Dynamic Transcriptome Analysis


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Documentation for package ‘DTA’ version 2.40.0

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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.