ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Version 1.32.0

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
Bioconductor views DifferentialExpression GeneExpression MicrotitrePlateAssay qPCR
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseLGPL-3
Version1.32.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ddCt")

Popular man pages

ddCtExpression-class: ddCt Expression
ddCtExpression-methods: Apply the ddCt algorithm for a given data set
elistWrite-methods: Write ddCtExpression object into data frame or files
getDir: Auxillary functions for the executive scripts
InputFrame: Build an InputFrame from a ReaderClass or a data frame
removeNTC-methods: Remove NTC samples
SDMFrame: Read an SDM file
See all...

All man pages Function index File listing

Man pages

barploterrbar: Barplot with error bars.
ddCtAbsolute: absolute quantification for Taqman data
ddCtExpression-class: ddCt Expression
ddCtExpression-methods: Apply the ddCt algorithm for a given data set
elistWrite-methods: Write ddCtExpression object into data frame or files
errBarchart-methods: Draw barchart of relative expression level with error-bars
errBarchartParameter-class: Class "errBarchartParameter"
getDir: Auxillary functions for the executive scripts
InputFrame: Build an InputFrame from a ReaderClass or a data frame
InputReader-class: Class "InputReader"
QuantStudioFrame: Read QuantStudio file(s)
removeNTC-methods: Remove NTC samples
replaceVectorByEquality: REPLACE ITEMS OF VECTOR BY EQUALITY
SDMFrame: Read an SDM file
SDMFrame-class: Working with SDM files
write.htmltable: Write a data frame into an html table within a html page
writeSimpleTabCsv: Write a data frame into a tab delimited file

Functions

"fData<-" Man page
"featureData<-" Man page
"featureNames<-" Man page
"pData<-" Man page
"phenoData<-" Man page
"varMetadata<-" Man page
$,InputFrame-method Man page
ColMap Man page Source code
ColMap-class Man page
Ct Man page
Ct,InputFrame-method Man page
Ct,ddCtExpression-method Man page
Ct<- Man page
Ct<-,InputFrame,numeric-method Man page
CtErr Man page
CtErr,ddCtExpression-method Man page
DEFAULT.CT.COLNAME Man page
DEFAULT.FEATURE.COLNAME Man page
DEFAULT.SAMPLE.COLNAME Man page
DataFrame Source code
InputFrame Man page
InputFrame,InputReader-method Man page
InputFrame,data.frame-method Man page
InputFrame-class Man page
InputReader-class Man page
QuantStudioFrame Man page Source code
QuantStudioReader-class Man page
SDMFrame Man page Source code
SDMFrame-class Man page
SDMReader-class Man page
TSVFrame Man page Source code
TSVReader-class Man page
[,InputFrame-method Man page
[[,InputFrame-method Man page
as.data.frame.InputFrame Source code
assayData Man page
barchart Man page
barploterrbar Man page Source code
brewer.pal Man page
brewer.pal.info Man page
checkParams Source code
coreData Man page
coreData,InputFrame-method Man page
coreData<- Man page
coreData<-,InputFrame,data.frame-method Man page
dCt Man page
dCt,ddCtExpression-method Man page
dCtErr Man page
dCtErr,ddCtExpression-method Man page
ddCt Man page
ddCt,ddCtExpression-method Man page
ddCtAbsolute Man page Source code
ddCtErr Man page
ddCtErr,ddCtExpression-method Man page
ddCtErrBarchart Source code
ddCtExpression Man page
ddCtExpression,InputFrame-method Man page
ddCtExpression,SDMFrame-method Man page
ddCtExpression-class Man page
ddCtExpression-methods Man page
ddCtReport Source code
ddCtSplit Source code
detectorNames Man page
detectorNames,InputFrame-method Man page
detectorNames<- Man page
detectorNames<-,InputFrame,character-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
factor2char Source code
featureData Man page
featureNames Man page
fileNames Man page
fileNames,InputFrame-method Man page
getCmdParans Source code
getConfParams Source code
getDefaultParams Source code
getDiff Source code
getDir Man page Source code
getExecMode Source code
getParams Source code
getSysParams Source code
isGrep Source code
level Man page
level,ddCtExpression-method Man page
levelErr Man page
levelErr,ddCtExpression-method Man page
levelfkt Source code
na.mad Source code
na.mean Source code
na.median Source code
na.sd Source code
names,InputFrame-method Man page
numberCt Man page
numberCt,ddCtExpression-method Man page
numberNA Man page
numberNA,ddCtExpression-method Man page
pData Man page
panel.abline Man page
panel.barchart Man page
panel.barchart.errbar Source code
panel.ddCtErrBarchart Source code
panel.grid Man page
panel.segments Man page
panel.text Man page
phenoData 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,InputFrame-method Man page
removeNTC,ddCtExpression-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
replaceNames Source code
replaceSample Man page
replaceSample,InputFrame,character,character-method Man page
replaceSample-methods Man page
replaceVectorByEquality Man page Source code
rightCensoring Man page
rightCensoring,InputFrame,numeric-method Man page
rightCensoring,SDMFrame,numeric-method Man page
sampleNames Man page
sampleNames,InputFrame-method Man page
sampleNames<- Man page
sampleNames<-,InputFrame,character-method Man page
show,InputFrame-method Man page
show,errBarchartParameter-method Man page
summary Man page
uniqueDetectorNames Man page
uniqueDetectorNames,InputFrame-method Man page
uniqueDetectorNames<- Man page
uniqueDetectorNames<-,InputFrame,character,character-method Man page
uniqueDetectorNames<-,InputFrame,missing,character-method Man page
uniquePlate Source code
uniqueSampleNames Man page
uniqueSampleNames,InputFrame-method Man page
uniqueSampleNames<- Man page
uniqueSampleNames<-,InputFrame,character,character-method Man page
uniqueSampleNames<-,InputFrame,missing,character-method Man page
varLabels Man page
varMetadata Man page
write.htmltable Man page Source code
writeLines.ddCt Source code
writeSimpleTabCsv Man page Source code
xtable Man page
xtable.ddCt Source code

