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'...

Functions

AICc Man page
akaike.weights Man page
eff Man page
efficiency Man page
evidence Man page
expcomp Man page
expfit Man page
LRE Man page
modlist Man page
mselect Man page
pcrbatch Man page
pcrfit Man page
pcrGOF Man page
pcrimport Man page
pcrimport2 Man page
pcropt1 Man page
plot.pcrfit Man page
PRESS Man page
propagate Man page
ratiocalc Man page
refmean Man page
resplot Man page
resVar Man page
RMSE Man page
Rsq Man page
RSS Man page
sliwin Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

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