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tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
tigre User Guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription
Version 1.56.0
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License AGPL-3
Depends R (>= 2.11.0), BiocGenerics, Biobase
Imports methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite
System Requirements
URL https://github.com/ahonkela/tigre
Bug Reports https://github.com/ahonkela/tigre/issues
See More
Suggests drosgenome1.db, puma, lumi, BiocStyle, BiocManager
Linking To
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Build Report Build Report

Package Archives

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

Source Package tigre_1.56.0.tar.gz
Windows Binary tigre_1.56.0.zip
macOS Binary (x86_64) tigre_1.56.0.tgz
macOS Binary (arm64) tigre_1.56.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tigre
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tigre
Bioc Package Browser https://code.bioconductor.org/browse/tigre/
Package Short Url https://bioconductor.org/packages/tigre/
Package Downloads Report Download Stats