ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

AuthorJitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseLGPL-3
Version1.30.0

View on Bioconductor

Functions

assayData Man page
barchart Man page
barploterrbar Man page
brewer.pal Man page
brewer.pal.info Man page
ColMap Man page
ColMap-class Man page
coreData Man page
coreData<- Man page
coreData<-,InputFrame,data.frame-method Man page
coreData,InputFrame-method Man page
Ct Man page
Ct<- Man page
Ct,ddCtExpression-method Man page
CtErr Man page
CtErr,ddCtExpression-method Man page
Ct,InputFrame-method Man page
Ct<-,InputFrame,numeric-method Man page
dCt Man page
dCt,ddCtExpression-method Man page
dCtErr Man page
dCtErr,ddCtExpression-method Man page
ddCt Man page
ddCtAbsolute Man page
ddCt,ddCtExpression-method Man page
ddCtErr Man page
ddCtErr,ddCtExpression-method Man page
ddCtExpression Man page
ddCtExpression-class Man page
ddCtExpression,InputFrame-method Man page
ddCtExpression-methods Man page
ddCtExpression,SDMFrame-method Man page
DEFAULT.CT.COLNAME Man page
DEFAULT.FEATURE.COLNAME Man page
DEFAULT.SAMPLE.COLNAME Man page
detectorNames Man page
detectorNames<- Man page
detectorNames<-,InputFrame,character-method Man page
detectorNames,InputFrame-method Man page
elist Man page
elist,ddCtExpression-method Man page
elistWrite Man page
elistWrite,ddCtExpression,character-method Man page
errBarchart Man page
errBarchart,ddCtExpression,character-method Man page
errBarchart,ddCtExpression,missing-method Man page
errBarchart-methods Man page
errBarchartParameter-class Man page
exprs Man page
exprsUndeterminedLabel,errBarchartParameter-method Man page
fData Man page
"fData<-" Man page
featureData Man page
"featureData<-" Man page
featureNames Man page
"featureNames<-" Man page
fileNames Man page
fileNames,InputFrame-method Man page
getDir Man page
InputFrame Man page
InputFrame-class Man page
InputFrame,data.frame-method Man page
InputFrame,InputReader-method Man page
[,InputFrame-method Man page
[[,InputFrame-method Man page
$,InputFrame-method Man page
InputReader-class Man page
level Man page
level,ddCtExpression-method Man page
levelErr Man page
levelErr,ddCtExpression-method Man page
names,InputFrame-method Man page
numberCt Man page
numberCt,ddCtExpression-method Man page
numberNA Man page
numberNA,ddCtExpression-method Man page
panel.abline Man page
panel.barchart Man page
panel.grid Man page
panel.segments Man page
panel.text Man page
pData Man page
"pData<-" Man page
phenoData Man page
"phenoData<-" Man page
QuantStudioFrame Man page
QuantStudioReader-class Man page
readQuantStudio Man page
readSDM Man page
removeDetector Man page
removeDetector,InputFrame,character-method Man page
removeDetector-methods Man page
removeNTC Man page
removeNTC,ddCtExpression-method Man page
removeNTC,InputFrame-method Man page
removeNTC-methods Man page
removeSample Man page
removeSample,InputFrame,character-method Man page
removeSample-methods Man page
replaceDetector Man page
replaceDetector,InputFrame,character,character-method Man page
replaceDetector-methods Man page
replaceSample Man page
replaceSample,InputFrame,character,character-method Man page
replaceSample-methods Man page
replaceVectorByEquality Man page
rightCensoring Man page
rightCensoring,InputFrame,numeric-method Man page
rightCensoring,SDMFrame,numeric-method Man page
sampleNames Man page
sampleNames<- Man page
sampleNames<-,InputFrame,character-method Man page
sampleNames,InputFrame-method Man page
SDMFrame Man page
SDMFrame-class Man page
SDMReader-class Man page
show,errBarchartParameter-method Man page
show,InputFrame-method Man page
summary Man page
TSVFrame Man page
TSVReader-class Man page
uniqueDetectorNames Man page
uniqueDetectorNames<- Man page
uniqueDetectorNames<-,InputFrame,character,character-method Man page
uniqueDetectorNames,InputFrame-method Man page
uniqueDetectorNames<-,InputFrame,missing,character-method Man page
uniqueSampleNames Man page
uniqueSampleNames<- Man page
uniqueSampleNames<-,InputFrame,character,character-method Man page
uniqueSampleNames,InputFrame-method Man page
uniqueSampleNames<-,InputFrame,missing,character-method Man page
varLabels Man page
varMetadata Man page
"varMetadata<-" Man page
write.htmltable Man page
writeSimpleTabCsv Man page
xtable Man page

