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qpcR (version 1.3-7.1)

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

1,795

Version

1.3-7.1

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

April 18th, 2013

Functions in qpcR (1.3-7.1)

R-square value of a fitted model

Advanced qPCR data import function

Calculation of qPCR efficiency by the 'linear regression of efficiency' method

General error analysis function using different methods

Hannan-Quinn Information Criterion

Akaike's second-order corrected Information Criterion

Calculation of PCR efficiency by fitting an exponential model

Building a model which averages a batch of qPCR curves

The amplification efficiency curve of a fitted object

Calculation of ratios from qPCR runs with/without reference genes

Combinatorial elimination of plateau and ground phase cycles

Workhorse function for qPCR model fitting

Evidence ratio for model comparisons with AIC, AICc or BIC

Averaging of multiple reference genes

Comparison of all sigmodal models within the exponential region

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

Calculation of qPCR efficiency by the 'window-of-linearity' method

Residual variance of a fitted model

Batch calculation of qPCR efficiency and other qPCR parameters

An (overlayed) residuals barplot

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

Residual sum-of-squares of a fitted model

Sigmoidal model selection by different criteria

Calculation of qPCR efficiency and other important qPCR parameters

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

Root-mean-squared-error of a fitted model

qPCR data of the S27a transcript in 15 testicular biopsies

Calculation of qPCR efficiency by dilution curve analysis

Calculation of Akaike weights/relative likelihoods/delta-AICs

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

Summarize measures for the goodness-of-fit

Calculation of the qPCR takeoff point

Calculation of qPCR efficiency by dilution curve bootstrapping

Elimination of qPCR cycles with low/high impact on fitted parameters

Display news and changes of qpcR package versions

Cy0 alternative to threshold cycles as in Guescini et al. (2008)

Value prediction from a fitted qPCR model

The maxRatio method as in Shain et al. (2008)

The chi-square goodness-of-fit

Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput data

Calculation of the 'midpoint' region

Amalgamation of single data models into an averaged model

Converts a 'replist' back to a 'modlist'

Outlier summary for objects of class 'modlist' or 'replist'

Updating and refitting a qPCR model

Melting curve analysis with (iterative) Tm identification and peak area calculation/cutoff

Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA model

Bootstrapping and jackknifing qPCR data

Adjusted R-square value of a fitted model

The nonlinear/mechanistic models implemented in qpcR

Neill's lack-of-fit test when replicates are lacking

Amalgamation of single data models into a model containing replicates

Parameters that can be changed to tweak the kinetic outlier methods

Calculation of likelihood ratios for nested models

The (published) datasets implemented in qpcR

(K)inetic (O)utlier (D)etection using several methods

Calculation of ratios in a batch format from external PCR parameters

Simulation of sigmoidal qPCR data with goodness-of-fit analysis

Concatenating or calculating statistics on a 'pcrbatch'

Calculation of ratios in a batch format for multiple genes/samples