{
  "_id": "6a1acb531d7bb097a09ddf91",
  "Package": "HPAanalyze",
  "Type": "Package",
  "Title": "Retrieve and analyze data from the Human Protein Atlas",
  "Date": "2025-12-07",
  "Version": "1.31.0",
  "Authors@R": "person(\"Anh Nhat\", \"Tran\", email = \"trannhatanh89@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Provide functions for retrieving, exploratory analyzing\nand visualizing the Human Protein Atlas data. HPAanalyze is\ndesigned to fullfill 3 main tasks: (1) Import, subsetting and\nexport downloadable datasets; (2) Visualization of downloadable\ndatasets for exploratory analysis; and (3) Working with the\nindividual XML files. This package aims to serve researchers\nwith little programming experience, but also allow power users\nto use the imported data as desired.",
  "License": "GPL-3 + file LICENSE",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "Proteomics, CellBiology, Visualization, Software",
  "URL": "https://github.com/anhtr/HPAanalyze",
  "BugReports": "https://github.com/anhtr/HPAanalyze/issues",
  "LazyData": "true",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:34 UTC",
  "RemoteUrl": "https://github.com/bioc/HPAanalyze",
  "RemoteRef": "HEAD",
  "RemoteSha": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:01:04 UTC",
    "User": "root"
  },
  "Author": "Anh Nhat Tran [aut, cre]",
  "Maintainer": "Anh Nhat Tran <trannhatanh89@gmail.com>",
  "MD5sum": "89e4aa76144e7c1b0b212eb18e4bb9a6",
  "_user": "bioc",
  "_type": "src",
  "_file": "HPAanalyze_1.31.0.tar.gz",
  "_fileid": "6bc737a9887c264861e42a46cec6cf021db362e6ca633cfaf9008721706bf70b",
  "_filesize": 3408775,
  "_sha256": "6bc737a9887c264861e42a46cec6cf021db362e6ca633cfaf9008721706bf70b",
  "_created": "2026-05-30T08:01:04.000Z",
  "_published": "2026-05-30T11:34:43.898Z",
  "_jobs": [
    {
      "job": 78635217947,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306689725"
    },
    {
      "job": 78635217942,
      "time": 263,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306696623"
    },
    {
      "job": 78635217939,
      "time": 201,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306690824"
    },
    {
      "job": 78635217932,
      "time": 109,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307876167"
    },
    {
      "job": 78635217938,
      "time": 134,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307878911"
    },
    {
      "job": 78635003156,
      "time": 235,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306671334"
    },
    {
      "job": 78635217945,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306684556"
    },
    {
      "job": 78635217950,
      "time": 142,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306685188"
    },
    {
      "job": 78635217935,
      "time": 138,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306684821"
    },
    {
      "job": 78635217963,
      "time": 148,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306685706"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/HPAanalyze",
  "_commit": {
    "id": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
    "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": 1777380514
  },
  "_maintainer": {
    "name": "Anh Nhat Tran",
    "email": "trannhatanh89@gmail.com",
    "login": "anhtr",
    "mastodon": "@anhtr@fosstodon.org",
    "description": "",
    "uuid": 22552876
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 35
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-49",
      "n": 6
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "proteomics",
    "cellbiology",
    "visualization",
    "software"
  ],
  "_stars": 39,
  "_contributors": [
    {
      "user": "anhtr",
      "count": 359,
      "uuid": 22552876
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 546,
    "source": "https://www.bioconductor.org/packages/stats/bioc/HPAanalyze"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/anhtr/hpaanalyze",
  "_searchresults": 40,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HPAanalyze.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/anhtr/hpaanalyze",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "hpaDownload",
    "hpaExport",
    "hpaListParam",
    "hpaSubset",
    "hpaVis",
    "hpaVisPatho",
    "hpaVisSubcell",
    "hpaVisTissue",
    "hpaXml",
    "hpaXmlAntibody",
    "hpaXmlGet",
    "hpaXmlProtClass",
    "hpaXmlTissueExpr",
    "hpaXmlTissueExprSum"
  ],
  "_datasets": [
    {
      "name": "hpa_histology_data",
      "title": "HPA histology dataset",
      "object": "hpa_histology_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "hpa_histology_data",
      "title": "HPA histology dataset",
      "topics": [
        "hpa_histology_data"
      ]
    },
    {
      "page": "hpaDownload",
      "title": "Download datasets",
      "concept": [
        "downloadable datasets functions"
      ],
      "topics": [
        "hpaDownload"
      ]
    },
    {
      "page": "hpaExport",
      "title": "Export the subset data",
      "concept": [
        "downloadable datasets functions"
      ],
      "topics": [
        "hpaExport"
      ]
    },
    {
      "page": "hpaListParam",
      "title": "Subset downloaded data",
      "concept": [
        "downloadable datasets functions"
      ],
      "topics": [
        "hpaListParam",
        "hpaSubset"
      ]
    },
    {
      "page": "hpaVis",
      "title": "Visualize data in one function",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "hpaVis"
      ]
    },
    {
      "page": "hpaVisPatho",
      "title": "Visualize pathology data",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "hpaVisPatho"
      ]
    },
    {
      "page": "hpaVisSubcell",
      "title": "Visualize subcellular location data",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "hpaVisSubcell"
      ]
    },
    {
      "page": "hpaVisTissue",
      "title": "Visualize tissue data",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "hpaVisTissue"
      ]
    },
    {
      "page": "hpaXml",
      "title": "Extract details about an individual protein from XML file in one function",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXml"
      ]
    },
    {
      "page": "hpaXmlAntibody",
      "title": "Extract antibody information",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXmlAntibody"
      ]
    },
    {
      "page": "hpaXmlGet",
      "title": "Download and import xml file",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXmlGet"
      ]
    },
    {
      "page": "hpaXmlProtClass",
      "title": "Extract protein classes",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXmlProtClass"
