ddCt

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

Bioconductor version: 2.8

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

Maintainer: Jitao David Zhang <j.zhang at dkfz.de>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ddCt")

To cite this package in a publication, start R and enter:

    citation("ddCt")

Documentation

PDF R Script Analyse RT-PCR data with the end-to-end script in ddCt package
PDF R Script How to apply the ddCt method
PDF R Script Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and example
PDF   Reference Manual

Details

biocViews GeneExpression, DifferentialExpression, RT-PCR
Depends R (>= 2.3.0), Biobase(>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods
Imports
Suggests
System Requirements
License LGPL-3
URL
Depends On Me
Imports Me
Suggests Me
Version 1.6.0
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source ddCt_1.6.0.tar.gz
Windows Binary ddCt_1.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary ddCt_1.6.0.tgz
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