# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "tigre" in publications use:'
type: software
license: AGPL-3.0-only
title: 'tigre: Transcription factor Inference through Gaussian process Reconstruction
  of Expression'
version: 1.59.0
doi: 10.1093/bioinformatics/btr057
identifiers:
- type: doi
  value: 10.32614/CRAN.package.tigre
abstract: The tigre package implements our methodology of Gaussian process differential
  equation models for analysis of gene expression time series from single input motif
  networks. The package can be used for inferring unobserved transcription factor
  (TF) protein concentrations from expression measurements of known target genes,
  or for ranking candidate targets of a TF.
authors:
- family-names: Honkela
  given-names: Antti
  email: antti.honkela@helsinki.fi
- family-names: Gao
  given-names: Pei
- family-names: Ropponen
  given-names: Jonatan
- family-names: Matikainen
  given-names: Miika-Petteri
- family-names: Rattray
  given-names: Magnus
- family-names: Lawrence
  given-names: Neil D.
preferred-citation:
  type: article
  title: 'tigre: Transcription factor Inference through Gaussian process Reconstruction
    of Expression for Bioconductor'
  authors:
  - family-names: Honkela
    given-names: Antti
    email: antti.honkela@helsinki.fi
  - family-names: Gao
    given-names: Pei
  - family-names: Ropponen
    given-names: Jonatan
  - family-names: Rattray
    given-names: Magnus
  - family-names: Lawrence
    given-names: Neil D
  journal: Bioinformatics
  year: '2011'
  volume: '27'
  issue: '7'
  doi: 10.1093/bioinformatics/btr057
  url: http://dx.doi.org/10.1093/bioinformatics/btr057
  start: 1026-1027
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ahonkela/tigre
commit: 59d8655c9ffe35fc8958564da49fbfa7451b13d7
url: https://github.com/ahonkela/tigre
date-released: '2021-08-04'
contact:
- family-names: Honkela
  given-names: Antti
  email: antti.honkela@helsinki.fi
references:
- type: article
  title: Model-based method for transcription factor target identification with limited
    data
  authors:
  - family-names: Honkela
    given-names: Antti
  - family-names: Girardot
    given-names: Charles
  - family-names: Gustafson
    given-names: E. Hilary
  - family-names: Liu
    given-names: Ya-Hsin
  - family-names: Furlong
    given-names: Eileen E.M.
  - family-names: Lawrence
    given-names: Neil D.
  - family-names: Rattray
    given-names: Magnus
  journal: Proc Natl Acad Sci USA
  year: '2010'
  volume: '107'
  issue: '17'
  doi: 10.1073/pnas.0914285107
  url: http://dx.doi.org/10.1073/pnas.0914285107
  start: 7793-7798
- type: article
  title: 'Gaussian process modelling of latent chemical species: applications to inferring
    transcription factor activities'
  authors:
  - family-names: Gao
    given-names: Pei
  - family-names: Honkela
    given-names: Antti
  - family-names: Rattray
    given-names: Magnus
  - family-names: Lawrence
    given-names: Neil D
  journal: Bioinformatics
  year: '2008'
  volume: '24'
  issue: '16'
  doi: 10.1093/bioinformatics/btn278
  start: i70-i75
- type: generic
  title: Modelling transcriptional regulation using Gaussian processes
  authors:
  - family-names: Lawrence
    given-names: Neil D.
  - family-names: Sanguinetti
    given-names: Guido
  - family-names: Rattray
    given-names: Magnus
  collection-title: Advances in Neural Information Processing Systems
  collection-type: collection
  publisher:
    name: MIT Press
    address: Cambridge, MA
  year: '2007'
  editors:
  - family-names: Sch\"olkopf
    given-names: B.
  - family-names: Platt
    given-names: J. C.
  - family-names: Hofmann
    given-names: T.
  volume: '19'
  start: 785-792