To install this package, start R and enter:

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

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

tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: Release (3.0)

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:

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 Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription
Version 1.20.0
In Bioconductor since BioC 2.6 (R-2.11)
License AGPL-3
Depends R (>= 2.11.0), BiocGenerics, Biobase
Imports methods, AnnotationDbi, gplots, graphics, stats, utils, annotate, DBI, RSQLite
Suggests drosgenome1.db, puma, lumi, BiocStyle
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_1.20.0.tar.gz
Windows Binary tigre_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) tigre_1.20.0.tgz
Mac OS X 10.9 (Mavericks) tigre_1.20.0.tgz
Browse/checkout source (username/password: readonly)
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