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

Antti HonkelaPei Gao, Jonatan Ropponen, Magnus RattrayNeil D. Lawrence
,  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
@InProceedings{pmlr-v-honkela-tigre11, title = {tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor}, author = {Antti Honkela and Pei Gao and Jonatan Ropponen and Magnus Rattray and Neil D. Lawrence}, pages = {1026--1027}, year = {}, editor = {}, volume = {27}, 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} }
Endnote
%0 Conference Paper %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 %B %C Proceedings of Machine Learning Research %D %E %F pmlr-v-honkela-tigre11 %I PMLR %J Proceedings of Machine Learning Research %P 1026--1027 %R 10.1093/bioinformatics/btr057 %U http://inverseprobability.com %V %W PMLR %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 - 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 BT - PY - DA - ED - ID - pmlr-v-honkela-tigre11 PB - PMLR SP - 1026 DP - PMLR EP - 1027 DO - 10.1093/bioinformatics/btr057 L1 - 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 -
APA
Honkela, A., Gao, P., Ropponen, J., Rattray, M. & Lawrence, N.D.. (). tigre: Transcription factor inference through Gaussian process reconstruction of expression for Bioconductor. , in PMLR :1026-1027

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