{
  "_id": "6a15e349acfb0bcc41d6bfe1",
  "Package": "iSEEtree",
  "Version": "1.7.0",
  "Authors@R": "c(person(given = \"Giulio\", family = \"Benedetti\", role = c(\"aut\", \"cre\"),\nemail = \"giulio.benedetti@utu.fi\",\ncomment = c(ORCID = \"0000-0002-8732-7692\")),\nperson(given = \"Ely\", family = \"Seraidarian\", role = c(\"ctb\"),\nemail = \"ely.seraidarian@utu.fi\",\ncomment = c(ORCID = \"0009-0008-8602-093X\")),\nperson(given = \"Leo\", family = \"Lahti\", role = c(\"aut\"),\nemail = \"leo.lahti@iki.fi\",\ncomment = c(ORCID = \"0000-0001-5537-637X\")))",
  "Title": "Interactive visualisation for microbiome data",
  "Description": "iSEEtree is an extension of iSEE for the\nTreeSummarizedExperiment data container. It provides\ninteractive panel designs to explore hierarchical datasets,\nsuch as the microbiome and cell lines.",
  "biocViews": "Software, Visualization, Microbiome, GUI, ShinyApps,\nDataImport",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "URL": "https://github.com/microbiome/iSEEtree",
  "BugReports": "https://github.com/microbiome/iSEEtree/issues",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-20 12:57:33 UTC",
  "RemoteUrl": "https://github.com/bioc/iSEEtree",
  "RemoteRef": "HEAD",
  "RemoteSha": "e4fd1ef538117635f8010f37eb2244ed112605aa",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 18:05:48 UTC",
    "User": "root"
  },
  "Author": "Giulio Benedetti [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8732-7692>),\nEly Seraidarian [ctb] (ORCID: <https://orcid.org/0009-0008-8602-093X>),\nLeo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>)",
  "Maintainer": "Giulio Benedetti <giulio.benedetti@utu.fi>",
  "MD5sum": "735ff2623c77fb6918d96a2d497ba108",
  "_user": "bioc",
  "_type": "src",
  "_file": "iSEEtree_1.7.0.tar.gz",
  "_fileid": "9c72efe222e9b73f43609c9bedb016aed72d6044e375f7d460eb5a2f24a954ec",
  "_filesize": 7461048,
  "_sha256": "9c72efe222e9b73f43609c9bedb016aed72d6044e375f7d460eb5a2f24a954ec",
  "_created": "2026-05-26T18:05:48.000Z",
  "_published": "2026-05-26T18:15:37.316Z",
  "_jobs": [
    {
      "job": 77926972315,
      "time": 252,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7222480875"
    },
    {
      "job": 77926972249,
      "time": 509,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7222569600"
    },
    {
      "job": 77926972247,
      "time": 445,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7222547879"
    },
    {
      "job": 77926972264,
      "time": 226,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7222472290"
    },
    {
      "job": 77926972357,
      "time": 276,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7222489358"
    },
    {
      "job": 77925722698,
      "time": 409,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222395406"
    },
    {
      "job": 77926972253,
      "time": 201,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7222463840"
    },
    {
      "job": 77926972471,
      "time": 501,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7222566807"
    },
    {
      "job": 77926972256,
      "time": 368,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7222522643"
    },
    {
      "job": 77926972433,
      "time": 369,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7222522121"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/iSEEtree",
  "_commit": {
    "id": "e4fd1ef538117635f8010f37eb2244ed112605aa",
    "author": "Giulio Benedetti <giuliobene2000@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #51 from federicomarini/patch-1\n\nUpdate iSEEtree.Rmd",
    "time": 1779281853
  },
  "_maintainer": {
    "name": "Giulio Benedetti",
    "email": "giulio.benedetti@utu.fi",
    "login": "riborings",
    "linkedin": "in/giulio-benedetti-00a5621b2",
    "orcid": "0000-0002-8732-7692",
    "description": "Bioengineering student interested in Bioinformatics, Neuroscience, Machine Learning and Data Science",
    "uuid": 82203661
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "iSEE",
      "version": ">= 2.19.4",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggtree",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "miaViz",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "mia",
      "role": "Imports"
    },
    {
      "package": "shinyWidgets",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "TreeSummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "biomformat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "RefManageR",
