{
  "_id": "6a1ac86a1d7bb097a09dc116",
  "Package": "iSEEfier",
  "Title": "Streamlining the creation of initial states for starting an iSEE\ninstance",
  "Version": "1.9.0",
  "Authors@R": "c(\nperson(given = \"Najla\", family = \"Abassi\", role = c(\"aut\", \"cre\"),\nemail = \"abassi.nejla96@gmail.com\", comment = c(ORCID = \"0000-0001-8357-0938\")\n),\nperson(given = \"Federico\", family = \"Marini\", role = c(\"aut\"),\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n)\n)",
  "Description": "iSEEfier provides a set of functionality to quickly and\nintuitively create, inspect, and combine initial configuration\nobjects. These can be conveniently passed in a straightforward\nmanner to the function call to launch iSEE() with the specified\nconfiguration. This package currently works seamlessly with the\nsets of panels provided by the iSEE and iSEEu packages, but can\nbe extended to accommodate the usage of any custom panel (e.g.\nfrom iSEEde, iSEEpathways, or any panel developed independently\nby the user).",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "biocViews": "CellBasedAssays, Clustering, DimensionReduction,\nFeatureExtraction, GUI, GeneExpression, ImmunoOncology,\nShinyApps, SingleCell, Software, Transcription,\nTranscriptomics, Visualization",
  "URL": "https://github.com/NajlaAbassi/iSEEfier",
  "BugReports": "https://github.com/NajlaAbassi/iSEEfier/issues",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:46 UTC",
  "RemoteUrl": "https://github.com/bioc/iSEEfier",
  "RemoteRef": "HEAD",
  "RemoteSha": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:45:20 UTC",
    "User": "root"
  },
  "Author": "Najla Abassi [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8357-0938>),\nFederico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)",
  "Maintainer": "Najla Abassi <abassi.nejla96@gmail.com>",
  "MD5sum": "c78b014b3876b5fb1803b30caf5f5966",
  "_user": "bioc",
  "_type": "src",
  "_file": "iSEEfier_1.9.0.tar.gz",
  "_fileid": "da6a0014a86b3932a9a59386224cfd2e060bea5b4a950d6b45ea9581a2cb43f0",
  "_filesize": 429065,
  "_sha256": "da6a0014a86b3932a9a59386224cfd2e060bea5b4a950d6b45ea9581a2cb43f0",
  "_created": "2026-05-30T07:45:20.000Z",
  "_published": "2026-05-30T11:22:18.108Z",
  "_jobs": [
    {
      "job": 78634429042,
      "time": 285,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306606490"
    },
    {
      "job": 78634429041,
      "time": 539,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306631202"
    },
    {
      "job": 78634429039,
      "time": 538,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306631124"
    },
    {
      "job": 78634429040,
      "time": 324,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307788959"
    },
    {
      "job": 78634429093,
      "time": 602,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307812992"
    },
    {
      "job": 78634100956,
      "time": 395,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306578743"
    },
    {
      "job": 78634429038,
      "time": 276,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306605542"
    },
    {
      "job": 78634429060,
      "time": 1908,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306765771"
    },
    {
      "job": 78634429053,
      "time": 1926,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7306767591"
    },
    {
      "job": 78634429045,
      "time": 1710,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306746916"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/iSEEfier",
  "_commit": {
    "id": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381366
  },
  "_maintainer": {
    "name": "Najla Abassi",
    "email": "abassi.nejla96@gmail.com",
    "login": "najlaabassi",
    "bluesky": "@guigadraws.bsky.social",
    "linkedin": "in/najla-abassi",
    "description": "Bioinformatician/Research Associate",
    "uuid": 112277365,
    "orcid": "0000-0001-8357-0938"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "iSEE",
      "role": "Imports"
    },
    {
      "package": "iSEEu",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "visNetwork",
      "role": "Imports"
    },
    {
      "package": "BiocBaseUtils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "scuttle",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 3
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "cellbasedassays",
    "clustering",
    "dimensionreduction",
    "featureextraction",
    "gui",
    "geneexpression",
    "immunooncology",
    "shinyapps",
    "singlecell",
    "software",
    "transcription",
    "transcriptomics",
    "visualization"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "najlaabassi",
      "count": 124,
      "uuid": 112277365
    },
    {
      "user": "federicomarini",
      "count": 88,
      "uuid": 7447478
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 234,
    "source": "https://www.bioconductor.org/packages/stats/bioc/iSEEfier"
  },
  "_devurl": "https://github.com/najlaabassi/iseefier",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/iSEEfier.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/najlaabassi/iseefier",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "glue_initials",
