{
  "_id": "6a55c137ff0138dec5d68807",
  "Package": "imageFeatureTCGA",
  "Title": "Import features from hovernet, provgigapath into a\nMultiAssayExperiment",
  "Version": "1.1.6",
  "Authors@R": "c(\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\", \"aut\",\nc(ORCID = \"0000-0002-3242-0582\", affiliation =\n\"CUNY Graduate School of Public Health and Health Policy,\nNew York, NY USA\")\n),\nperson(\"Ilaria\", \"Billato\", , \"ilaria.billato@phd.unipd.it\",\nc(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3335-3254\",\naffiliation = \"Department of Biology, University of Padova\")\n),\nperson(\"Eslam\", \"Abousamra\", role = \"aut\", comment = c(\naffiliation = \"CUNY Graduate School of Public Health and Health Policy,\nNew York, NY USA\")\n),\nperson(\"Sehyun\", \"Oh\", , \"shbrief@gmail.com\", \"aut\",\nc(ORCID = \"0000-0002-9490-3061\", affiliation =\n\"CUNY Graduate School of Public Health and Health Policy,\nNew York, NY USA\")\n))",
  "Description": "The package imports data from HoverNet, and ProvGigaPath\npipelines. Pipeline output data are hosted in a self-owned\nonline repository. Package functionality conveniently\nincorporates pipeline data into existing MultiAssayExperiment\ninstances from curatedTCGAData.",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Infrastructure, DataImport, DataRepresentation",
  "BugReports": "https://github.com/waldronlab/imageFeatureTCGA/issues",
  "URL": "https://github.com/waldronlab/imageFeatureTCGA",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Date": "2026-07-13",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make libmagick++-dev gsfonts libbz2-dev libicu-dev\nliblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-13 20:24:24 UTC",
  "RemoteUrl": "https://github.com/bioc/imageFeatureTCGA",
  "RemoteRef": "HEAD",
  "RemoteSha": "cce042259ff781afbaaff5c4a1958716a9039368",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-14 04:43:17 UTC",
    "User": "root"
  },
  "Author": "Marcel Ramos [aut] (ORCID: <https://orcid.org/0000-0002-3242-0582>,\naffiliation: CUNY Graduate School of Public Health and Health\nPolicy, New York, NY USA),\nIlaria Billato [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3335-3254>, affiliation: Department of\nBiology, University of Padova),\nEslam Abousamra [aut] (affiliation: CUNY Graduate School of Public\nHealth and Health Policy, New York, NY USA),\nSehyun Oh [aut] (ORCID: <https://orcid.org/0000-0002-9490-3061>,\naffiliation: CUNY Graduate School of Public Health and Health\nPolicy, New York, NY USA)",
  "Maintainer": "Ilaria Billato <ilaria.billato@phd.unipd.it>",
  "_user": "bioc",
  "_type": "src",
  "_file": "imageFeatureTCGA_1.1.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/020153761c88557d669727edfc680fa0dc42c53ea087d8417b3bc3a6d95b7564",
  "_filesize": 174235,
  "_sha256": "020153761c88557d669727edfc680fa0dc42c53ea087d8417b3bc3a6d95b7564",
  "_expires": "2026-10-22T04:55:17.000Z",
  "_created": "2026-07-14T04:43:17.000Z",
  "_published": "2026-07-14T04:55:18.782Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682",
  "_status": "success",
  "_upstream": "https://github.com/bioc/imageFeatureTCGA",
  "_commit": {
    "id": "cce042259ff781afbaaff5c4a1958716a9039368",
    "author": "LiNk-NY <marcel.ramos@sph.cuny.edu>",
    "committer": "LiNk-NY <marcel.ramos@sph.cuny.edu>",
    "message": "version bump 1.1.6\n",
    "time": 1783974264
  },
  "_maintainer": {
    "name": "Ilaria Billato",
    "email": "ilaria.billato@phd.unipd.it",
    "orcid": "0000-0002-3335-3254"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 87001359777,
      "time": 262,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8300538760"
    },
    {
      "job": 87001359774,
      "time": 540,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8300606682"
    },
    {
      "job": 87001359790,
      "time": 420,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8300577535"
    },
    {
      "job": 87001359853,
      "time": 367,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8300636077"
    },
    {
      "job": 87001359834,
      "time": 374,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8300634203"
    },
    {
      "job": 87000488165,
      "time": 427,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8300474385"
    },
    {
      "job": 87001359761,
      "time": 244,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8300534878"
    },
    {
