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>

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 1.6.2
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source tigre_1.6.2.tar.gz
Windows Binary tigre_1.6.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary tigre_1.6.2.tgz
Package Downloads Report Download Stats

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