TraRe
This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TraRe.
Transcriptional Rewiring
Bioconductor version: 3.13
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("TraRe")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, Classification, GeneRegulation, GeneTarget, GraphAndNetwork, RNASeq, Software |
| Version | 1.0.0 |
| 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 | |
| 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 | TraRe_1.0.0.tar.gz |
| Windows Binary | TraRe_1.0.0.zip |
| macOS 10.13 (High Sierra) | TraRe_1.0.0.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 3.13 | Source Archive |