tigre: Transcription Factor Inference through Gaussian Process Reconstruction of Expression for Bioconductor

Antti Honkela; Pei Gao; Jonatan Ropponen; Magnus Rattray; Neil D. Lawrence

doi:10.1093/bioinformatics/btr057

edit

Back to publications

tigre: Transcription Factor Inference through Gaussian Process Reconstruction of Expression for Bioconductor

Antti Honkela, Pei Gao, Jonatan Ropponen, Magnus Rattray, Neil D. Lawrence

Bioinformatics, 27:1026-1027, 2011.

Abstract

Summary: tigre is an R/Bioconductor package for inference of transcription factor activity and ranking candidate target genes from gene expression time series. The underlying methodology is based on Gaussian process inference on a differential equation model that allows the use of short, unevenly sampled, time series. The method has been designed with efficient parallel implementation in mind, and the package supports parallel operation even without additional software.

Availability: The tigre package is included in Bioconductor since release 2.6 for R 2.11. The package and a user’s guide are available at http://www.bioconductor.org.

Contact: antti.honkela@hiit.fi; m.rattray@sheffield.ac.uk; n.lawrence@dcs.shef.ac.uk

Links

Cite this Paper

BibTeX


@Article{Honkela-tigre11,
  title = 	 {tigre: Transcription Factor Inference through {G}aussian Process Reconstruction of Expression for Bioconductor},
  author = 	 {Honkela, Antti and Gao, Pei and Ropponen, Jonatan and Rattray, Magnus and Lawrence, Neil D.},
  journal =      {Bioinformatics},
  pages = 	 {1026--1027},
  year = 	 {2011},
  volume = 	 {27},
  doi = 	 {10.1093/bioinformatics/btr057},
  pdf = 	 {http://bioinformatics.oxfordjournals.org/content/27/7/1026.full.pdf+html},
  url = 	 {/publications/transcription-factor-inference-through-gaussian-process-reconstruction-of-expression-for-bioconductor.mdhonkela-tigre11.html},
  abstract = 	 {**Summary**: tigre is an R/Bioconductor package for inference of transcription
factor activity and ranking candidate target genes from gene expression time series.
The underlying methodology is based on Gaussian process inference on a differential
equation model that allows the use of short, unevenly sampled, time series. The
method has been designed with efficient parallel implementation in mind, and the
package supports parallel operation even without additional software.

**Availability**: The tigre package is included in Bioconductor since release 2.6 for R 2.11. The
package and a user's guide are available at http://www.bioconductor.org.

**Contact**: antti.honkela@hiit.fi; m.rattray@sheffield.ac.uk; n.lawrence@dcs.shef.ac.uk
}
}

Endnote

%0 Journal Article
%T tigre: Transcription Factor Inference through Gaussian Process Reconstruction of Expression for Bioconductor
%A Antti Honkela
%A Pei Gao
%A Jonatan Ropponen
%A Magnus Rattray
%A Neil D. Lawrence
%J Bioinformatics
%D 2011	
%F Honkela-tigre11
%P 1026--1027
%R 10.1093/bioinformatics/btr057
%U /publications/transcription-factor-inference-through-gaussian-process-reconstruction-of-expression-for-bioconductor.mdhonkela-tigre11.html
%V 27
%X **Summary**: tigre is an R/Bioconductor package for inference of transcription
factor activity and ranking candidate target genes from gene expression time series.
The underlying methodology is based on Gaussian process inference on a differential
equation model that allows the use of short, unevenly sampled, time series. The
method has been designed with efficient parallel implementation in mind, and the
package supports parallel operation even without additional software.

**Availability**: The tigre package is included in Bioconductor since release 2.6 for R 2.11. The
package and a user's guide are available at http://www.bioconductor.org.

**Contact**: antti.honkela@hiit.fi; m.rattray@sheffield.ac.uk; n.lawrence@dcs.shef.ac.uk

RIS


TY  - JOUR
TI  - tigre: Transcription Factor Inference through Gaussian Process Reconstruction of Expression for Bioconductor
AU  - Antti Honkela
AU  - Pei Gao
AU  - Jonatan Ropponen
AU  - Magnus Rattray
AU  - Neil D. Lawrence
DA  - 2011/02/07	
ID  - Honkela-tigre11
VL  - 27
SP  - 1026
EP  - 1027
DO  - 10.1093/bioinformatics/btr057
L1  - http://bioinformatics.oxfordjournals.org/content/27/7/1026.full.pdf+html
UR  - /publications/transcription-factor-inference-through-gaussian-process-reconstruction-of-expression-for-bioconductor.mdhonkela-tigre11.html
AB  - **Summary**: tigre is an R/Bioconductor package for inference of transcription
factor activity and ranking candidate target genes from gene expression time series.
The underlying methodology is based on Gaussian process inference on a differential
equation model that allows the use of short, unevenly sampled, time series. The
method has been designed with efficient parallel implementation in mind, and the
package supports parallel operation even without additional software.

**Availability**: The tigre package is included in Bioconductor since release 2.6 for R 2.11. The
package and a user's guide are available at http://www.bioconductor.org.

**Contact**: antti.honkela@hiit.fi; m.rattray@sheffield.ac.uk; n.lawrence@dcs.shef.ac.uk

ER  -

APA


Honkela, A., Gao, P., Ropponen, J., Rattray, M. & Lawrence, N.D.. (2011). tigre: Transcription Factor Inference through Gaussian Process Reconstruction of Expression for Bioconductor. Bioinformatics 27:1026-1027 doi:10.1093/bioinformatics/btr057 Available from /publications/transcription-factor-inference-through-gaussian-process-reconstruction-of-expression-for-bioconductor.mdhonkela-tigre11.html.