GitHub - adeschen/enrichViewNet: From functional enrichment results to biological networks (original) (raw)

R-CMD-check-bioc codecov License: Artistic-2.0

The enrichViewNet package enables the transformation of functional enrichment results, formatted as the results obtained by gprofiler2, into networks.

First, the enrichViewNet package enables the visualization of enrichment results a Cytoscapenetwork where significant terms (Gene Ontology/Reactome/Transcription Factor/etc..) and genes are nodes. In this network, edges connect genes that are part of the enrichment request to their terms.

In addition, the enrichViewNet package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps, as introduced in the Bioconductorenrichplot package, enable the visualization of enriched terms into a network with edges connecting overlapping genes. Thus, enriched terms with overlapping genes cluster together.

Bioconductor Package

Bioconductor Time

The enrichViewNet package is now an official package of Bioconductor.

The current Bioconductor release can be directly downloaded from their website:Current release

Authors

Astrid Deschênes,Pascal Belleau,Robert L Faure,Maria J Fernandes,Alexander Krasnitz andDavid A Tuveson

License

This package and the underlying enrichViewNet code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License seehttp://opensource.org/licenses/Artistic-2.0

Documentation

enrichViewNet Website

enrichViewNet Get Started

Installation

To install the latest version accessible, thedevtoolspackage is required.

 ## Load required package
 library(devtools)

 ## Install the latest version of enrichViewNet
 devtools::install_github('adeschen/enrichViewNet')

To install this package from Bioconductor, start R (version 4.3 or later) and enter:

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

 BiocManager::install("enrichViewNet")

Bugs/Feature requests

If you have any bugs or feature requests,let us know.

Thanks!