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qpcR (version 1.4-1)

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

1,626

Version

1.4-1

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

June 14th, 2018

Functions in qpcR (1.4-1)

The chi-square goodness-of-fit

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

Amalgamation of single data models into a model containing replicates

Sigmoidal model selection by different criteria

Plotting qPCR data with fitted curves

Calculation of likelihood ratios for nested models

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

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

Averaging of multiple reference genes

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

Calculation of the 'midpoint' region

Combinatorial elimination of plateau and ground phase cycles

Calculation of the qPCR takeoff point

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

Parameters that can be changed to tweak the kinetic outlier methods

Workhorse function for qPCR model fitting

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

Summarize measures for the goodness-of-fit

Bootstrapping and jackknifing qPCR data

Batch calculation of qPCR efficiency and other qPCR parameters

Value prediction from a fitted qPCR model

Display news and changes of qpcR package versions

Error propagation using different methods

The nonlinear/mechanistic models implemented in qpcR

Calculation of ratios in a batch format from external PCR parameters

An (overlayed) residuals barplot

Residual variance of a fitted model

Updating and refitting a qPCR model

Advanced qPCR data import function

The (published) datasets implemented in qpcR

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

Calculation of ratios from qPCR runs with/without reference genes

Residual sum-of-squares of a fitted model

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

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

Adjusted R-square value of a fitted model

R-square value of a fitted model

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

Root-mean-squared-error of a fitted model

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

Calculation of Akaike weights/relative likelihoods/delta-AICs

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

Akaike's second-order corrected Information Criterion

Calculation of PCR efficiency by fitting an exponential model

The amplification efficiency curve of a fitted object

Calculation of qPCR efficiency using dilution curves and replicate bootstrapping

Comparison of all sigmodal models within the exponential region

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

Evidence ratio for model comparisons with AIC, AICc or BIC

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

Calculation of qPCR efficiency and other important qPCR parameters