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DTA (version 2.18.0)

Dynamic Transcriptome Analysis

Description

Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.

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Version

Version

2.18.0

License

Artistic-2.0

Maintainer

Bjoern Schwalb

Last Published

February 15th, 2017

Functions in DTA (2.18.0)

Mapping function to switch between different identifiers.

Simulation of DTA experiments

Plots in any format and any quality

Sc.ensg.reliable

Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.

Mapping of SaccharomycesCerevisiae Affymetrix Yeast 2.0 and gene identifiers.

Design of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) cDTA experiment from Sun et al.

Transcription factors.

Estimation of synthesis and decay rates

Gene expression profiles of the Homo Sapiens DTA experiment from Doelken et al.

The amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.

Ribosomal protein genes.

Weighted Total Least Square Regression.

The amount of thymines in the cDNA of each transcript of Drosophila Melanogaster.

Design of the Homo Sapiens DTA experiment from Doelken et al.

DTA.dynamic.generate

Simulation of DTA experiments upon perturbation

Create a phenomat that suits your experiment.

Sc.phenomat.dynamic

Design of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.

Miller2011dynamic

Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.

Dynamic Transcriptome Analysis

Gene expression profiles of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.

Gene identifiers valid for parameter estimation from the Mus Musculus Doelken et al. DTA experiment.

Mapping of Homo Sapiens gene and transcript identifiers.

Sc.datamat.dynamic

Gene expression profiles of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.

Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. wild-type DTA experiment.

The amount of thymines in the cDNA of each transcript of Mus Musculus.

The amount of thymines in the cDNA of each transcript of Schizosaccharomyces Pombe.

DTA.dynamic.estimate

Estimation of synthesis and decay rates upon perturbation

The amount of thymines in the cDNA of each transcript of Homo Sapiens.

Design of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.

Sc.reliable.dynamic

Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. salt stress DTA experiment.

Gene expression profiles of the Mus Musculus DTA experiment from Doelken et al.

Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.

Sp.affy.reliable

Gene identifiers valid for cDTA normalization from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.

Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.

Gene identifiers valid for parameter estimation from the Homo Sapiens Doelken et al. DTA experiment.

Design of the Saccharomyces Cerevisiae wild-type cDTA experiment from Sun et al.

cDTA normalization procedure.

Mus Musculus and Homo Sapiens DTA experiment from Doelken et al.

Mapping of Mus Musculus gene and transcript identifiers.

Design of the Mus Musculus DTA experiment from Doelken et al.

ISA stress module.

Ribosome biogenesis genes.

Gene expression profiles of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.