Files

ddCt/DESCRIPTION
ddCt/Makefile
ddCt/NAMESPACE
ddCt/NEWS
ddCt/R
ddCt/R/AllClasses.R ddCt/R/AllFunctions.R ddCt/R/AllGenerics.R ddCt/R/AllGlobals.R ddCt/R/AllMethods.R ddCt/R/absoluteQ.R ddCt/R/ddCtSplit.R ddCt/R/output.R ddCt/R/visualization.R
ddCt/build
ddCt/build/vignette.rds
ddCt/inst
ddCt/inst/doc
ddCt/inst/doc/RT-PCR-Script-ddCt.R
ddCt/inst/doc/RT-PCR-Script-ddCt.Rnw
ddCt/inst/doc/RT-PCR-Script-ddCt.pdf
ddCt/inst/doc/rtPCR-usage.R
ddCt/inst/doc/rtPCR-usage.Rnw
ddCt/inst/doc/rtPCR-usage.pdf
ddCt/inst/doc/rtPCR.R
ddCt/inst/doc/rtPCR.Rnw
ddCt/inst/doc/rtPCR.pdf
ddCt/inst/extdata
ddCt/inst/extdata/Experiment1.txt
ddCt/inst/extdata/Experiment2.txt
ddCt/inst/extdata/ExperimentWithNTC.txt
ddCt/inst/extdata/QuantStudio_File1.txt
ddCt/inst/extdata/QuantStudio_File2.txt
ddCt/inst/extdata/sampleData.txt
ddCt/inst/scripts
ddCt/inst/scripts/ddCt.R
ddCt/inst/scripts/ddCt.conf
ddCt/man
ddCt/man/InputFrame.Rd ddCt/man/InputReader-class.Rd ddCt/man/QuantStudioFrame.Rd ddCt/man/SDMFrame-class.Rd ddCt/man/SDMFrame.Rd ddCt/man/barploterrbar.Rd ddCt/man/ddCtAbsolute.Rd ddCt/man/ddCtExpression-class.Rd ddCt/man/ddCtExpression-methods.Rd ddCt/man/elistWrite-methods.Rd ddCt/man/errBarchart-methods.Rd ddCt/man/errBarchartParameter-class.Rd ddCt/man/getDir.Rd ddCt/man/removeNTC-methods.Rd ddCt/man/replaceVectorByEquality.Rd ddCt/man/write.htmltable.Rd ddCt/man/writeSimpleTabCsv.Rd
ddCt/tests
ddCt/tests/unit.R
ddCt/tests/units
ddCt/tests/units/runit.SDMFrame.R
ddCt/tests/units/runit.SDMFrame.RData
ddCt/tests/units/runit.ddCtExpression.R
ddCt/tests/units/runit.ddCtExpression.RData
ddCt/vignettes
ddCt/vignettes/RT-PCR-Script-ddCt.Rnw
ddCt/vignettes/Result_Experiment1
ddCt/vignettes/Result_Experiment1/CtResult.pdf
ddCt/vignettes/Result_Experiment1/HTML
ddCt/vignettes/Result_Experiment1/HTML/Ct.html
ddCt/vignettes/Result_Experiment1/HTML/dCt.html
ddCt/vignettes/Result_Experiment1/HTML/ddCt.html
ddCt/vignettes/Result_Experiment1/HTML/level.html
ddCt/vignettes/Result_Experiment1/Tables
ddCt/vignettes/Result_Experiment1/Tables/Ct_matrix.txt
ddCt/vignettes/Result_Experiment1/Tables/dCt_matrix.txt
ddCt/vignettes/Result_Experiment1/Tables/ddCt_matrix.txt
ddCt/vignettes/Result_Experiment1/Tables/levelPlusError.txt
ddCt/vignettes/Result_Experiment1/Tables/level_matrix.txt
ddCt/vignettes/Result_Experiment1/allValues.csv
ddCt/vignettes/Result_Experiment1/correlationResult.pdf
ddCt/vignettes/Result_Experiment1/levelResult.pdf
ddCt/vignettes/rtPCR-usage.Rnw
ddCt/vignettes/rtPCR.Rnw
ddCt/vignettes/rtPCR.bib

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