ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Bioconductor version: 3.23 · Package version: 1.68.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ddCt")Details
| Maintainer | Jitao David Zhang <jitao_david.zhang@roche.com> |
| Author | Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt |
| License | LGPL-3 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR |
| Package Short Url | https://bioconductor.org/packages/ddCt/ |
Citation
From within R, enter citation("ddCt"):
Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt. ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR). doi:10.18129/B9.bioc.ddCt, R package version 1.68.0, https://bioconductor.org/packages/ddCt.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Analyse RT-PCR data with the end-to-end script in ddCt package
- How to apply the ddCt method
- Introduction to the ddCt method for qRT-PCR data analysis: background, algorithm and example
Download
Follow the installation instructions to use this package in your R session.
| Source package | ddCt_1.68.0.tar.gz |
| Windows binary (x86_64) | ddCt_1.68.0.zip |
| macOS binary (arm64) | ddCt_1.68.0.tgz |
| macOS binary (x86_64) | ddCt_1.68.0.tgz |
Dependencies
Depends: R (>= 2.3.0), methods
Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics
Suggests: testthat (>= 3.0.0), RUnit