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TTCA
View on CRAN: Click
here
Download and install TTCA package within the R console
Install from CRAN:
install.packages("TTCA")
Install from Github:
library("remotes")
install_github("cran/TTCA")
Install by package version:
library("remotes")
install_version("TTCA", "0.1.1")
Attach the package and use:
library("TTCA")
Maintained by
Marco Albrecht
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-06-20
Latest Update: 2017-01-29
Description:
The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)<doi:10.1186/s12859-016-1440-8>.
How to cite:
Marco Albrecht (2016). TTCA: Transcript Time Course Analysis. R package version 0.1.1, https://cran.r-project.org/web/packages/TTCA
Previous versions and publish date:
0.1.0 (2016-06-20 08:19)
Other packages that cited TTCA R package
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imports, suggests or enhances
Functions, R codes and Examples using
the TTCA R package
Some associated functions: Control . EGF . TTCA . annot . annotation .
Some associated R codes: TTCA.R . Full TTCA package functions and examples
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