{
  "_id": "6a5494a8ff0138dec5d65605",
  "Package": "volcano3D",
  "Type": "Package",
  "Title": "3D Volcano Plots and Polar Plots for Three-Class Data",
  "Version": "2.0.11",
  "Authors@R": "c(person(\"Katriona\", \"Goldmann\", role = c(\"aut\", \"cre\"),\nemail = \"katrionagoldmann@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9073-6323\")),\nperson(\"Myles\", \"Lewis\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-9365-5345\")))",
  "Maintainer": "Katriona Goldmann <katrionagoldmann@gmail.com>",
  "URL": "https://katrionagoldmann.github.io/volcano3D/index.html,\nhttps://github.com/KatrionaGoldmann/volcano3D",
  "BugReports": "https://github.com/KatrionaGoldmann/volcano3D/issues",
  "Description": "Generates interactive plots for analysing and visualising\nthree-class high dimensional data. It is particularly suited to\nvisualising differences in continuous attributes such as\ngene/protein/biomarker expression levels between three groups.\nDifferential gene/biomarker expression analysis between two\nclasses is typically shown as a volcano plot. However, with\nthree groups this type of visualisation is particularly\ndifficult to interpret. This package generates 3D volcano plots\nand 3-way polar plots for easier interpretation of three-class\ndata.",
  "Language": "en-gb",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
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  "Packaged": {
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    "User": "root"
  },
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://katrionagoldmann.r-universe.dev",
  "Date/Publication": "2026-01-14 14:54:10 UTC",
  "RemoteUrl": "https://github.com/katrionagoldmann/volcano3d",
  "RemoteRef": "HEAD",
  "RemoteSha": "51e9d423296c8610ab48e8cfd6a69370702a77c8",
  "Author": "Katriona Goldmann [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9073-6323>),\nMyles Lewis [aut] (ORCID: <https://orcid.org/0000-0001-9365-5345>)",
  "_user": "katrionagoldmann",
  "_type": "src",
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  "_expires": "2026-10-21T07:32:55.000Z",
  "_created": "2026-07-13T07:28:14.000Z",
  "_published": "2026-07-13T07:32:56.846Z",
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    {
      "package": "rlang",
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    },
    {
      "package": "matrixTests",
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    },
    {
      "package": "DESeq2",
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    },
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  "_selfowned": true,
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      "week": "2026-02",
      "n": 9
    },
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  ],
  "_tags": [],
  "_topics": [
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    "differential-expression",
    "differential-expression-analysis",
    "gene-expression",
    "interactive",
    "omics",
    "plotly",
    "rna-seq",
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/volcano3D"
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  "_devurl": "https://github.com/katrionagoldmann/volcano3d",
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  "_assets": [
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    "extra/NEWS.txt",
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    "manual.pdf"
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  "_realowner": "katrionagoldmann",
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      "date": "2020-06-04"
    },
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      "version": "1.0.1",
      "date": "2020-06-26"
    },
    {
      "version": "1.1.0",
      "date": "2021-02-22"
    },
    {
      "version": "1.2.0",
      "date": "2021-03-31"
    },
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      "date": "2022-07-06"
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      "date": "2023-05-17"
    },
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      "date": "2026-01-15"
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    "boxplot_trio",
    "calc_pvals",
    "calc_stats_2x3",
    "deseq_2x3",
    "deseq_2x3_polar",
    "deseq_polar",
    "forest_ggplot",
    "forest_plot",
    "forest_plotly",
    "polar_coords",
    "polar_coords_2x3",
    "polar_grid",
    "radial_ggplot",
    "radial_plotly",
    "show_grid",
    "significance_subset",
    "volcano3D",
    "voom_polar"
  ],
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      "name": "syn_example_meta",
      "title": "PEAC synovial sample data",
      "object": "example_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Pathotype"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "syn_example_rld",
      "title": "PEAC synovial gene expression data",
      "object": "example_data",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "SYN001",
        "SYN002",
        "SYN003",
        "SYN004",
        "SYN005",
        "SYN006",
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        "SYN032",
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        "SYN034",
        "SYN035",
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        "SYN037",
        "SYN038",
        "SYN039",
        "SYN040",
        "SYN041",
        "SYN042",
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        "SYN075",
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        "SYN078",
        "SYN079",
        "SYN080",
        "SYN081"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_animation",
      "title": "Add mode bar button to rotate the plot",
      "concept": [
        "volcanoplot"
      ],
      "topics": [
        "add_animation"
      ]
    },
    {
      "page": "boxplot_trio",
      "title": "Boxplot to compare groups",
      "topics": [
        "boxplot_trio"
      ]
    },
    {
      "page": "calc_pvals",
      "title": "Calculate one-way test and pairwise tests",
      "topics": [
        "calc_pvals"
      ]
    },
    {
      "page": "calc_stats_2x3",
      "title": "Calculate p-values for 2x3-way analysis",
      "topics": [
        "calc_stats_2x3"
      ]
    },
    {
      "page": "deseq_2x3",
      "title": "2 x 3 factor DESeq2 analysis",
      "topics": [
        "deseq_2x3"
      ]
    },
    {
      "page": "deseq_2x3_polar",
      "title": "Convert 2x3 design DESeq2 objects to a volcano3d object",
      "topics": [
        "deseq_2x3_polar"
      ]
    },
    {
      "page": "deseq_polar",
      "title": "Convert DESeq2 objects to a volcano3d object",
      "topics": [
        "deseq_polar"
      ]
    },
    {
      "page": "forest_plot",
      "title": "Forest plot individual gene from 2x3 factor analysis",
      "topics": [
        "forest_ggplot",
        "forest_plot",
        "forest_plotly"
      ]
    },
    {
      "page": "grid-class",
      "title": "An S4 class to define the polar grid coordinates system.",
      "topics": [
        "grid-class"
      ]
    },
    {
      "page": "polar_coords",
      "title": "Coordinates for Three Way Polar Plot",
      "topics": [
        "polar_coords"
      ]
    },
    {
      "page": "polar_coords_2x3",
      "title": "Coordinates for three way polar plot from 2x3 factor analysis",
      "topics": [
        "polar_coords_2x3"
      ]
    },
    {
      "page": "polar_grid",
      "title": "Grid required for 3D volcano plot and 2D radial plots",
      "topics": [
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      ]
    },
    {
      "page": "radial_ggplot",
      "title": "'Ggplot' for Three Way Polar Plot",
      "topics": [
        "radial_ggplot"
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    },
    {
      "page": "radial_plotly",
      "title": "Three-way radial comparison Polar Plot (using plotly)",
      "topics": [
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      ]
    },
    {
      "page": "show_grid",
      "title": "Plots grid objects for inspection using plotly",
      "topics": [
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      ]
    },
    {
      "page": "significance_subset",
      "title": "Extract a subset population",
      "topics": [
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    },
    {
      "page": "syn_example_meta",
      "title": "PEAC synovial sample data",
      "topics": [
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      ]
    },
    {
      "page": "syn_example_rld",
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    },
    {
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        "volc3d-class"
      ]
    },
    {
      "page": "volcano3D",
      "title": "Three-Dimensional Volcano Plot",
      "topics": [
        "volcano3D"
      ]
    },
    {
      "page": "voom_polar",
      "title": "Convert RNA-Seq count data to a volcano3d object using 'limma voom'",
      "topics": [
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