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qpcR (version 1.2-1)

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

1,227

Version

1.2-1

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

August 13th, 2009

Functions in qpcR (1.2-1)

R-square value of a fitted model

Bayesian Information Criterion

Building a model which averages a batch of qPCR curves

Calculation of PCR efficiency by fitting an exponential model

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

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

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

PCR data from 15 different testicular biopsies (Roche Lightcycler)

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

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

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

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

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

Residual sum-of-squares of a fitted model

Calculation of Akaike weights/relative likelihoods/delta-AICs

Combinatorial elimination of plateau and ground phase cycles

Root-mean-squared-error of a fitted model

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

Calculation of qPCR efficiency and several other important qPCR parameters

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

A residuals bar-plot with colour-coded bars

Evidence ratio for model comparison with AIC or AICc

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

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

Residual variance of a fitted model

Function for qPCR model fitting

qPCR dilution experiment with replicates (Roche Lightcycler)

Another qPCR dilution experiment with replicates (Roche Lightcycler)

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

The amplification efficiency curve of a fitted object

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)

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

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

Summarize measures for the goodness-of-fit