ddCt

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

Bioconductor version: Release (2.14)

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 <jitao_david.zhang at roche.com>

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
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR
Version 1.18.0
In Bioconductor since BioC 2.5 (R-2.10)
License LGPL-3
Depends R (>= 2.3.0), Biobase(>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods
Imports
Suggests RUnit
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ddCt_1.18.0.tar.gz
Windows Binary ddCt_1.18.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ddCt_1.18.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center