ddCt
This is the released version of ddCt; for the devel version, see ddCt.
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.68.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 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 | testthat (>= 3.0.0), 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_1.68.0.tar.gz |
| Windows Binary (x86_64) | ddCt_1.68.0.zip |
| macOS Binary (big-sur-x86_64) | ddCt_1.68.0.tgz |
| macOS Binary (sonoma-arm64) | ddCt_1.68.0.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/ |
| Package Downloads Report | Download Stats |