qpcR: Modelling and analysis of real-time PCR data
Version 1.4-0

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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AuthorAndrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Date of publication2014-09-15 20:33:00
MaintainerAndrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
LicenseGPL (>= 2)
Version1.4-0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("qpcR")

Man pages

AICc: Akaike's second-order corrected Information Criterion
akaike.weights: Calculation of Akaike weights/relative likelihoods/delta-AICs
calib: Calculation of qPCR efficiency using dilution curves and...
Cy0: Cy0 alternative to threshold cycles as in Guescini et al....
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
fitchisq: The chi-square goodness-of-fit
getPar: Batch calculation of qPCR fit...
is.outlier: Outlier summary for objects of class 'modlist' or 'replist'
KOD: (K)inetic (O)utlier (D)etection using several methods
llratio: Calculation of likelihood ratios for nested models
LOF.test: Formal lack-Of-Fit test of a nonlinear model against a...
LRE: Calculation of qPCR efficiency by the 'linear regression of...
maxRatio: The maxRatio method as in Shain et al. (2008)
meltcurve: Melting curve analysis with (iterative) Tm identification and...
midpoint: Calculation of the 'midpoint' region
modlist: Create nonlinear models from a dataframe and coerce them into...
mselect: Sigmoidal model selection by different criteria
parKOD: Parameters that can be changed to tweak the kinetic outlier...
pcrbatch: Batch calculation of qPCR efficiency and other qPCR...
pcrboot: Bootstrapping and jackknifing qPCR data
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
pcrsim: Simulation of sigmoidal qPCR data with goodness-of-fit...
plot.pcrfit: Plotting qPCR data with fitted curves/confidence bands/error...
predict.pcrfit: Value prediction from a fitted qPCR model
PRESS: Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka...
propagate: Error propagation using different methods
qpcR_datasets: The (published) datasets implemented in qpcR
qpcR_functions: The nonlinear/mechanistic models implemented in qpcR
qpcR.news: Display news and changes of qpcR package versions
ratiobatch: Calculation of ratios in a batch format for multiple...
ratiocalc: Calculation of ratios from qPCR runs with/without reference...
ratioPar: Calculation of ratios in a batch format from external PCR...
refmean: Averaging of multiple reference genes
replist: Amalgamation of single data models into a model containing...
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
Rsq.ad: Adjusted 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'...
takeoff: Calculation of the qPCR takeoff point
update.pcrfit: Updating and refitting a qPCR model

Functions

AICc Man page Source code
Cy0 Man page Source code
EMA Source code
KOD Man page Source code
LOF.test Man page Source code
LRE Man page Source code
PRESS Man page Source code
RMSE Man page Source code
RSS Man page Source code
Rsq Man page Source code
Rsq.ad Man page Source code
TmFind Source code
akaike.weights Man page Source code
aq.plot Source code
arw Source code
b4 Man page
b5 Man page
b6 Man page
b7 Man page
baseline Source code
batsch1 Man page
batsch2 Man page
batsch3 Man page
batsch4 Man page
batsch5 Man page
boggy Man page
bubbleplot Source code
calib Man page Source code
cbind.na Source code
cm3 Man page
cmean Source code
competimer Man page
counter Source code
data.frame.na Source code
delete Source code
dil4reps94 Man page
dyemelt Man page
eff Man page Source code
efficiency Man page Source code
evidence Man page Source code
expGrowth Man page
expSDM Man page
expcomp Man page Source code
expfit Man page Source code
fetchData Source code
fitchisq Man page Source code
getPar Man page Source code
gmean Source code
guescini1 Man page
guescini2 Man page
hmean Source code
htPCR Man page
is.outlier Man page Source code
karlen1 Man page
karlen2 Man page
karlen3 Man page
l4 Man page
l5 Man page
l6 Man page
l7 Man page
lievens1 Man page
lievens2 Man page
lievens3 Man page
lin2 Man page
linexp Man page
llratio Man page Source code
mak2 Man page
mak2i Man page
mak3 Man page
mak3i Man page
makeStat Source code
maxRatio Man page Source code
meltcurve Man page Source code
midpoint Man page Source code
modlist Man page Source code
mselect Man page Source code
multi1 Source code
multi2 Source code
multi3 Source code
parKOD Man page Source code
pcrGOF Man page Source code
pcrbatch Man page Source code
pcrboot Man page Source code
pcrfit Man page Source code
pcrimport Man page Source code
pcrimport2 Man page Source code
pcropt1 Man page Source code
pcrpred Source code
pcrsim Man page Source code
peakArea Source code
peaks Source code
plot.pcrfit Man page Source code
predict.pcrfit Man page Source code
propagate Man page Source code
qpcR.news Man page Source code
ratioPar Man page Source code
ratiobatch Man page Source code
ratiocalc Man page Source code
rbind.na Source code
refmean Man page Source code
replist Man page Source code
reps Man page
reps2 Man page
reps3 Man page
reps384 Man page
resVar Man page Source code
rescale Source code
resplot Man page Source code
runmean Source code
rutledge Man page
savgol Source code
sliwin Man page Source code
smoothit Source code
spl3 Man page
takeoff Man page Source code
testdat Man page
tmvrnorm Source code
uni1 Source code
uni2 Source code
update.pcrfit Man page Source code
vermeulen1 Man page
vermeulen2 Man page
wfct Source code
whittaker Source code
xyy.plot Source code

