{
  "_id": "6a4de0b4d253724d3f6dd98f",
  "Package": "OncoScore",
  "Version": "1.41.0",
  "Date": "2026-03-09",
  "Title": "A tool to identify potentially oncogenic genes",
  "Authors@R": "c(person(\"Luca\", \"De Sano\", role=c(\"cre\",\"aut\"), email=\"luca.desano@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9618-3774\")),\nperson(\"Carlo\", \"Gambacorti Passerini\", role=c(\"ctb\"), email=\"carlo.gambacorti@unimib.it\"),\nperson(\"Rocco\", \"Piazza\", role=c(\"ctb\"), email=\"rocco.piazza@unimib.it\"),\nperson(\"Daniele\", \"Ramazzotti\", role=c(\"aut\"),email=\"daniele.ramazzotti@unimib.it\",\ncomment = c(ORCID = \"0000-0002-6087-2666\")),\nperson(\"Roberta\", \"Spinelli\", role=c(\"ctb\"), email=\"spinelli.roberta@gmail.com\"))",
  "Description": "OncoScore is a tool to measure the association of genes to\ncancer based on citation frequencies in biomedical literature.\nThe score is evaluated from PubMed literature by dynamically\nupdatable web queries.",
  "Encoding": "UTF-8",
  "License": "file LICENSE",
  "URL": "https://github.com/danro9685/OncoScore",
  "BugReports": "https://github.com/danro9685/OncoScore",
  "biocViews": "BiomedicalInformatics",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:05 UTC",
  "RemoteUrl": "https://github.com/bioc/OncoScore",
  "RemoteRef": "HEAD",
  "RemoteSha": "5f63256c882b1dedef96fcbc08852538f7c78115",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-08 05:25:54 UTC",
    "User": "root"
  },
  "Author": "Luca De Sano [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-9618-3774>),\nCarlo Gambacorti Passerini [ctb],\nRocco Piazza [ctb],\nDaniele Ramazzotti [aut] (ORCID:\n<https://orcid.org/0000-0002-6087-2666>),\nRoberta Spinelli [ctb]",
  "Maintainer": "Luca De Sano <luca.desano@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "OncoScore_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6e7491d0e03fc5a976bc6d783895f47481b657c6280341fb5771e28cf698ac6e",
  "_filesize": 456400,
  "_sha256": "6e7491d0e03fc5a976bc6d783895f47481b657c6280341fb5771e28cf698ac6e",
  "_expires": "2026-10-16T05:31:30.000Z",
  "_created": "2026-07-08T05:25:54.000Z",
  "_published": "2026-07-08T05:31:32.338Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395",
  "_status": "success",
  "_upstream": "https://github.com/bioc/OncoScore",
  "_commit": {
    "id": "5f63256c882b1dedef96fcbc08852538f7c78115",
    "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": 1777380185
  },
  "_maintainer": {
    "name": "Luca De Sano",
    "email": "luca.desano@gmail.com",
    "login": "luca-dex",
    "description": "",
    "uuid": 3315913,
    "orcid": "0000-0002-9618-3774"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85794147380,
      "time": 190,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159022208"
    },
    {
      "job": 85794147369,
      "time": 240,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8159034925"
    },
    {
      "job": 85794147382,
      "time": 293,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8159048839"
    },
    {
      "job": 85794147386,
      "time": 136,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8159008029"
    },
    {
      "job": 85794147366,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8159004561"
    },
    {
      "job": 85793603198,
      "time": 262,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8158971858"
    },
    {
      "job": 85794147429,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8159012506"
    },
    {
      "job": 85794147385,
      "time": 142,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8159009844"
    },
    {
      "job": 85794147374,
      "time": 172,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8159017923"
    },
    {
      "job": 85794147371,
      "time": 147,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8159012281"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "biomedicalinformatics"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "danro9685",
      "count": 332,
      "uuid": 5859159
    },
    {
      "user": "luca-dex",
      "count": 76,
      "uuid": 3315913
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 374,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OncoScore"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/danro9685/oncoscore",
  "_searchresults": 3,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OncoScore.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/danro9685/oncoscore",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "combine.query.results",
    "compute.oncoscore",
    "compute.oncoscore.from.region",
    "compute.oncoscore.timeseries",
    "get.genes.from.biomart",
    "perform.query",
    "perform.query.from.region",
    "perform.query.timeseries",
    "plot.oncoscore",
    "plot.oncoscore.timeseries"
  ],
  "_datasets": [
    {
      "name": "genes",
      "title": "A list of genes",
      "object": "genes",
      "file": "genes.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "query",
      "title": "The result of perform.web.query on genes",
      "object": "query",
      "file": "query.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "CitationsGene",
        "CitationsGeneInCancer"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "query.timepoints",
      "title": "The result of perform.time.series.query on genes and timepoints",
      "object": "query.timepoints",
      "file": "query.timepoints.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "timepoints",
      "title": "A list of timepoints",
      "object": "timepoints",
      "file": "timepoints.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "combine.query.results",
