DTA: Dynamic Transcriptome Analysis

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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.

Author
Bjoern Schwalb, Benedikt Zacher, Sebastian Duemcke, Achim Tresch
Date of publication
None
Maintainer
Bjoern Schwalb <schwalb@lmb.uni-muenchen.de>
License
Artistic-2.0
Version
2.20.0

View on Bioconductor

Man pages

Dm.tnumber
The amount of thymines in the cDNA of each transcript of...
Doelken2008
Mus Musculus and Homo Sapiens DTA experiment from Doelken et...
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-package
Dynamic Transcriptome Analysis
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...
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...
Hs.tnumber
The amount of thymines in the cDNA of each transcript of Homo...
Miller2011
Saccharomyces Cerevisiae wild-type DTA experiment from Miller...
Miller2011dynamic
Saccharomyces Cerevisiae salt stress DTA experiment from...
Mm.datamat
Gene expression profiles of the Mus Musculus DTA experiment...
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...
Mm.tnumber
The amount of thymines in the cDNA of each transcript of Mus...
Pol.phenomat
Design of the Saccharomyces Cerevisiae rpb1-N488D (Slow...
Raw.datamat
Gene expression profiles of the Saccharomyces Cerevisiae...
Sc.affy2ensg
Mapping of SaccharomycesCerevisiae Affymetrix Yeast 2.0 and...
Sc.datamat
Gene expression profiles of the Saccharomyces Cerevisiae...
Sc.datamat.dynamic
Gene expression profiles of the Saccharomyces Cerevisiae salt...
Sc.ensg.reliable
Gene identifiers valid for parameter estimation from the...
Sc.phenomat
Design of the Saccharomyces Cerevisiae wild-type DTA...
Sc.phenomat.dynamic
Design of the Saccharomyces Cerevisiae salt stress DTA...
Sc.reliable
Gene identifiers valid for parameter estimation from the...
Sc.reliable.dynamic
Gene identifiers valid for parameter estimation from the...
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...
Sp.affy.reliable
Gene identifiers valid for cDTA normalization from the...
Sp.tnumber
The amount of thymines in the cDNA of each transcript of...
Sun2011
Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and...
tls
Weighted Total Least Square Regression.
Wt.phenomat
Design of the Saccharomyces Cerevisiae wild-type cDTA...

Files in this package

DTA/DESCRIPTION
DTA/NAMESPACE
DTA/R
DTA/R/DTA.dynamic.estimate.r
DTA/R/DTA.dynamic.generate.R
DTA/R/DTA.estimate.r
DTA/R/DTA.generate.r
DTA/R/DTA.map.it.R
DTA/R/DTA.normalize.R
DTA/R/DTA.phenomat.R
DTA/R/DTA.plots.R
DTA/R/DTA.utilities.R
DTA/R/wtls.R
DTA/build
DTA/build/vignette.rds
DTA/data
DTA/data/Dm.tnumber.RData
DTA/data/Doelken2008.RData
DTA/data/Hs.tnumber.RData
DTA/data/Miller2011.RData
DTA/data/Miller2011dynamic.RData
DTA/data/Mm.tnumber.RData
DTA/data/Sc.ribig.ensg.RData
DTA/data/Sc.rpg.ensg.RData
DTA/data/Sc.stress.ensg.RData
DTA/data/Sc.tf.ensg.RData
DTA/data/Sc.tnumber.RData
DTA/data/Sp.tnumber.RData
DTA/data/Sun2011.RData
DTA/data/datalist
DTA/inst
DTA/inst/doc
DTA/inst/doc/DTA.R
DTA/inst/doc/DTA.Rnw
DTA/inst/doc/DTA.pdf
DTA/man
DTA/man/DTA-package.Rd
DTA/man/DTA.dynamic.estimate.Rd
DTA/man/DTA.dynamic.generate.Rd
DTA/man/DTA.estimate.Rd
DTA/man/DTA.generate.Rd
DTA/man/DTA.map.it.Rd
DTA/man/DTA.normalize.Rd
DTA/man/DTA.phenomat.Rd
DTA/man/DTA.plot.it.Rd
DTA/man/Dm.tnumber.Rd
DTA/man/Doelken2008.Rd
DTA/man/Hs.datamat.Rd
DTA/man/Hs.enst2ensg.Rd
DTA/man/Hs.phenomat.Rd
DTA/man/Hs.reliable.Rd
DTA/man/Hs.tnumber.Rd
DTA/man/Miller2011.Rd
DTA/man/Miller2011dynamic.Rd
DTA/man/Mm.datamat.Rd
DTA/man/Mm.enst2ensg.Rd
DTA/man/Mm.phenomat.Rd
DTA/man/Mm.reliable.Rd
DTA/man/Mm.tnumber.Rd
DTA/man/Pol.phenomat.Rd
DTA/man/Raw.datamat.Rd
DTA/man/Sc.affy2ensg.Rd
DTA/man/Sc.datamat.Rd
DTA/man/Sc.datamat.dynamic.Rd
DTA/man/Sc.ensg.reliable.Rd
DTA/man/Sc.phenomat.Rd
DTA/man/Sc.phenomat.dynamic.Rd
DTA/man/Sc.reliable.Rd
DTA/man/Sc.reliable.dynamic.Rd
DTA/man/Sc.ribig.ensg.Rd
DTA/man/Sc.rpg.ensg.Rd
DTA/man/Sc.stress.ensg.Rd
DTA/man/Sc.tf.ensg.Rd
DTA/man/Sc.tnumber.Rd
DTA/man/Sp.affy.reliable.Rd
DTA/man/Sp.tnumber.Rd
DTA/man/Sun2011.Rd
DTA/man/Wt.phenomat.Rd
DTA/man/tls.Rd
DTA/vignettes
DTA/vignettes/DTA.Rnw
DTA/vignettes/bibliography.bib