tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: Development (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>

To install this package, start R and enter:

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

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

Documentation

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 1.19.0
In Bioconductor since BioC 2.6 (R-2.11)
License AGPL-3
Depends R (>= 2.11.0), BiocGenerics, Biobase
Imports methods, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite
Suggests drosgenome1.db, lumi
System Requirements
URL http://www.bioinf.manchester.ac.uk/resources/tiger/
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source tigre_1.19.0.tar.gz
Windows Binary tigre_1.19.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) tigre_1.19.0.tgz
Mac OS X 10.9 (Mavericks) tigre_1.19.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center