tigre

This is the development version of tigre; for the stable release version, see tigre.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor version: Development (3.24)

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")):

Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence. tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression. doi:10.18129/B9.bioc.tigre, R package version 1.67.0, https://bioconductor.org/packages/tigre.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription
Version	1.67.0
In Bioconductor since	BioC 2.6 (R-2.11) (16.5 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

Suggests	drosgenome1.db, puma, lumi, BiocStyle, BiocManager
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	tigre_1.67.0.tar.gz
Windows Binary (x86_64)	tigre_1.67.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	tigre_1.67.0.tgz
macOS Binary (sonoma-arm64)	tigre_1.67.0.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