enrichViewNet

This is the released version of enrichViewNet; for the devel version, see enrichViewNet.

From functional enrichment results to biological networks

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-7846-6749 , Pascal Belleau [aut] ORCID: 0000-0002-0802-1071 , Robert L. Faure [aut] ORCID: 0000-0003-1798-4723 , Maria J. Fernandes [aut] ORCID: 0000-0002-3973-025X , Alexander Krasnitz [aut], David A. Tuveson [aut] ORCID: 0000-0002-8017-2712

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, GO, Network, NetworkEnrichment, Software
Version	1.6.0
In Bioconductor since	BioC 3.18 (R-4.3) (1.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods
System Requirements
URL	https://github.com/adeschen/enrichViewNet https://adeschen.github.io/enrichViewNet/
Bug Reports	https://github.com/adeschen/enrichViewNet/issues

Suggests	BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick
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_1.6.0.tar.gz
Windows Binary (x86_64)	enrichViewNet_1.6.0.zip
macOS Binary (x86_64)	enrichViewNet_1.6.0.tgz
macOS Binary (arm64)	enrichViewNet_1.6.0.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