TraRe

DOI: 10.18129/B9.bioc.TraRe  

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TraRe.

Transcriptional Rewiring

Bioconductor version: 3.16

TraRe (Transcriptional Rewiring) is an R package which contains the necessary tools to carry out several functions. Identification of module-based gene regulatory networks (GRN); score-based classification of these modules via a rewiring test; visualization of rewired modules to analyze condition-based GRN deregulation and drop out genes recovering via cliques methodology. For each tool, an html report can be generated containing useful information about the generated GRN and statistical data about the performed tests. These tools have been developed considering sequenced data (RNA-Seq).

Author: Jesus De La Fuente Cedeño [aut, cre, cph] , Mikel Hernaez [aut, cph, ths] , Charles Blatti [aut, cph]

Maintainer: Jesus De La Fuente Cedeño <jdelafuentec at unav.es>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("TraRe")

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("TraRe")

 

HTML	R Script	TraRe: Identification of conditions dependant Gene Regulatory Networks
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, Classification, GeneRegulation, GeneTarget, GraphAndNetwork, RNASeq, Software
Version	1.5.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	hash, ggplot2, stats, methods, igraph, utils, glmnet, vbsr, grDevices, gplots, gtools, pvclust, R.utils, dqrng, SummarizedExperiment, BiocParallel, matrixStats
LinkingTo
Suggests	knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/ubioinformat/TraRe/tree/master
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	TraRe_1.5.0.tar.gz
Windows Binary	TraRe_1.6.3.zip (64-bit only)
macOS Binary (x86_64)	TraRe_1.6.3.tgz
macOS Binary (arm64)	TraRe_1.6.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TraRe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TraRe
Bioc Package Browser	https://code.bioconductor.org/browse/TraRe/
Package Short Url	https://bioconductor.org/packages/TraRe/
Package Downloads Report	Download Stats