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

tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tigre")

 

PDF	R Script	tigre Quick Guide
PDF	R Script	tigre User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, GeneExpression, Microarray, Software, TimeCourse, Transcription
Version	1.16.1
In Bioconductor since	BioC 2.6 (R-2.11)
License	AGPL-3
Depends	R (>= 2.11.0), BiocGenerics, Biobase
Imports	methods, BiocGenerics, Biobase, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite
Suggests	puma, drosgenome1.db, annotate, lumi
System Requirements
URL	http://www.bioinf.manchester.ac.uk/resources/tiger/
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	tigre_1.16.1.tar.gz
Windows Binary	tigre_1.16.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	tigre_1.16.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats