Welcome to the new bioconductor.org!

enrichViewNet

From functional enrichment results to biological networks


Bioconductor version: Release (3.18)

This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

Author: Astrid DeschĂȘnes [aut, cre] , Pascal Belleau [aut] , Robert L. Faure [aut] , Maria J. Fernandes [aut] , Alexander Krasnitz [aut], David A. Tuveson [aut]

Maintainer: Astrid DeschĂȘnes <adeschen at hotmail.com>

Citation (from within R, enter citation("enrichViewNet")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("enrichViewNet")

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("enrichViewNet")
From functional enrichment results to biological networks HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, GO, Network, NetworkEnrichment, Software
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, methods
System Requirements
URL https://github.com/adeschen/enrichViewNet https://adeschen.github.io/enrichViewNet/
Bug Reports https://github.com/adeschen/enrichViewNet/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
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 enrichViewNet_1.0.0.tar.gz
Windows Binary enrichViewNet_1.0.0.zip
macOS Binary (x86_64) enrichViewNet_1.0.0.tgz
macOS Binary (arm64) enrichViewNet_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/enrichViewNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/enrichViewNet
Bioc Package Browser https://code.bioconductor.org/browse/enrichViewNet/
Package Short Url https://bioconductor.org/packages/enrichViewNet/
Package Downloads Report Download Stats