To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tigre")

In most cases, you don't need to download the package archive at all.

tigre

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see tigre.

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: 2.8

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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		tigre-009.pdf
PDF		tigre-010.pdf
PDF		tigre-011.pdf
PDF		tigre.pdf
PDF		tigre_quick.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, GeneExpression, Microarray, Software, TimeCourse, Transcription
Version	1.6.2
In Bioconductor since	BioC 2.6 (R-2.11) (6 years)
License	AGPL-3
Depends	R (>= 2.11.0), Biobase
Imports	Biobase, methods, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite
LinkingTo
Suggests	puma, drosgenome1.db, annotate
SystemRequirements
Enhances
URL	http://www.bioinf.manchester.ac.uk/resources/tiger/
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	tigre_1.6.2.tar.gz
Windows Binary	tigre_1.6.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/tigre/tree/release-2.8
Package Short Url	http://bioconductor.org/packages/tigre/
Package Downloads Report	Download Stats