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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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Install
install.packages('qpcR')
Monthly Downloads
1,795
Version
1.4-1
License
GPL (>= 2)
Maintainer
Andrej-Nikolai Spiess
Last Published
June 14th, 2018
Functions in qpcR (1.4-1)
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fitchisq
The chi-square goodness-of-fit
pcrsim
Simulation of sigmoidal qPCR data with goodness-of-fit analysis
replist
Amalgamation of single data models into a model containing replicates
mselect
Sigmoidal model selection by different criteria
plot.pcrfit
Plotting qPCR data with fitted curves
llratio
Calculation of likelihood ratios for nested models
pcrimport2
Simple qPCR data import function (i.e. from text files or clipboard)
sliwin
Calculation of qPCR efficiency by the 'window-of-linearity' method
refmean
Averaging of multiple reference genes
modlist
Create nonlinear models from a dataframe and coerce them into a list
midpoint
Calculation of the 'midpoint' region
pcropt1
Combinatorial elimination of plateau and ground phase cycles
takeoff
Calculation of the qPCR takeoff point
meltcurve
Melting curve analysis with (iterative) Tm identification and peak area calculation/cutoff
parKOD
Parameters that can be changed to tweak the kinetic outlier methods
pcrfit
Workhorse function for qPCR model fitting
maxRatio
The maxRatio method as in Shain et al. (2008)
pcrGOF
Summarize measures for the goodness-of-fit
pcrboot
Bootstrapping and jackknifing qPCR data
pcrbatch
Batch calculation of qPCR efficiency and other qPCR parameters
predict.pcrfit
Value prediction from a fitted qPCR model
qpcR.news
Display news and changes of qpcR package versions
propagate
Error propagation using different methods
qpcR_functions
The nonlinear/mechanistic models implemented in qpcR
ratioPar
Calculation of ratios in a batch format from external PCR parameters
resplot
An (overlayed) residuals barplot
resVar
Residual variance of a fitted model
update.pcrfit
Updating and refitting a qPCR model
pcrimport
Advanced qPCR data import function
qpcR_datasets
The (published) datasets implemented in qpcR
ratiobatch
Calculation of ratios in a batch format for multiple genes/samples
ratiocalc
Calculation of ratios from qPCR runs with/without reference genes
RSS
Residual sum-of-squares of a fitted model
KOD
(K)inetic (O)utlier (D)etection using several methods
LRE
Calculation of qPCR efficiency by the 'linear regression of efficiency' method
Rsq.ad
Adjusted R-square value of a fitted model
Rsq
R-square value of a fitted model
Cy0
Cy0 alternative to threshold cycles as in Guescini et al. (2008)
RMSE
Root-mean-squared-error of a fitted model
PRESS
Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-square
akaike.weights
Calculation of Akaike weights/relative likelihoods/delta-AICs
LOF.test
Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA model
AICc
Akaike's second-order corrected Information Criterion
expfit
Calculation of PCR efficiency by fitting an exponential model
eff
The amplification efficiency curve of a fitted object
calib
Calculation of qPCR efficiency using dilution curves and replicate bootstrapping
expcomp
Comparison of all sigmodal models within the exponential region
is.outlier
Outlier summary for objects of class 'modlist' or 'replist'
evidence
Evidence ratio for model comparisons with AIC, AICc or BIC
getPar
Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput data
efficiency
Calculation of qPCR efficiency and other important qPCR parameters