{
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  "Package": "enrichViewNet",
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  "Version": "1.11.0",
  "Date": "2023-08-12",
  "Title": "From functional enrichment results to biological networks",
  "Description": "This package enables the visualization of functional\nenrichment results as network graphs. First the package enables\nthe visualization of enrichment results, in a format\ncorresponding to the one generated by gprofiler2, as a\ncustomizable Cytoscape network. In those networks, both gene\ndatasets (GO terms/pathways/protein complexes) and genes\nassociated to the datasets are represented as nodes. While the\nedges connect each gene to its dataset(s). The package also\nprovides the option to create enrichment maps from functional\nenrichment results. Enrichment maps enable the visualization of\nenriched terms into a network with edges connecting overlapping\ngenes.",
  "Authors@R": "c(person(\"Astrid\", \"Deschênes\", email = \"adeschen@hotmail.com\",\nrole=c(\"aut\", \"cre\"), comment=c(ORCID = \"0000-0001-7846-6749\")),\nperson(\"Pascal\", \"Belleau\", email = \"pascal_belleau@hotmail.com\",\nrole=c(\"aut\"), comment = c(ORCID = \"0000-0002-0802-1071\")),\nperson(\"Robert L.\", \"Faure\", email=\"robert.faure@crchudequebec.ulaval.ca\",\nrole=c(\"aut\"), comment=c(ORCID=\"0000-0003-1798-4723\")),\nperson(\"Maria J.\", \"Fernandes\",\nemail=\"maria.fernandes@crchudequebec.ulaval.ca\", role = c(\"aut\"),\ncomment=c(ORCID=\"0000-0002-3973-025X\")),\nperson(given=\"Alexander\", family=\"Krasnitz\", email=\"krasnitz@cshl.edu\",\nrole=c(\"aut\")),\nperson(given=\"David A.\", family=\"Tuveson\",\nemail=\"dtuveson@cshl.edu\",\nrole=c(\"aut\"), comment=c(ORCID=\"0000-0002-8017-2712\")))",
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  "biocViews": "BiologicalQuestion, Software, Network, NetworkEnrichment, GO",
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  "URL": "https://github.com/adeschen/enrichViewNet,\nhttps://adeschen.github.io/enrichViewNet/",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:49 UTC",
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  "Author": "Astrid Deschênes [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7846-6749>),\nPascal Belleau [aut] (ORCID: <https://orcid.org/0000-0002-0802-1071>),\nRobert L. Faure [aut] (ORCID: <https://orcid.org/0000-0003-1798-4723>),\nMaria J. Fernandes [aut] (ORCID:\n<https://orcid.org/0000-0002-3973-025X>),\nAlexander Krasnitz [aut],\nDavid A. Tuveson [aut] (ORCID: <https://orcid.org/0000-0002-8017-2712>)",
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      "source": "enrichViewNet.Rmd",
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      "title": "From functional enrichment results to biological networks",
      "author": "Astrid Deschênes, Pascal Belleau, Robert L Faure and Maria J Fernandes",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Licensing",
        "Citing",
        "Introduction",
        "Installation",
        "General workflow",
        "Gene-Term network loadable in Cytoscape",
        "Run an enrichment analysis",
        "Start Cytoscape",
        "Create a gene-term network",
        "Enrichment map",
        "Create an enrichment map in a ggplot format",
        "Using list of term IDs",
        "Enrichment map customization",
        "Create an enrichment map in an igraph format",
        "Effect of seed value",
        "Enrichment map with groups from different enrichment analyses",
        "Create an enrichment map using multiple enrichment analyses in a ggplot format",
        "Create an enrichment map using multiple enrichment analyses in an igraph format",
        "Enrichment map with groups from same enrichment analysis or from complex designs",
        "Create an enrichment map using mutliple subsections of one enrichment analysis in a ggplot format",
        "Create an enrichment map using a complex design",
        "Create an enrichment map using mutliple subsections of one enrichment analysis in a igraph format",
        "Create an enrichment map using mutliple subsections of multiple enrichment analyses in a igraph format",
        "Code Ocean Capsule",
        "Acknowledgments",
        "Session info",
        "References"
      ],
      "created": "2023-09-14 21:23:22",
      "modified": "2026-04-20 21:56:10",
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