tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor | Zendy

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

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tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor

Author(s) -

Antti Honkela,

Pei Gao,

Jonatan Ropponen,

Magnus Rattray,

Neil D. Lawrence

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr057

Subject(s) - bioconductor , inference , computer science , r package , software , ranking (information retrieval) , software package , data mining , artificial intelligence , biology , gene , programming language , genetics

igre 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.

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