 8th, 2010

Functions in qpcR (1.3-2)

Calculation of Akaike weights/relative likelihoods/delta-AICs

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

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

Another qPCR dilution experiment with replicates (Roche Lightcycler)

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

Residual sum-of-squares of a fitted model

Function for qPCR model fitting

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

Residual variance of a fitted model

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

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

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

The amplification efficiency curve of a fitted object

Root-mean-squared-error of a fitted model

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

R-square value of a fitted model

PCR data from 15 different testicular biopsies (Roche Lightcycler)

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

Calculation of qPCR efficiency and several other important qPCR parameters

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

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

Summarize measures for the goodness-of-fit

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

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

Building a model which averages a batch of qPCR curves

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

Calculation of PCR efficiency by fitting an exponential model

qPCR dilution experiment with replicates (Roche Lightcycler)

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

Combinatorial elimination of plateau and ground phase cycles

A residuals bar-plot with colour-coded bars

Evidence ratio for model comparison with AIC or AICc

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)