      "role": "Suggests"
    },
    {
      "package": "remotes",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "vegan",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "visualization",
    "microbiome",
    "gui",
    "shinyapps",
    "dataimport",
    "shiny-apps",
    "visualisation"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "riborings",
      "count": 182,
      "uuid": 82203661
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "federicomarini",
      "count": 2,
      "uuid": 7447478
    },
    {
      "user": "elyseraidarian",
      "count": 1,
      "uuid": 167744870
    },
    {
      "user": "antagomir",
      "count": 1,
      "uuid": 1228382
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 300,
    "source": "https://www.bioconductor.org/packages/stats/bioc/iSEEtree"
  },
  "_devurl": "https://github.com/microbiome/iseetree",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/iSEEtree.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/microbiome/iseetree",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".check_all_panels",
    ".check_panel",
    "AbundanceDensityPlot",
    "AbundancePlot",
    "ColumnGraphPlot",
    "ColumnTreePlot",
    "iSEE",
    "LoadingPlot",
    "PrevalencePlot",
    "RDAPlot",
    "RowGraphPlot",
    "RowTreePlot",
    "ScreePlot"
  ],
  "_help": [
    {
      "page": "AbundanceDensityPlot",
      "title": "Abundance density plot",
      "topics": [
        "AbundanceDensityPlot",
        "AbundanceDensityPlot-class"
      ]
    },
    {
      "page": "AbundancePlot",
      "title": "Abundance plot",
      "topics": [
        "AbundancePlot",
        "AbundancePlot-class"
      ]
    },
    {
      "page": "ColumnGraphPlot",
      "title": "Column graph plot",
      "topics": [
        "ColumnGraphPlot",
        "ColumnGraphPlot-class"
      ]
    },
    {
      "page": "ColumnTreePlot",
      "title": "Column tree plot",
      "topics": [
        "ColumnTreePlot",
        "ColumnTreePlot-class"
      ]
    },
    {
      "page": "GraphPlot",
      "title": "Graph plot",
      "topics": [
        "GraphPlot",
        "GraphPlot-class"
      ]
    },
    {
      "page": "iSEE",
      "title": "iSEE layout for TreeSE",
      "topics": [
        "iSEE",
        "iSEE,TreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "LoadingPlot",
      "title": "Loading plot",
      "topics": [
        "LoadingPlot",
        "LoadingPlot-class"
      ]
    },
    {
      "page": "PrevalencePlot",
      "title": "Prevalence plot",
      "topics": [
        "PrevalencePlot",
        "PrevalencePlot-class"
      ]
    },
    {
      "page": "RDAPlot",
      "title": "RDA plot",
      "topics": [
        "RDAPlot",
        "RDAPlot-class"
      ]
    },
    {
      "page": "RowGraphPlot",
      "title": "Row graph plot",
      "topics": [
        "RowGraphPlot",
        "RowGraphPlot-class"
      ]
    },
    {
      "page": "RowTreePlot",
      "title": "Row tree plot",
      "topics": [
        "RowTreePlot",
        "RowTreePlot-class"
      ]
    },
    {
      "page": "ScreePlot",
      "title": "Scree plot",
      "topics": [
        "ScreePlot",
        "ScreePlot-class"
      ]
    },
    {
      "page": "TreePlot",
      "title": "Tree plot",
      "topics": [
        "TreePlot",
        "TreePlot-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/iSEEtree/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "aplot",
    "assorthead",
    "base64enc",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bluster",
    "bslib",
    "cachem",
    "Cairo",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "colourpicker",
    "commonmark",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "crosstalk",
    "DBI",
    "DECIPHER",
    "decontam",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "DirichletMultinomial",
    "doParallel",
    "dplyr",
    "dqrng",
    "DT",
    "ecodive",
    "evaluate",
    "farver",
    "fastmap",
    "FNN",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "gdtools",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggbeeswarm",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggraph",
    "ggrastr",
    "ggrepel",
    "ggtree",
    "GlobalOptions",
    "glue",
    "graphlayouts",
    "gridExtra",
    "gridGraphics",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "IRanges",
    "irlba",
    "iSEE",
    "isoband",
    "iterators",
    "janeaustenr",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listviewer",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mia",
