Package: enrichViewNet 1.5.0

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]

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enrichViewNet.pdf |enrichViewNet.html✨
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NEWS

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

Peer review:

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

Pkgdown: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-1.5.0(bioc 3.21)enrichViewNet-1.4.0(bioc 3.20)

biologicalquestionsoftwarenetworknetworkenrichmentgocystocapefunctional-enrichment

5.68 score 5 stars 6 scripts 141 downloads 4 exports 152 dependencies

Last updated 2 months agofrom:b9b8a23dda. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:createEnrichMapcreateEnrichMapMultiBasiccreateEnrichMapMultiComplexcreateNetwork

Dependencies:AnnotationDbiapeaplotaskpassbackportsbase64encbase64urlBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcachemcaToolscheckmateclicodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdigestDOSEdplyrenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgprofiler2graphgridExtragridGraphicsgtablegtoolshighrhtmltoolshtmlwidgetshttrigraphIRangesIRdisplayIRkernelisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpbdZMQpillarpkgconfigplogrplotlyplyrpngpolyclippromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlRCy3reprreshape2RJSONIOrlangrmarkdownRSQLiteS4VectorssassscalesscatterpiesnowstrexstringistringrsyssystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8uuidvctrsviridisLitewithrxfunXMLXVectoryamlyulab.utilszlibbioc

From functional enrichment results to biological networks

Astrid Deschênes, Pascal Belleau, Robert L Faure and Maria J Fernandes

Rendered fromenrichViewNet.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-10-28
Started: 2023-09-14

Readme and manuals

Help Manual

Help pageTopics
From functional enrichment results to biological networksenrichViewNet-package enrichViewNet
Using functional enrichment results in gprofiler2 format to create an enrichment mapcreateEnrichMap
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from different enrichment analysescreateEnrichMapMultiBasic
Using functional enrichment results in gprofiler2 format to create an enrichment map with multiple groups from same or different enrichment analysescreateEnrichMapMultiComplex
Using functional enrichment results from gprofiler2 to create a Cytoscape networkcreateNetwork
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