    "iSEEinit",
    "iSEEmarker",
    "iSEEnrich",
    "view_initial_network",
    "view_initial_tiles"
  ],
  "_help": [
    {
      "page": "constants-iSEEfier",
      "title": "Constant values used throughout iSEEfier",
      "topics": [
        "constants-iSEEfier",
        "iSEE_panel_colors"
      ]
    },
    {
      "page": "glue_initials",
      "title": "Glue together initial objects into one",
      "topics": [
        "glue_initials"
      ]
    },
    {
      "page": "iSEEinit",
      "title": "iSEEinit: Create an initial state of an iSEE instance for gene expression visualization",
      "topics": [
        "iSEEinit"
      ]
    },
    {
      "page": "iSEEmarker",
      "title": "iSEEmarker",
      "topics": [
        "iSEEmarker"
      ]
    },
    {
      "page": "iSEEnrich",
      "title": "iSEEnrich",
      "topics": [
        "iSEEnrich"
      ]
    },
    {
      "page": "view_initial_network",
      "title": "View an initial object as a network",
      "topics": [
        "view_initial_network"
      ]
    },
    {
      "page": "view_initial_tiles",
      "title": "View an initial object as a set of tiles",
      "topics": [
        "view_initial_tiles"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/iSEEfier/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "bslib",
    "cachem",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "colourpicker",
    "commonmark",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "crosstalk",
    "DelayedArray",
    "digest",
    "doParallel",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "fs",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "ggrepel",
    "GlobalOptions",
    "glue",
    "gtable",
    "hexbin",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "IRanges",
    "iSEE",
    "iSEEhex",
    "iSEEu",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listviewer",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "miniUI",
    "nlme",
    "otel",
    "pkgconfig",
    "png",
    "promises",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rintrojs",
    "rjson",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "shiny",
    "shinyAce",
    "shinydashboard",
    "shinyjs",
    "shinyWidgets",
    "SingleCellExperiment",
    "sourcetools",
    "SparseArray",
    "SummarizedExperiment",
    "tinytex",
    "vctrs",
    "vipor",
    "viridisLite",
    "visNetwork",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "iSEEfier_userguide.Rmd",
      "filename": "iSEEfier_userguide.html",
      "title": "The iSEEfier User's Guide",
      "author": "Najla Abassi, Federico Marini",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "Create an initial state for gene expression visualization using iSEEinit()",
        "Create an initial state for feature sets exploration using iSEEnrich()",
        "Create an initial state for marker gene exploration using iSEEmarker()",
        "Visualize a preview of the initial configurations with view_initial_tiles()",
        "Visualize network connections between panels with view_initial_network()",
        "Merge different initial configurations with glue_initials()",
        "Related work",
        "Session info"
      ],
      "created": "2024-03-12 16:02:31",
      "modified": "2025-07-23 10:06:37",
      "commits": 17
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "iseefier",
  "_universes": [
    "bioc",
    "najlaabassi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T07:50:59.000Z",
      "distro": "noble",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "478819b911eb26c4a0dea5f408bad910f9aa72f6b8183b31c74dac08dda5c494",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T07:50:30.000Z",
      "distro": "noble",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "c18487d88931c363852bf25ed4b35e78b7dcd45718d6583dabe909942f1c7e22",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T11:14:02.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "138ca828cb69fc5e590955c6bf13a7b7ba140c199c755c214083901749f5484f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T11:14:15.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "f05e1da8ad47ead829297cfcb6416c49a7fa386bfeea1c15e442b93cb7747135",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-05-30T07:50:28.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "afa05eeb30acca27abb7ae036f1fbe26570e33cf5ae13eba00a36eac9e332810",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T08:13:47.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "3556e75062e60a1b9b03a8a0d24c3e599cab5027d5e0999a55e5ea3c5ee8730e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T08:14:06.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "cd96048197b4723652704b685cbae46e53f9ef28ab145f8d327101c6f315aced",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T08:06:12.000Z",
      "commit": "5c275bebae4da36a3e82e37f2b08895a08a945e5",
      "fileid": "5b7afd068ba22c4033909485fd04e45b371026e10320ea6b5e80d5b0f2f81828",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678285879"
    }
  ]
}