tigre

DOI: 10.18129/B9.bioc.tigre    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see tigre.

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: 3.9

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 helsinki.fi>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tigre")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.38.0
In Bioconductor since	BioC 2.6 (R-2.11) (9.5 years)
License	AGPL-3
Depends	R (>= 2.11.0), BiocGenerics, Biobase
Imports	methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite
LinkingTo
Suggests	drosgenome1.db, puma, lumi, BiocStyle, BiocManager
SystemRequirements
Enhances
URL	https://github.com/ahonkela/tigre
BugReports	https://github.com/ahonkela/tigre/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	tigre_1.38.0.tar.gz
Windows Binary	tigre_1.38.0.zip
Mac OS X 10.11 (El Capitan)	tigre_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tigre
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tigre
Package Short Url	https://bioconductor.org/packages/tigre/
Package Downloads Report	Download Stats