TraRe

DOI: 10.18129/B9.bioc.TraRe    

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

Transcriptional Rewiring

Bioconductor version: Development (3.15)

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) TraRe_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TraRe
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TraRe
Package Short Url https://bioconductor.org/packages/TraRe/
Package Downloads Report Download Stats

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