Dynamic Transcriptome Analysis

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Documentation for package ‘DTA’ version 2.55.0

• 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.