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>
citation("ddCt")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| How to apply the ddCt method | R Script | |
| Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and example | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR |
| Version | 1.40.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]:packages/ddCt |
| Bioc Package Browser | https://code.bioconductor.org/browse/ddCt/ |
| Package Short Url | https://bioconductor.org/packages/ddCt/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |