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>

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HTML R Script TraRe: Identification of conditions dependant Gene Regulatory Networks
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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
Suggests knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle
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