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

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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.

Author
Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt
Date of publication
None
Maintainer
Jitao David Zhang <jitao_david.zhang@roche.com>
License
LGPL-3
Version
1.30.0

View on Bioconductor

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

Files in this package

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