      ]
    },
    {
      "page": "hpaXmlTissueExpr",
      "title": "Extract tissue expression details",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXmlTissueExpr"
      ]
    },
    {
      "page": "hpaXmlTissueExprSum",
      "title": "Extract tissue expression and download images",
      "concept": [
        "xml functions"
      ],
      "topics": [
        "hpaXmlTissueExprSum"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/HPAanalyze/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "openxlsx",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xml2",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "a_HPAanalyze_quick_start.Rmd",
      "filename": "a_HPAanalyze_quick_start.html",
      "title": "Quick-start guide: Acquire and visualize the Human Protein Atlas (HPA) data in one function with HPAanalyze ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "The different HPA data formats",
        "HPAanalyze overview",
        "Visualize protein expression data",
        "Acquiring individual sample data from the Human Protein Atlas",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 11
    },
    {
      "source": "b_HPAanalyze_indepth.Rmd",
      "filename": "b_HPAanalyze_indepth.html",
      "title": "In-depth: Working with Human Protein Atlas (HPA) data in R with HPAanalyze ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Summary",
        "Background",
        "The different HPA data formats",
        "HPAanalyze overview",
        "Obtaining HPAanalyze",
        "Full dataset import, subsetting and export",
        "Download and import data with hpaDownload()",
        "The \"histology\" datasets",
        "Other datasets",
        "List available parameter for subsetting with hpaListParam()",
        "Subset data with hpaSubset()",
        "Export data with hpaExport()",
        "Visualization",
        "Unbrella function hpaVis()",
        "Visualize tissue data with hpaVisTissue()",
        "Visualize expression in cancer with hpaVisPatho()",
        "Visualize subcellular location data with hpaVisSubcell()",
        "Individual xml import and image downloading",
        "The umbrella function hpaXml",
        "Import xml file with hpaXmlGet()",
        "View protein classes with hpaXmlProtClass()",
        "Get summary and images of tissue expression with hpaXmlTissueExprSum()",
        "Get details of individual IHC samples with hpaXmlAntibody() and hpaXmlTissueExpr()",
        "Compatibility with hpar Bioconductor package",
        "Acknowledgements",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 12
    },
    {
      "source": "c_HPAanalyze_case_query.Rmd",
      "filename": "c_HPAanalyze_case_query.html",
      "title": "Tutorial: Combine HPAanalyze with your Human Protein Atlas (HPA) queries ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The case",
        "The solution",
        "Create your query",
        "Visualization",
        "XML extraction",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 12
    },
    {
      "source": "d_HPAanalyze_case_offline_xml.Rmd",
      "filename": "d_HPAanalyze_case_offline_xml.html",
      "title": "Tutorial: Working with Human Protein Atlas (HPA) xml files offline ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The case",
        "The solution",
        "Download and keep a local version of the xml files for yourself",
        "Business as usual with hpaXml functions",
        "Save your parsed objects",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 11
    },
    {
      "source": "e_HPAanalyze_case_json.Rmd",
      "filename": "e_HPAanalyze_case_json.html",
      "title": "Tutorial: Export Human Protein Atlas (HPA) data as JSON ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The case",
        "The solution",
        "Download and subset data",
        "Convert dataframes to JSON",
        "Write JSON file",
        "In one function",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 11
    },
    {
      "source": "f_HPAanalyze_case_images.Rmd",
      "filename": "f_HPAanalyze_case_images.html",
      "title": "Tutorial: Download histology images from the Human Protein Atlas ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The case",
        "The solution",
        "Get the download links",
        "Download the images",
        "Notes",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 14
    },
    {
      "source": "z_HPAanalyze_paper_figures.Rmd",
      "filename": "z_HPAanalyze_paper_figures.html",
      "title": "Code for figures from HPAanalyze paper ",
      "author": "Anh N. Tran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Figure 2",
        "Figure 3",
        "Figure 4",
        "Figure 5",
        "Copyright"
      ],
      "created": "2019-11-08 22:20:09",
      "modified": "2025-05-28 20:28:16",
      "commits": 10
    }
  ],
  "_score": 7.816373888752363,
  "_indexed": true,
  "_nocasepkg": "hpaanalyze",
  "_universes": [
    "bioc",
    "anhtr"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T08:04:51.000Z",
      "distro": "noble",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "52e0ddf950d82f781bca3c1fca9731def537568f3a257754b6a2a1106bcb387e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-30T08:03:53.000Z",
      "distro": "noble",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "b16f71a03dfad7a21e55be375f771dd71e319302c6a5b3f4b8970137fe8214aa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T11:33:13.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "8034fb08ffdc94673c9abb9361808e0cdd649432e5ba8c29b6cda35e4aa80eba",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-30T11:33:33.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "3c100c2becd4c795c702e036e0488a37692a736073e26471a5821216881f4faf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-05-30T08:03:43.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "de1e823e427301ed67375bfe3814042a26eedab71f50c8b721a80a1883be67f7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:02:52.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "7443623a4bad36266a5b51b9dda74214b074cee0d3d983ad09f6ed54da7857dc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:02:43.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "bf2a69750afc5f0c5121342a22841eb53f7394d8935d2c14fdfbfc70b0cc786a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-30T08:02:48.000Z",
      "commit": "9926657cf2e6f5110b30e31b2e0392bec901ad61",
      "fileid": "d00bcb5f0285517923d98a6e209f0f0fa64bc0ba30d74ea9d2cdb7c479f783d7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678639197"
    }
  ]
}