      "title": "combine.query.results",
      "topics": [
        "combine.query.results"
      ]
    },
    {
      "page": "combine.single.matrix",
      "title": "combine.single.matrix",
      "topics": [
        "combine.single.matrix"
      ]
    },
    {
      "page": "compute.frequencies.scores",
      "title": "compute.frequencies.scores",
      "topics": [
        "compute.frequencies.scores"
      ]
    },
    {
      "page": "compute.oncoscore",
      "title": "compute.oncoscore",
      "topics": [
        "compute.oncoscore"
      ]
    },
    {
      "page": "compute.oncoscore.from.region",
      "title": "compute.oncoscore.from.region",
      "topics": [
        "compute.oncoscore.from.region"
      ]
    },
    {
      "page": "compute.oncoscore.timeseries",
      "title": "compute.oncoscore.timeseries",
      "topics": [
        "compute.oncoscore.timeseries"
      ]
    },
    {
      "page": "estimate.oncogenes",
      "title": "estimate.oncogenes",
      "topics": [
        "estimate.oncogenes"
      ]
    },
    {
      "page": "genes",
      "title": "A list of genes",
      "topics": [
        "genes"
      ]
    },
    {
      "page": "get.genes.from.biomart",
      "title": "get.genes.from.biomart",
      "topics": [
        "get.genes.from.biomart"
      ]
    },
    {
      "page": "get.list.from.xml",
      "title": "get.list.from.xml",
      "topics": [
        "get.list.from.xml"
      ]
    },
    {
      "page": "get.pubmed.driver.analysis",
      "title": "get.pubmed.driver.analysis",
      "topics": [
        "get.pubmed.driver.analysis"
      ]
    },
    {
      "page": "perform.query",
      "title": "perform.query",
      "topics": [
        "perform.query"
      ]
    },
    {
      "page": "perform.query.from.region",
      "title": "perform.query.from.region",
      "topics": [
        "perform.query.from.region"
      ]
    },
    {
      "page": "perform.query.timeseries",
      "title": "perform.query.timeseries",
      "topics": [
        "perform.query.timeseries"
      ]
    },
    {
      "page": "plot.oncoscore",
      "title": "plot.oncoscore",
      "topics": [
        "plot.oncoscore"
      ]
    },
    {
      "page": "plot.oncoscore.timeseries",
      "title": "plot.oncoscore.timeseries",
      "topics": [
        "plot.oncoscore.timeseries"
      ]
    },
    {
      "page": "query",
      "title": "The result of perform.web.query on genes",
      "topics": [
        "query"
      ]
    },
    {
      "page": "query.timepoints",
      "title": "The result of perform.time.series.query on genes and timepoints",
      "topics": [
        "query.timepoints"
      ]
    },
    {
      "page": "timepoints",
      "title": "A list of timepoints",
      "topics": [
        "timepoints"
      ]
    },
    {
      "page": "try.scan",
      "title": "try.scan",
      "topics": [
        "try.scan"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/OncoScore/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "dplyr",
    "fastmap",
    "filelock",
    "generics",
    "glue",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "xml2",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "v1_introduction.Rmd",
      "filename": "v1_introduction.html",
      "title": "Introduction",
      "author": "Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Installing OncoScore",
        "Debug"
      ],
      "created": "2023-04-10 20:45:18",
      "modified": "2023-04-10 20:45:18",
      "commits": 1
    },
    {
      "source": "v2_running_OncoScore.Rmd",
      "filename": "v2_running_OncoScore.html",
      "title": "Running OncoScore",
      "author": "Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2023-04-10 20:45:18",
      "modified": "2023-04-10 20:45:18",
      "commits": 1
    }
  ],
  "_score": 6.146128035678238,
  "_indexed": true,
  "_nocasepkg": "oncoscore",
  "_universes": [
    "bioc",
    "luca-dex",
    "danro9685"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-08T05:29:05.000Z",
      "distro": "resolute",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/961fe60da03532fec9c597e1fe045d26206756f6b57e5c8b334db921b705abc5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-08T05:29:55.000Z",
      "distro": "resolute",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/4d714bcd061c6d6d4c7405e9671072c1474d6b8461548fb25ac73436416fbd9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-08T05:27:47.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/f292eeb7bab4b7cb2f0aa566a80430beb043a970b8f4befe0490dc5165f79737",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-08T05:27:22.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/c9aa284eb54bca2b9a644ed305b211e17203ce3cbf10ef97bac47fc8e676be9d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-07-08T05:28:49.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/70146233f0fdbbbeffa48c93e497e7c3bf6e136440cb8f46dee5b6712418c034",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:27:17.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/d6e23c426886f7061b85570097b5862ed441324a5bf13a83b10290f14f446a09",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:27:59.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/8eabad16496734db35ab850d56aecc3a575ac811e90dbcad768e149df0c51e95",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:27:32.000Z",
      "commit": "5f63256c882b1dedef96fcbc08852538f7c78115",
      "fileid": "https://r2.ropensci.org/f929b2b1053ffb3dabb5e49c1386dcc87b7ad7fa8e35f87d5fd5d16a6f7a65b0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919552395"
    }
  ]
}