    "miaViz",
    "mime",
    "miniUI",
    "MultiAssayExperiment",
    "nlme",
    "otel",
    "patchwork",
    "permute",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "promises",
    "purrr",
    "R6",
    "ragg",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "reshape2",
    "rintrojs",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSpectra",
    "rsvd",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "ScaledMatrix",
    "scales",
    "scater",
    "scuttle",
    "Seqinfo",
    "shape",
    "shiny",
    "shinyAce",
    "shinydashboard",
    "shinyjs",
    "shinyWidgets",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SnowballC",
    "sourcetools",
    "SparseArray",
    "sparseMatrixStats",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidytext",
    "tidytree",
    "tinytex",
    "tokenizers",
    "treeio",
    "TreeSummarizedExperiment",
    "tweenr",
    "utf8",
    "uwot",
    "vctrs",
    "vegan",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "iSEEtree.Rmd",
      "filename": "iSEEtree.html",
      "title": "iSEEtree: interactive explorer for hierarchical data",
      "author": "Giulio Benedetti",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Motivation",
        "Panels",
        "Compositional Analysis",
        "Ordination Analysis",
        "Structural Analysis",
        "Other Panels",
        "Tutorial",
        "Installation",
        "Example",
        "Resources",
        "Open datasets",
        "Other tutorials",
        "Citation",
        "Acknowledgements",
        "Help",
        "Reproducibility",
        "References"
      ],
      "created": "2024-04-20 06:29:45",
      "modified": "2026-05-20 12:57:33",
      "commits": 16
    },
    {
      "source": "panels.Rmd",
      "filename": "panels.html",
      "title": "Panel Catalogue",
      "author": "Giulio Benedetti",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Compositional Analysis",
        "Abundance plot",
        "Abundance density plot",
        "Prevalence plot",
        "Feature assay plot",
        "Complex heatmap plot",
        "Ordination Analysis",
        "RDA plot",
        "Scree plot",
        "Loading plot",
        "Reduced dimension plot",
        "Structural Analysis",
        "Row/Column tree plots",
        "Row/Column graph plots",
        "Other panels",
        "Row/Column tile plots",
        "Mediation plot",
        "Row/Column data tables",
        "Row/Column data plots",
        "Reproducibility",
        "References"
      ],
      "created": "2025-03-10 19:27:22",
      "modified": "2026-05-20 12:57:07",
      "commits": 4
    }
  ],
  "_score": 6.158362492095249,
  "_indexed": true,
  "_nocasepkg": "iseetree",
  "_universes": [
    "bioc",
    "riborings",
    "microbiome"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-26T18:10:52.000Z",
      "distro": "noble",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "ba370842ea623f471d9bf0f698d6933f4fcfc20244e85be7f150e2abfda3fe83",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-05-26T18:10:13.000Z",
      "distro": "noble",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "4942a7f80fbeb580cb0aa7ee6617ed40cc4738cabd6d5da26a28c36d076c91fb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-26T18:08:20.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "2ca06d9c8b193d8640b777e11d49d2d4f5ec130247ad40449a3120b5a1d08910",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-05-26T18:08:31.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "ae1f15f24947b389a824a616297561a1fa821dd0c868ce4768ae7d6e0103f00e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-05-26T18:10:03.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "73a42a453d785ee7b9c99741ee5979c60c5b97c636c19d1a7515180c8cd7ae0f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-26T18:09:22.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "c555cc18772bd27223ae39b7b05c3f95032a5fa904633df2677513a3150515d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-26T18:08:46.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "beeb592a20faaa5307860420221db486c540cb1e8c0fa3c54d50ff5ab066b88c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-05-26T18:08:28.000Z",
      "commit": "e4fd1ef538117635f8010f37eb2244ed112605aa",
      "fileid": "3e653ae980925db000a50124dd247956aeb56c157af812983d056da4a19e9ab6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26465825559"
    }
  ]
}