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enrichViewNet
This is thereleased version of enrichViewNet; for the devel version, seeenrichViewNet.
From functional enrichment results to biological networks
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion,GO,Network,NetworkEnrichment,Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | gprofiler2,strex,RCy3,jsonlite,stringr,enrichplot,DOSE,igraph,reshape2, methods |
| System Requirements | |
| URL | https://github.com/adeschen/enrichViewNethttps://adeschen.github.io/enrichViewNet/ |
| Bug Reports | https://github.com/adeschen/enrichViewNet/issues |
See More
| Suggests | BiocStyle,knitr,rmarkdown,ggplot2,scatterpie,ggtangle,ggrepel,testthat,ggnetwork,magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | enrichViewNet_1.8.0.tar.gz |
| Windows Binary (x86_64) | enrichViewNet_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | enrichViewNet_1.8.0.tgz |
| macOS Binary (arm64) | enrichViewNet_1.8.0.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 |