Files

DESCRIPTION
Makefile
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllFunctions.R
R/AllGenerics.R
R/AllGlobals.R
R/AllMethods.R
R/absoluteQ.R
R/ddCtSplit.R
R/output.R
R/visualization.R
build
build/vignette.rds
inst
inst/doc
inst/doc/RT-PCR-Script-ddCt.R
inst/doc/RT-PCR-Script-ddCt.Rnw
inst/doc/RT-PCR-Script-ddCt.pdf
inst/doc/rtPCR-usage.R
inst/doc/rtPCR-usage.Rnw
inst/doc/rtPCR-usage.pdf
inst/doc/rtPCR.R
inst/doc/rtPCR.Rnw
inst/doc/rtPCR.pdf
inst/extdata
inst/extdata/Experiment1.txt
inst/extdata/Experiment2.txt
inst/extdata/ExperimentWithNTC.txt
inst/extdata/QuantStudio_File1.txt
inst/extdata/QuantStudio_File2.txt
inst/extdata/sampleData.txt
inst/scripts
inst/scripts/ddCt.R
inst/scripts/ddCt.conf
man
man/InputFrame.Rd
man/InputReader-class.Rd
man/QuantStudioFrame.Rd
man/SDMFrame-class.Rd
man/SDMFrame.Rd
man/barploterrbar.Rd
man/ddCtAbsolute.Rd
man/ddCtExpression-class.Rd
man/ddCtExpression-methods.Rd
man/elistWrite-methods.Rd
man/errBarchart-methods.Rd
man/errBarchartParameter-class.Rd
man/getDir.Rd
man/removeNTC-methods.Rd
man/replaceVectorByEquality.Rd
man/write.htmltable.Rd
man/writeSimpleTabCsv.Rd
tests
tests/unit.R
tests/units
tests/units/runit.SDMFrame.R
tests/units/runit.SDMFrame.RData
tests/units/runit.ddCtExpression.R
tests/units/runit.ddCtExpression.RData
vignettes
vignettes/RT-PCR-Script-ddCt.Rnw
vignettes/Result_Experiment1
vignettes/Result_Experiment1/CtResult.pdf
vignettes/Result_Experiment1/HTML
vignettes/Result_Experiment1/HTML/Ct.html
vignettes/Result_Experiment1/HTML/dCt.html
vignettes/Result_Experiment1/HTML/ddCt.html
vignettes/Result_Experiment1/HTML/level.html
vignettes/Result_Experiment1/Tables
vignettes/Result_Experiment1/Tables/Ct_matrix.txt
vignettes/Result_Experiment1/Tables/dCt_matrix.txt
vignettes/Result_Experiment1/Tables/ddCt_matrix.txt
vignettes/Result_Experiment1/Tables/levelPlusError.txt
vignettes/Result_Experiment1/Tables/level_matrix.txt
vignettes/Result_Experiment1/allValues.csv
vignettes/Result_Experiment1/correlationResult.pdf
vignettes/Result_Experiment1/levelResult.pdf
vignettes/rtPCR-usage.Rnw
vignettes/rtPCR.Rnw
vignettes/rtPCR.bib
ddCt documentation built on May 20, 2017, 10:28 p.m.