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>

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

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

Details

biocViews Bayesian, Classification, GeneRegulation, GeneTarget, GraphAndNetwork, RNASeq, Software
Version 1.5.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
System Requirements
URL https://github.com/ubioinformat/TraRe/tree/master
See More
Suggests knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle
Linking To
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Depends On Me
Imports Me
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Build Report 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
Old Source Packages for BioC 3.16 Source Archive