Package: DTA 2.59.0

Bjoern Schwalb

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.

Authors:Bjoern Schwalb, Benedikt Zacher, Sebastian Duemcke, Achim Tresch

DTA_2.59.0.tar.gz
DTA_2.59.0.zip(r-4.7)DTA_2.59.0.zip(r-4.6)DTA_2.59.0.zip(r-4.5)
DTA_2.59.0.tgz(r-4.6-any)DTA_2.59.0.tgz(r-4.5-any)
DTA_2.59.0.tar.gz(r-4.7-any)DTA_2.59.0.tar.gz(r-4.6-any)
DTA_2.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DTA/json (API)

# Install 'DTA' in R:

install.packages('DTA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Dm.tnumber - The amount of thymines in the cDNA of each transcript of Drosophila Melanogaster.
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.
Hs.tnumber - The amount of thymines in the cDNA of each transcript of Homo Sapiens.
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.
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.
Sc.tnumber - The amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
Sc.tnumber - The amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
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.
Wt.phenomat - Design of the Saccharomyces Cerevisiae wild-type cDTA experiment from Sun et al.

On BioConductor:DTA-2.59.0(bioc 3.24)DTA-2.58.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray differentialexpression geneexpression transcription

4.78 score 1 packages 7 scripts 21 mentions 9 exports 2 dependencies

Last updated from:6f0c322f9b. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	141
linux-devel-x86_64	NOTE	261
source / vignettes	OK	682
linux-release-x86_64	NOTE	235
macos-release-arm64	NOTE	138
macos-oldrel-arm64	NOTE	150
windows-devel	NOTE	241
windows-release	NOTE	259
windows-oldrel	NOTE	218
wasm-release	OK	85

Exports:DTA.dynamic.estimate DTA.dynamic.generate DTA.estimate DTA.generate DTA.map.it DTA.normalize DTA.phenomat DTA.plot.it tls

Dependencies:LSD scatterplot3d

A guide to Dynamic Transcriptome Analysis (DTA)

Rendered fromDTA.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Dynamic Transcriptome Analysis	DTA-package DTA
The amount of thymines in the cDNA of each transcript of Drosophila Melanogaster.	Dm.tnumber
Mus Musculus and Homo Sapiens DTA experiment from Doelken et al.	Doelken2008
Estimation of synthesis and decay rates upon perturbation	DTA.dynamic.estimate
Simulation of DTA experiments upon perturbation	DTA.dynamic.generate
Estimation of synthesis and decay rates	DTA.estimate
Simulation of DTA experiments	DTA.generate
Mapping function to switch between different identifiers.	DTA.map.it
cDTA normalization procedure.	DTA.normalize
Create a phenomat that suits your experiment.	DTA.phenomat
Plots in any format and any quality	DTA.plot.it
Gene expression profiles of the Homo Sapiens DTA experiment from Doelken et al.	Hs.datamat
Mapping of Homo Sapiens gene and transcript identifiers.	Hs.enst2ensg
Design of the Homo Sapiens DTA experiment from Doelken et al.	Hs.phenomat
Gene identifiers valid for parameter estimation from the Homo Sapiens Doelken et al. DTA experiment.	Hs.reliable
The amount of thymines in the cDNA of each transcript of Homo Sapiens.	Hs.tnumber
Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.	Miller2011
Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.	Miller2011dynamic
Gene expression profiles of the Mus Musculus DTA experiment from Doelken et al.	Mm.datamat
Mapping of Mus Musculus gene and transcript identifiers.	Mm.enst2ensg
Design of the Mus Musculus DTA experiment from Doelken et al.	Mm.phenomat
Gene identifiers valid for parameter estimation from the Mus Musculus Doelken et al. DTA experiment.	Mm.reliable
The amount of thymines in the cDNA of each transcript of Mus Musculus.	Mm.tnumber
Design of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) cDTA experiment from Sun et al.	Pol.phenomat
Gene expression profiles of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.	Raw.datamat
Mapping of SaccharomycesCerevisiae Affymetrix Yeast 2.0 and gene identifiers.	Sc.affy2ensg
Gene expression profiles of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.	Sc.datamat
Gene expression profiles of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.	Sc.datamat.dynamic
Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.	Sc.ensg.reliable
Design of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.	Sc.phenomat
Design of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.	Sc.phenomat.dynamic
Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. wild-type DTA experiment.	Sc.reliable
Gene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. salt stress DTA experiment.	Sc.reliable.dynamic
Ribosome biogenesis genes.	Sc.ribig.ensg
Ribosomal protein genes.	Sc.rpg.ensg
ISA stress module.	Sc.stress.ensg
Transcription factors.	Sc.tf.ensg
The amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.	Sc.tnumber
Gene identifiers valid for cDTA normalization from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.	Sp.affy.reliable
The amount of thymines in the cDNA of each transcript of Schizosaccharomyces Pombe.	Sp.tnumber
Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.	Sun2011
Weighted Total Least Square Regression.	tls
Design of the Saccharomyces Cerevisiae wild-type cDTA experiment from Sun et al.	Wt.phenomat