enrichViewNet

DOI: 10.18129/B9.bioc.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 Deschênes [aut, cre] , Pascal Belleau [aut] , Robert L. Faure [aut] , Maria J. Fernandes [aut] , Alexander Krasnitz [aut], David A. Tuveson [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

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")

 

HTML	R Script	From functional enrichment results to biological networks
PDF		Reference Manual
Text		NEWS

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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/adeschen/enrichViewNet https://adeschen.github.io/enrichViewNet/
BugReports	https://github.com/adeschen/enrichViewNet/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
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 (64-bit only)
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
Old Source Packages for BioC 3.18	Source Archive