      "job": 87001359827,
      "time": 413,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8300575969"
    },
    {
      "job": 87001359780,
      "time": 429,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8300580187"
    },
    {
      "job": 87001359786,
      "time": 436,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8300581728"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "BiocBaseUtils",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "BiocIO",
      "role": "Imports"
    },
    {
      "package": "BumpyMatrix",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rjsoncons",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "TCGAutils",
      "role": "Imports"
    },
    {
      "package": "TENxIO",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "anndataR",
      "role": "Suggests"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "curatedTCGAData",
      "role": "Suggests"
    },
    {
      "package": "curl",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "imageTCGAutils",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "png",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SpatialFeatureExperiment",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    },
    {
      "package": "yaml",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 16
    },
    {
      "week": "2025-45",
      "n": 14
    },
    {
      "week": "2025-46",
      "n": 47
    },
    {
      "week": "2025-47",
      "n": 17
    },
    {
      "week": "2025-48",
      "n": 26
    },
    {
      "week": "2025-49",
      "n": 10
    },
    {
      "week": "2025-50",
      "n": 6
    },
    {
      "week": "2025-51",
      "n": 29
    },
    {
      "week": "2026-02",
      "n": 28
    },
    {
      "week": "2026-03",
      "n": 8
    },
    {
      "week": "2026-04",
      "n": 33
    },
    {
      "week": "2026-05",
      "n": 13
    },
    {
      "week": "2026-06",
      "n": 61
    },
    {
      "week": "2026-07",
      "n": 66
    },
    {
      "week": "2026-08",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 9
    },
    {
      "week": "2026-10",
      "n": 5
    },
    {
      "week": "2026-11",
      "n": 11
    },
    {
      "week": "2026-12",
      "n": 11
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 8
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-26",
      "n": 13
    },
    {
      "week": "2026-28",
      "n": 13
    },
    {
      "week": "2026-29",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.5",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "infrastructure",
    "dataimport",
    "datarepresentation"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "link-ny",
      "count": 336,
      "uuid": 4392950
    },
    {
      "user": "billila",
      "count": 80,
      "uuid": 78036851
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "shbrief",
      "count": 2,
      "uuid": 15724490
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 446,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 220,
    "source": "https://www.bioconductor.org/packages/stats/bioc/imageFeatureTCGA"
  },
  "_devurl": "https://github.com/waldronlab/imagefeaturetcga",
  "_searchresults": 19,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/imageFeatureTCGA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/waldronlab/imagefeaturetcga",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "embeddingStack",
    "getCatalog",
    "getFileURLs",
    "HoverNet",
    "import",
    "linkTCGA",
    "path",
    "ProvGiga",
    "ProvGigaList",
    "show"
  ],
  "_help": [
    {
      "page": "embeddingStack",
      "title": "Create an embedding stack from a ProvGigaList object",
      "topics": [
        "embeddingStack"
      ]
    },
    {
      "page": "getCatalog",
      "title": "Download the catalog of available HoVerNet and ProvGigaPath files",
      "topics": [
        "getCatalog",
        "getFileURLs"
      ]
    },
    {
      "page": "HoverNet",
      "title": "Import Hovernet JSON, H5AD, and PNG files into Bioconductor classes",
      "topics": [
        ".HoverNetPNG",
        "HoverNet",
        "HoverNet-class",
        "HoverNetH5AD-class",
        "HoverNetJSON-class",
        "HoverNetParquet-class",
        "HoverNetPNG-class",
        "import,HoverNetH5AD,ANY,ANY-method",
        "import,HoverNetJSON,ANY,ANY-method",
        "import,HoverNetParquet,ANY,ANY-method",
        "import,HoverNetPNG,ANY,ANY-method",
