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 <email@example.com>|
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