DTA: Dynamic Transcriptome Analysis

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DTA")
AuthorBjoern Schwalb, Benedikt Zacher, Sebastian Duemcke, Achim Tresch
Bioconductor views DifferentialExpression GeneExpression Microarray Transcription
Date of publicationNone
MaintainerBjoern Schwalb <schwalb@lmb.uni-muenchen.de>
LicenseArtistic-2.0
Version2.20.0

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...

Functions

Dm.tnumber Man page
Doelken2008 Man page
DTA Man page
DTA.dynamic.estimate Man page
DTA.dynamic.generate Man page
DTA.estimate Man page
DTA.generate Man page
DTA.map.it Man page
DTA.normalize Man page
DTA-package Man page
DTA.phenomat Man page
DTA.plot.it Man page
Hs.datamat Man page
Hs.enst2ensg Man page
Hs.phenomat Man page
Hs.reliable Man page
Hs.tnumber Man page
Miller2011 Man page
Miller2011dynamic Man page
Mm.datamat Man page
Mm.enst2ensg Man page
Mm.phenomat Man page
Mm.reliable Man page
Mm.tnumber Man page
Pol.phenomat Man page
Raw.datamat Man page
Sc.affy2ensg Man page
Sc.datamat Man page
Sc.datamat.dynamic Man page
Sc.ensg.reliable Man page
Sc.phenomat Man page
Sc.phenomat.dynamic Man page
Sc.reliable Man page
Sc.reliable.dynamic Man page
Sc.ribig.ensg Man page
Sc.rpg.ensg Man page
Sc.stress.ensg Man page
Sc.tf.ensg Man page
Sc.tnumber Man page
Sp.affy.reliable Man page
Sp.tnumber Man page
Sun2011 Man page
tls Man page
Wt.phenomat Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.