        "show,HoverNetJSON-method"
      ]
    },
    {
      "page": "linkTCGA",
      "title": "Link MultiAssayExperiment object to TCGA data",
      "topics": [
        "linkTCGA"
      ]
    },
    {
      "page": "ProvGiga",
      "title": "Import ProvGiga slide-level data into a Bioconductor class object",
      "topics": [
        "import,ProvGigaCSV,ANY,ANY-method",
        "ProvGiga",
        "ProvGiga-class",
        "ProvGigaCSV-class",
        "show,ProvGiga-method"
      ]
    },
    {
      "page": "ProvGigaList",
      "title": "ProvGigaList class for handling lists of ProvGiga objects",
      "topics": [
        ".ProvGigaList",
        "import,ProvGigaList,ANY,ANY-method",
        "path,ProvGigaList-method",
        "ProvGigaList",
        "ProvGigaList-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/imageFeatureTCGA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BumpyMatrix",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dir.expiry",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicDataCommons",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "MultiAssayExperiment",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RaggedExperiment",
    "rappdirs",
    "Rcpp",
    "RCurl",
    "readr",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rjsoncons",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "selectr",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "TCGAutils",
    "TENxIO",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "imageFeatureTCGA.Rmd",
      "filename": "imageFeatureTCGA.html",
      "title": "Import HoverNet and ProvGigaPath features with imageFeatureTCGA",
      "author": "Ilaria Billato",
      "engine": "knitr::rmarkdown",
      "headings": [
        "imageFeatureTCGA",
        "Overview",
        "Installation",
        "Data structure and technical details",
        "HoVerNet outputs",
        "ProvGigaPath embeddings",
        "Slide-level embeddings",
        "Tile-level embeddings",
        "Available Data",
        "Formats",
        "HoVerNet data",
        "ProvGigaPath data",
        "Importing HoVerNet data",
        "Importing ProvGigaPath embeddings",
        "Importing multiple ProvGigaPath files",
        "Mixed level imports",
        "See also",
        "Shiny App: imageTCGA",
        "Session Info"
      ],
      "created": "2026-02-10 17:12:44",
      "modified": "2026-03-02 11:35:41",
      "commits": 12
    }
  ],
  "_score": 6.630936119064192,
  "_indexed": true,
  "_nocasepkg": "imagefeaturetcga",
  "_universes": [
    "bioc",
    "waldronlab"
  ],
  "_previous": "1.1.5",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.6",
      "date": "2026-07-14T04:48:48.000Z",
      "distro": "resolute",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/f7f092b476da5037dba2e1032f992c20b52533e12a04c8c0e8e10967cc8ec925",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.6",
      "date": "2026-07-14T04:47:59.000Z",
      "distro": "resolute",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/15d52d2a943d0b0cc9eda11b91296f9f0395be42fd1909bab356eb4d77a6da62",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.6",
      "date": "2026-07-14T04:50:44.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/f953efd1a414074f915ea306032267f9ec74610c39e203b8d48392bc08f51c5d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.6",
      "date": "2026-07-14T04:50:36.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/26aca2978d91c0c4655fe36de9adaf7f25ed7296d9f1ffad9da922fb9ea3d8bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.6",
      "date": "2026-07-14T04:47:57.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/f59846d52fea20938ea32f0d80c40799883a498aae13ffb7b71afb8b6cadab5e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-07-14T04:46:21.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/62bdb6cda9f5a9cfcc3847dfb6ff21d671ec7038f30f5fd332c456b0160d8660",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-07-14T04:46:54.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/d55c287695c9f4687edf2c4d2e50aaea6810890be900d412fc9cc82800f9f038",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.6",
      "date": "2026-07-14T04:46:56.000Z",
      "commit": "cce042259ff781afbaaff5c4a1958716a9039368",
      "fileid": "https://r2.ropensci.org/b2c0c4c34b168dfa1e4095dcceb7dd65c278e3950d170fd2805435c617c40bb7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29306393682"
    }
  ]
}