tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor

[edit]

Antti Honkela, University of Helsinki
Pei Gao, Peking University
Jonatan Ropponen
Magnus Rattray, University of Manchester
Neil D. Lawrence, University of Sheffield

Bioinformatics 27, pp 1026-1027

Related Material

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


@Article{honkela-tigre11,
  title = 	 {tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor},
  journal =  	 {Bioinformatics},
  author = 	 {Antti Honkela and Pei Gao and Jonatan Ropponen and Magnus Rattray and Neil D. Lawrence},
  pages = 	 {1026},
  year = 	 {2011},
  volume = 	 {27},
  month = 	 {00},
  edit = 	 {https://github.com/lawrennd//publications/edit/gh-pages/_posts/2011-01-01-honkela-tigre11.md},
  url =  	 {http://inverseprobability.com/publications/honkela-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},
  key = 	 {Honkela-tigre11},
  doi = 	 {10.1093/bioinformatics/btr057},
  linkpdf = 	 {http://bioinformatics.oxfordjournals.org/content/27/7/1026.full.pdf+html},
  OPTgroup = 	 {}
 

}
%T tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor
%A Antti Honkela and Pei Gao and Jonatan Ropponen and Magnus Rattray and Neil D. Lawrence
%B 
%C Bioinformatics
%D 
%F honkela-tigre11
%J Bioinformatics	
%P 1026--1027
%R 10.1093/bioinformatics/btr057
%U http://inverseprobability.com/publications/honkela-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
TY  - CPAPER
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
PY  - 2011/01/01
DA  - 2011/01/01	
ID  - honkela-tigre11	
SP  - 1026
EP  - 1027
DO  - 10.1093/bioinformatics/btr057
L1  - http://bioinformatics.oxfordjournals.org/content/27/7/1026.full.pdf+html
UR  - http://inverseprobability.com/publications/honkela-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  -

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