Package: enrichViewNet 1.11.0

Astrid Deschênes

enrichViewNet: From functional enrichment results to biological networks

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.

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

enrichViewNet_1.11.0.tar.gz
enrichViewNet_1.11.0.zip(r-4.7)enrichViewNet_1.11.0.zip(r-4.6)enrichViewNet_1.11.0.zip(r-4.5)
enrichViewNet_1.11.0.tgz(r-4.6-any)enrichViewNet_1.11.0.tgz(r-4.5-any)
enrichViewNet_1.11.0.tar.gz(r-4.7-any)enrichViewNet_1.11.0.tar.gz(r-4.6-any)
enrichViewNet_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
enrichViewNet/json (API)

# Install 'enrichViewNet' in R:

install.packages('enrichViewNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeschen/enrichviewnet/issues

Pkgdown/docs site:https://adeschen.github.io

Datasets:

demoGOST - The result of a functional enrichment analysis done with 'gprofiler2' (<https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html>).
parentalNapaVsDMSODEG - The result of a differential expression analysis done between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
parentalNapaVsDMSOEnrichment - The result of an enrichment analysis has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
rosaNapaVsDMSODEG - The result of a differential expression analysis done between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
rosaNapaVsDMSOEnrichment - The result of an enrichment analysis that has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.

On BioConductor:enrichViewNet-1.11.0(bioc 3.24)enrichViewNet-1.10.0(bioc 3.23)

biologicalquestion software network networkenrichment go cystocape functional-enrichment

5.48 score 6 stars 6 scripts 7 exports 139 dependencies

Last updated from:6c5350e130. Checks:1 NOTE, 8 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	213
linux-devel-x86_64	OK	405
source / vignettes	OK	290
linux-release-x86_64	OK	355
macos-release-arm64	OK	183
macos-oldrel-arm64	OK	195
windows-devel	ERROR	269
windows-release	OK	295
windows-oldrel	OK	273
wasm-release	OK	207

Exports:createEnrichMap createEnrichMapAsIgraph createEnrichMapMultiBasic createEnrichMapMultiBasicAsIgraph createEnrichMapMultiComplex createEnrichMapMultiComplexAsIgraph createNetwork

Dependencies:AnnotationDbi ape aplot askpass backports base64enc base64url Biobase BiocGenerics Biostrings bit bit64 bitops blob bslib cachem caTools checkmate cli cluster cpp11 crayon crosstalk curl data.table DBI digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gplots gprofiler2 graph gridExtra gridGraphics gtable gtools highr htmltools htmlwidgets httr igraph IRanges IRdisplay IRkernel isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme openssl otel patchwork pbdZMQ pillar pkgconfig plotly plyr png polyclip promises purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl RCy3 repr reshape2 RJSONIO rlang rmarkdown RSQLite S4Vectors S7 sass scales scatterpie Seqinfo strex stringi stringr sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 uuid vctrs viridisLite withr xfun XML XVector yaml yulab.utils

From functional enrichment results to biological networks

Rendered fromenrichViewNet.Rmdusingknitr::rmarkdown

Last update: 2026-04-20
Started: 2023-09-14

Help page	Topics
From functional enrichment results to biological networks	enrichViewNet-package enrichViewNet
Using functional enrichment results in gprofiler2 format to create an enrichment map	createEnrichMap
Using functional enrichment results in gprofiler2 format to create an enrichment map in an igraph format	createEnrichMapAsIgraph
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from different enrichment analyses	createEnrichMapMultiBasic
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from different enrichment analyses as an igraph	createEnrichMapMultiBasicAsIgraph
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from same or different enrichment analyses	createEnrichMapMultiComplex
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from same or different enrichment analyses in an igraph format	createEnrichMapMultiComplexAsIgraph
Using functional enrichment results from gprofiler2 to create a Cytoscape network	createNetwork
The result of a functional enrichment analysis done with 'gprofiler2' (<https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html>).	demoGOST
The result of a differential expression analysis done between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.	parentalNapaVsDMSODEG
The result of an enrichment analysis has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.	parentalNapaVsDMSOEnrichment
The result of a differential expression analysis done between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.	rosaNapaVsDMSODEG
The result of an enrichment analysis that has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.	rosaNapaVsDMSOEnrichment
Validate arguments passed to validateCreateEnrichMapMultiComplex() function	validateCreateEnrichMapMultiComplexAsIgraphArg

Package: enrichViewNet 1.11.0

enrichViewNet: From functional enrichment results to biological networks

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