tigre
Transcription factor Inference through Gaussian process Reconstruction of Expression
Bioconductor version: Release (3.20)
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("tigre")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, GeneRegulation, Microarray, NetworkInference, Software, TimeCourse, Transcription |
| Version | 1.60.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14.5 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 |
See More
| Suggests | drosgenome1.db, puma, lumi, BiocStyle, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tigre_1.60.0.tar.gz |
| Windows Binary (x86_64) | tigre_1.60.0.zip |
| macOS Binary (x86_64) | tigre_1.60.0.tgz |
| macOS Binary (arm64) | tigre_1.59.0.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 |