qpcR: Modelling and analysis of real-time PCR data

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Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).

Author
Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Date of publication
2014-09-15 20:33:00
Maintainer
Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
License
GPL (>= 2)
Version
1.4-0

View on CRAN

Man pages

AICc
Akaike's second-order corrected Information Criterion
akaike.weights
Calculation of Akaike weights/relative likelihoods/delta-AICs
eff
The amplification efficiency curve of a fitted object
efficiency
Calculation of qPCR efficiency and other important qPCR...
evidence
Evidence ratio for model comparisons with AIC, AICc or BIC
expcomp
Comparison of all sigmodal models within the exponential...
expfit
Calculation of PCR efficiency by fitting an exponential model
LRE
Calculation of qPCR efficiency by the 'linear regression of...
modlist
Create nonlinear models from a dataframe and coerce them into...
mselect
Sigmoidal model selection by different criteria
pcrbatch
Batch calculation of qPCR efficiency and other qPCR...
pcrfit
Workhorse function for qPCR model fitting
pcrGOF
Summarize measures for the goodness-of-fit
pcrimport
Advanced qPCR data import function
pcrimport2
Simple qPCR data import function (i.e. from text files or...
pcropt1
Combinatorial elimination of plateau and ground phase cycles
plot.pcrfit
Plotting qPCR data with fitted curves/confidence bands/error...
PRESS
Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka...
propagate
Error propagation using different methods
ratiocalc
Calculation of ratios from qPCR runs with/without reference...
refmean
Averaging of multiple reference genes
resplot
An (overlayed) residuals barplot
resVar
Residual variance of a fitted model
RMSE
Root-mean-squared-error of a fitted model
Rsq
R-square value of a fitted model
RSS
Residual sum-of-squares of a fitted model
sliwin
Calculation of qPCR efficiency by the 'window-of-linearity'...

Files in this package

qpcR
qpcR/inst
qpcR/inst/add01
qpcR/inst/add01/format01.txt
qpcR/inst/add02
qpcR/inst/add02/format02d.txt
qpcR/inst/add02/format02c.txt
qpcR/inst/add02/format02b.txt
qpcR/inst/add02/format02a.txt
qpcR/src
qpcR/src/smth.c
qpcR/NAMESPACE
qpcR/NEWS
qpcR/data
qpcR/data/reps3.rda
qpcR/data/batsch1.rda
qpcR/data/reps2.rda
qpcR/data/batsch2.rda
qpcR/data/vermeulen1.rda
qpcR/data/htPCR.rda
qpcR/data/karlen2.rda
qpcR/data/sysdata.rda
qpcR/data/karlen1.rda
qpcR/data/guescini1.rda
qpcR/data/guescini2.rda
qpcR/data/karlen3.rda
qpcR/data/lievens3.rda
qpcR/data/dyemelt.rda
qpcR/data/batsch4.rda
qpcR/data/lievens2.rda
qpcR/data/competimer.rda
qpcR/data/vermeulen2.rda
qpcR/data/datalist
qpcR/data/testdat.rda
qpcR/data/reps384.rda
qpcR/data/rutledge.rda
qpcR/data/batsch5.rda
qpcR/data/boggy.rda
qpcR/data/dil4reps94.rda
qpcR/data/reps.rda
qpcR/data/lievens1.rda
qpcR/data/batsch3.rda
qpcR/R
qpcR/R/pcrfit.r
qpcR/R/pcrpred.R
qpcR/R/utils.R
qpcR/R/AICc.R
qpcR/R/qpcR.news.r
qpcR/R/RSS.R
qpcR/R/resVar.R
qpcR/R/Cy0.R
qpcR/R/pcrsim.r
qpcR/R/pcrimport.R
qpcR/R/Rsq.ad.r
qpcR/R/llratio.r
qpcR/R/maxRatio.r
qpcR/R/sysdata.rda
qpcR/R/mselect.r
qpcR/R/pcrGOF.R
qpcR/R/eff.R
qpcR/R/evidence.R
qpcR/R/replist.r
qpcR/R/refmean.R
qpcR/R/sliwin.R
qpcR/R/KOD.r
qpcR/R/modlist.r
qpcR/R/ratiocalc.r
qpcR/R/is.outlier.r
qpcR/R/akaike.weights.R
qpcR/R/meltcurve.r
qpcR/R/LRE.r
qpcR/R/takeoff.R
qpcR/R/update.pcrfit.r
qpcR/R/calib.r
qpcR/R/ratioPar.r
qpcR/R/expfit.R
qpcR/R/pcropt1.R
qpcR/R/midpoint.R
qpcR/R/predict.pcrfit.r
qpcR/R/RMSE.R
qpcR/R/getPar.r
qpcR/R/pcrbatch.r
qpcR/R/PRESS.R
qpcR/R/Rsq.R
qpcR/R/ratiobatch.r
qpcR/R/propagate.R
qpcR/R/plot.pcrfit.r
qpcR/R/LOF.test.r
qpcR/R/resplot.R
qpcR/R/pcrboot.r
qpcR/R/pcrimport2.R
qpcR/R/efficiency.R
qpcR/R/fitchisq.r
qpcR/R/expcomp.R
qpcR/MD5
qpcR/DESCRIPTION
qpcR/man
qpcR/man/is.outlier.rd
qpcR/man/calib.rd
qpcR/man/pcrGOF.Rd
qpcR/man/maxRatio.rd
qpcR/man/akaike.weights.Rd
qpcR/man/Cy0.rd
qpcR/man/pcrfit.Rd
qpcR/man/pcrboot.rd
qpcR/man/LOF.test.rd
qpcR/man/expfit.Rd
qpcR/man/refmean.Rd
qpcR/man/pcrimport.Rd
qpcR/man/ratioPar.rd
qpcR/man/resVar.Rd
qpcR/man/replist.rd
qpcR/man/eff.Rd
qpcR/man/resplot.Rd
qpcR/man/pcrbatch.Rd
qpcR/man/midpoint.rd
qpcR/man/ratiobatch.rd
qpcR/man/predict.pcrfit.rd
qpcR/man/pcrimport2.Rd
qpcR/man/qpcR_datasets.rd
qpcR/man/Rsq.ad.rd
qpcR/man/pcropt1.Rd
qpcR/man/expcomp.Rd
qpcR/man/evidence.Rd
qpcR/man/AICc.Rd
qpcR/man/ratiocalc.Rd
qpcR/man/takeoff.rd
qpcR/man/getPar.rd
qpcR/man/meltcurve.rd
qpcR/man/KOD.rd
qpcR/man/modlist.Rd
qpcR/man/llratio.rd
qpcR/man/mselect.Rd
qpcR/man/parKOD.rd
qpcR/man/fitchisq.rd
qpcR/man/propagate.Rd
qpcR/man/LRE.Rd
qpcR/man/efficiency.Rd
qpcR/man/PRESS.Rd
qpcR/man/pcrsim.rd
qpcR/man/qpcR.news.rd
qpcR/man/Rsq.Rd
qpcR/man/qpcR_functions.rd
qpcR/man/sliwin.Rd
qpcR/man/RMSE.Rd
qpcR/man/update.pcrfit.rd
qpcR/man/plot.pcrfit.Rd
qpcR/man/RSS.Rd