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ddCt

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("ddCt")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
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 R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR
Version 1.58.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)
License LGPL-3
Depends R (>= 2.3.0), methods
Imports Biobase(>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics
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Suggests testthat (>= 3.0.0), RUnit
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Package Archives

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

Source Package ddCt_1.58.0.tar.gz
Windows Binary ddCt_1.58.0.zip
macOS Binary (x86_64) ddCt_1.58.0.tgz
macOS Binary (arm64) ddCt_1.58.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ddCt
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ddCt
Bioc Package Browser https://code.bioconductor.org/browse/ddCt/
Package Short Url https://bioconductor.org/packages/ddCt/
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