title: tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.
abstract: 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.
  
  
  BACKGROUND
  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.
authors.affiliation: Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland. antti.honkela@hiit.fi
authors.forename: Antti
authors.initials: A
authors.lastname: Honkela
authors.forename: Pei
authors.initials: P
authors.lastname: Gao
authors.forename: Jonatan
authors.initials: J
authors.lastname: Ropponen
authors.forename: Magnus
authors.initials: M
authors.lastname: Rattray
authors.forename: Neil D
authors.initials: ND
authors.lastname: Lawrence
mesh_terms: D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors