qpcR: Modelling and analysis of real-time PCR data

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

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.