ddCt

DOI: 10.18129/B9.bioc.ddCt    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ddCt.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ddCt")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ddCt")

 

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	DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR
Version	1.40.0
In Bioconductor since	BioC 2.5 (R-2.10) (10 years)
License	LGPL-3
Depends	R (>= 2.3.0), methods
Imports	Biobase(>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics
LinkingTo
Suggests	RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ddCt_1.40.0.tar.gz
Windows Binary	ddCt_1.40.0.zip
Mac OS X 10.11 (El Capitan)	ddCt_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ddCt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ddCt
Package Short Url	https://bioconductor.org/packages/ddCt/
Package Downloads Report	Download Stats