CoRegNet
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CoRegNet.
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Bioconductor version: 3.17
This package provides methods to identify active transcriptional programs. Methods and classes are provided to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model Transcription Factor cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary. Transcriptional activity of the regulators in the network can be estimated using an measure of their influence in a given sample. Finally, an interactive UI can be used to navigate through the network of cooperative regulators and to visualize their activity in a specific sample or subgroup sample. The proposed visualization tool can be used to integrate gene expression, transcriptional activity, copy number status, sample classification and a transcriptional network including co-regulation information.
Author: Remy Nicolle, Thibault Venzac and Mohamed Elati
Maintainer: Remy Nicolle <remy.c.nicolle at gmail.com>
citation("CoRegNet")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CoRegNet")
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("CoRegNet")| Custom Print Methods | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, SystemsBiology, Transcription, Visualization |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.14), igraph, shiny, arules, methods |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | RColorBrewer, gplots, BiocStyle, knitr, rmarkdown |
| 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 | CoRegNet_1.38.0.tar.gz |
| Windows Binary | CoRegNet_1.38.0.zip |
| macOS Binary (x86_64) | CoRegNet_1.38.0.tgz |
| macOS Binary (arm64) | CoRegNet_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CoRegNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CoRegNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/CoRegNet/ |
| Package Short Url | https://bioconductor.org/packages/CoRegNet/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |