DOI: 10.18129/B9.bioc.tigre    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see tigre.

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: 3.12

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.

Author: Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence

Maintainer: Antti Honkela <antti.honkela at helsinki.fi>

Citation (from within R, enter citation("tigre")):


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PDF R Script tigre User Guide
PDF   Reference Manual
Text   NEWS


biocViews Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription
Version 1.44.0
In Bioconductor since BioC 2.6 (R-2.11) (11 years)
License AGPL-3
Depends R (>= 2.11.0), BiocGenerics, Biobase
Imports methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite
Suggests drosgenome1.db, puma, lumi, BiocStyle, BiocManager
URL https://github.com/ahonkela/tigre
BugReports https://github.com/ahonkela/tigre/issues
Depends On Me
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Source Package tigre_1.44.0.tar.gz
Windows Binary tigre_1.44.0.zip (32- & 64-bit)
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Source Repository git clone https://git.bioconductor.org/packages/tigre
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tigre
Package Short Url https://bioconductor.org/packages/tigre/
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