# Dynamic Transcriptome Analysis

## Documentation for package ‘DTA’ version 2.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

DTA-package | Dynamic Transcriptome Analysis
Dm.tnumber | The amount of thymines in the cDNA of each transcript of Drosophila Melanogaster.
Doelken2008 | Mus Musculus and Homo Sapiens DTA experiment from Doelken et al.
DTA | Dynamic Transcriptome Analysis
DTA.dynamic.estimate | Estimation of synthesis and decay rates upon perturbation
DTA.dynamic.generate | Simulation of DTA experiments upon perturbation
DTA.estimate | Estimation of synthesis and decay rates
DTA.generate | Simulation of DTA experiments
DTA.map.it | Mapping function to switch between different identifiers.
DTA.normalize | cDTA normalization procedure.
DTA.phenomat | Create a phenomat that suits your experiment.
DTA.plot.it | Plots in any format and any quality
Hs.datamat | Gene expression profiles of the Homo Sapiens DTA experiment from Doelken et al.
Hs.enst2ensg | Mapping of Homo Sapiens gene and transcript identifiers.
Hs.phenomat | Design of the Homo Sapiens DTA experiment from Doelken et al.
Hs.reliable | Gene identifiers valid for parameter estimation from the Homo Sapiens Doelken et al. DTA experiment.
Hs.tnumber | The amount of thymines in the cDNA of each transcript of Homo Sapiens.
Miller2011 | Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.
Miller2011dynamic | Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.
Mm.datamat | Gene expression profiles of the Mus Musculus DTA experiment from Doelken et al.
Mm.enst2ensg | Mapping of Mus Musculus gene and transcript identifiers.
Mm.phenomat | Design of the Mus Musculus DTA experiment from Doelken et al.
Mm.reliable | Gene identifiers valid for parameter estimation from the Mus Musculus Doelken et al. DTA experiment.
Mm.tnumber | The amount of thymines in the cDNA of each transcript of Mus Musculus.
Pol.phenomat | Design of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) cDTA experiment from Sun et al.
Raw.datamat | Gene expression profiles of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.
Sc.affy2ensg | Mapping of SaccharomycesCerevisiae Affymetrix Yeast 2.0 and gene identifiers.
Sc.datamat | Gene expression profiles of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.
Sc.datamat.dynamic | Gene expression profiles of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.
Sc.ensg.reliable | Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.
Sc.phenomat | Design of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.
Sc.phenomat.dynamic | Design of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.
Sc.reliable | Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. wild-type DTA experiment.
Sc.reliable.dynamic | Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. salt stress DTA experiment.
Sc.ribig.ensg | Ribosome biogenesis genes.
Sc.rpg.ensg | Ribosomal protein genes.
Sc.stress.ensg | ISA stress module.
Sc.tf.ensg | Transcription factors.
Sc.tnumber | The amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
Sp.affy.reliable | Gene identifiers valid for cDTA normalization from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.
Sp.tnumber | The amount of thymines in the cDNA of each transcript of Schizosaccharomyces Pombe.
Sun2011 | Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.
tls | Weighted Total Least Square Regression.
Wt.phenomat | Design of the Saccharomyces Cerevisiae wild-type cDTA experiment from Sun et al.