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

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 = {http://inverseprobability.com/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 http://inverseprobability.com/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 - http://inverseprobability.com/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 http://inverseprobability.com/publications/transcription-factor-inference-through-gaussian-process-reconstruction-of-expression-for-bioconductor.mdhonkela-tigre11.html.

Related Material