Files

inst
inst/add01
inst/add01/format01.txt
inst/add02
inst/add02/format02d.txt
inst/add02/format02c.txt
inst/add02/format02b.txt
inst/add02/format02a.txt
src
src/smth.c
NAMESPACE
NEWS
data
data/reps3.rda
data/batsch1.rda
data/reps2.rda
data/batsch2.rda
data/vermeulen1.rda
data/htPCR.rda
data/karlen2.rda
data/sysdata.rda
data/karlen1.rda
data/guescini1.rda
data/guescini2.rda
data/karlen3.rda
data/lievens3.rda
data/dyemelt.rda
data/batsch4.rda
data/lievens2.rda
data/competimer.rda
data/vermeulen2.rda
data/datalist
data/testdat.rda
data/reps384.rda
data/rutledge.rda
data/batsch5.rda
data/boggy.rda
data/dil4reps94.rda
data/reps.rda
data/lievens1.rda
data/batsch3.rda
R
R/pcrfit.r
R/pcrpred.R
R/utils.R
R/AICc.R
R/qpcR.news.r
R/RSS.R
R/resVar.R
R/Cy0.R
R/pcrsim.r
R/pcrimport.R
R/Rsq.ad.r
R/llratio.r
R/maxRatio.r
R/sysdata.rda
R/mselect.r
R/pcrGOF.R
R/eff.R
R/evidence.R
R/replist.r
R/refmean.R
R/sliwin.R
R/KOD.r
R/modlist.r
R/ratiocalc.r
R/is.outlier.r
R/akaike.weights.R
R/meltcurve.r
R/LRE.r
R/takeoff.R
R/update.pcrfit.r
R/calib.r
R/ratioPar.r
R/expfit.R
R/pcropt1.R
R/midpoint.R
R/predict.pcrfit.r
R/RMSE.R
R/getPar.r
R/pcrbatch.r
R/PRESS.R
R/Rsq.R
R/ratiobatch.r
R/propagate.R
R/plot.pcrfit.r
R/LOF.test.r
R/resplot.R
R/pcrboot.r
R/pcrimport2.R
R/efficiency.R
R/fitchisq.r
R/expcomp.R
MD5
DESCRIPTION
man
man/is.outlier.rd
man/calib.rd
man/pcrGOF.Rd
man/maxRatio.rd
man/akaike.weights.Rd
man/Cy0.rd
man/pcrfit.Rd
man/pcrboot.rd
man/LOF.test.rd
man/expfit.Rd
man/refmean.Rd
man/pcrimport.Rd
man/ratioPar.rd
man/resVar.Rd
man/replist.rd
man/eff.Rd
man/resplot.Rd
man/pcrbatch.Rd
man/midpoint.rd
man/ratiobatch.rd
man/predict.pcrfit.rd
man/pcrimport2.Rd
man/qpcR_datasets.rd
man/Rsq.ad.rd
man/pcropt1.Rd
man/expcomp.Rd
man/evidence.Rd
man/AICc.Rd
man/ratiocalc.Rd
man/takeoff.rd
man/getPar.rd
man/meltcurve.rd
man/KOD.rd
man/modlist.Rd
man/llratio.rd
man/mselect.Rd
man/parKOD.rd
man/fitchisq.rd
man/propagate.Rd
man/LRE.Rd
man/efficiency.Rd
man/PRESS.Rd
man/pcrsim.rd
man/qpcR.news.rd
man/Rsq.Rd
man/qpcR_functions.rd
man/sliwin.Rd
man/RMSE.Rd
man/update.pcrfit.rd
man/plot.pcrfit.Rd
man/RSS.Rd
qpcR documentation built on May 20, 2017, 5:55 a.m.