To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ddCt")
In most cases, you don't need to download the package archive at all.
ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Bioconductor version: 3.0
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ddCt")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ddCt")
| R Script | 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 | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, MicrotitrePlateAssay, Software, qPCR |
| Version | 1.20.0 |
| 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 | |
| LinkingTo | |
| Suggests | RUnit |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ddCt_1.20.0.tar.gz |
| Windows Binary | ddCt_1.20.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ddCt_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | ddCt_1.20.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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