tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: 2.7

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 hiit.fi>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("tigre")

To cite this package in a publication, start R and enter:

    citation("tigre")

Documentation

PDF	R Script	tigre Quick Guide
PDF	R Script	tigre User Guide
PDF		tigre-009.pdf
PDF		tigre-010.pdf
PDF		tigre-011.pdf
PDF		Reference Manual

Details

biocViews	Microarray, Bioinformatics, TimeCourse, GeneExpression, Transcription
Depends	R (>= 2.11.0), Biobase
Imports	Biobase, methods, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite
Suggests	puma, drosgenome1.db, annotate
System Requirements
License	AGPL-3
URL	http://www.bioinf.manchester.ac.uk/resources/tiger/
Depends On Me
Imports Me
Suggests Me
Version	1.4.2
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	tigre_1.4.2.tar.gz
Windows Binary	tigre_1.4.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	tigre_1.4.2.tgz
Package Downloads Report	Download Stats

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