{
  "_id": "6a1bd3ba1d7bb097a0a14f4c",
  "Package": "gINTomics",
  "Title": "Multi-Omics data integration",
  "Version": "1.9.0",
  "Authors@R": "c(person(\"Angelo\", \"Velle\", role = c(\"cre\", \"aut\"),\nemail = \"angelo.velle@unipd.it\",\ncomment = c(ORCID = \"0000-0002-4010-6390\")),\nperson(\"Francesco\", \"Patane'\", role = \"aut\",\nemail = \"francesco.patane@unipd.it\",\ncomment = c(ORCID = \"0009-0001-8619-447X\")),\nperson(\"Chiara\", \"Romualdi\", role = \"aut\",\nemail = \"chiara.romualdi@unipd.it\",\ncomment = c(ORCID = \"0000-0003-4792-9047\")))",
  "Description": "gINTomics is an R package for Multi-Omics data integration\nand visualization. gINTomics is designed to detect the\nassociation between the expression of a target and of its\nregulators, taking into account also their genomics\nmodifications such as Copy Number Variations (CNV) and\nmethylation. What is more, gINTomics allows integration results\nvisualization via a Shiny-based interactive app.",
  "License": "AGPL-3",
  "biocViews": "GeneExpression, RNASeq, Microarray, Visualization,\nCopyNumberVariation, GeneTarget",
  "Encoding": "UTF-8",
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  "BugReports": "https://github.com/angelovelle96/gINTomics/issues",
  "URL": "https://github.com/angelovelle96/gINTomics",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl libx11-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:03 UTC",
  "RemoteUrl": "https://github.com/bioc/gINTomics",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-05-30 08:26:47 UTC",
    "User": "root"
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  "Author": "Angelo Velle [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-4010-6390>),\nFrancesco Patane' [aut] (ORCID:\n<https://orcid.org/0009-0001-8619-447X>),\nChiara Romualdi [aut] (ORCID: <https://orcid.org/0000-0003-4792-9047>)",
  "Maintainer": "Angelo Velle <angelo.velle@unipd.it>",
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  "_created": "2026-05-30T08:26:47.000Z",
  "_published": "2026-05-31T06:22:50.920Z",
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      "title": "plotting enrichment",
      "topics": [
        "dot_plotly"
      ]
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    {
      "page": "extract_model_res",
      "title": "Setting method for extracting results",
      "topics": [
        "extract_model_res",
        "extract_model_res,list-method",
        "extract_model_res,MultiClass-method",
        "extract_model_res,MultiOmics-method"
      ]
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    {
      "page": "mirna_hsa",
      "title": "miRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).",
      "topics": [
        "mirna_hsa"
      ]
    },
    {
      "page": "mmultiassay_ov",
      "title": "Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.",
      "topics": [
        "mmultiassay_ov"
      ]
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      "page": "MultiClass-class",
      "title": "MultiClass Class",
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      "page": "MultiOmics-class",
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      "page": "plot_network",
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      "page": "plot_venn",
      "title": "plotting venn",
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      "page": "plot_volcano",
      "title": "plotting volcano",
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      "page": "run_cnv_integration",
      "title": "Integration of expression and Copy Number Variations",
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      "page": "run_genomic_enrich",
      "title": "Running genomic enrichment analysis",
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      "page": "run_multiomics",
      "title": "Complete Multi-Omics integration",
      "topics": [
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      "page": "run_shiny",
      "title": "Start a Shiny application for integrated multi-omics data analysis.",
      "concept": [
        "Data analysis",
        "Function",
        "Integration",
        "Interactive",
        "Multi-omics",
        "Shiny",
        "Visualization"
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  "_vignettes": [
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      "source": "gINTomics.Rmd",
      "filename": "gINTomics.html",
      "title": "gINTomics vignette",
      "author": "Angelo Velle, Francesco Patanè, Chiara Romualdi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "How to use gINTomics",
        "Structure of the package",
        "Generate a MultiAssayExperiment",
        "Run Genomic integration",
        "Run CNV integration",
        "Run methylation integration",
        "Run TF-target integration",
        "Run miRNA-target integration",
        "Run TF-miRNA integration",
        "Run complete Multi-Omics integration",
        "Visualization",
        "Shiny app",
        "plots",
        "network plot",
        "Venn Diagram",
        "Volcano plot",
        "Ridgeline plot",
        "Chromosome distribution plot",
        "TF distribution plot",
        "Enrichment plot",
        "Session info"
      ],
      "created": "2023-07-18 16:06:16",
      "modified": "2024-04-04 13:20:58",
      "commits": 19
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