{
  "_id": "6a20a422cd65a98ecbd17fc4",
  "Package": "PubMatrixR",
  "Title": "PubMed Pairwise Co-Occurrence Matrix Construction and\nVisualization",
  "Version": "1.0.0",
  "Authors@R": "c(\nperson(given = \"Tyler\", family = \"Laird\",\nemail = \"tylerscottlaird@gmail.com\", role = \"aut\"),\nperson(given = \"Enrique\", family = \"Toledo\",\nemail = \"enriquetoledo@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1460-4708\"))\n)",
  "Description": "Queries the 'NCBI' (National Center for Biotechnology\nInformation) Entrez 'E-utilities' API to count pairwise\nco-occurrences between two sets of terms in 'PubMed' or 'PubMed\nCentral'. It returns a matrix-like data frame of publication\ncounts and can export hyperlink-enabled results in CSV or ODS\nformat. The package also provides heatmap helpers for\nexploratory visualization of overlap patterns. Based on the\nmethod described in Becker et al. (2003) \"PubMatrix: a tool for\nmultiplex literature mining\" <doi:10.1186/1471-2105-4-61>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/ToledoEM/PubMatrixR-v2",
  "BugReports": "https://github.com/ToledoEM/PubMatrixR-v2/issues",
  "VignetteBuilder": "knitr",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev",
  "Repository": "https://toledoem.r-universe.dev",
  "Date/Publication": "2026-06-03 20:51:15 UTC",
  "RemoteUrl": "https://github.com/toledoem/pubmatrixr-v2",
  "RemoteRef": "HEAD",
  "RemoteSha": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 21:56:40 UTC",
    "User": "root"
  },
  "Author": "Tyler Laird [aut],\nEnrique Toledo [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1460-4708>)",
  "Maintainer": "Enrique Toledo <enriquetoledo@gmail.com>",
  "MD5sum": "aa81ae483c251b6f88a88a6b19a26d3c",
  "_user": "toledoem",
  "_type": "src",
  "_file": "PubMatrixR_1.0.0.tar.gz",
  "_fileid": "3d04f192844d979fe7413f2190ab6c0279f04f3c935e44b1633e1b3bcd13859f",
  "_filesize": 1431700,
  "_sha256": "3d04f192844d979fe7413f2190ab6c0279f04f3c935e44b1633e1b3bcd13859f",
  "_created": "2026-06-03T21:56:40.000Z",
  "_published": "2026-06-03T22:01:06.361Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79404121193,
      "time": 130,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7397722067"
    },
    {
      "job": 79404121151,
      "time": 179,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7397736263"
    },
    {
      "job": 79404121244,
      "time": 91,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7397710514"
    },
    {
      "job": 79404121219,
      "time": 110,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7397715731"
    },
    {
      "job": 79403626537,
      "time": 192,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7397680899"
    },
    {
      "job": 79404121180,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7397717263"
    },
    {
      "job": 79404121198,
      "time": 97,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7397712254"
    },
    {
      "job": 79404121186,
      "time": 72,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7397704650"
    },
    {
      "job": 79404121191,
      "time": 73,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7397704941"
    }
  ],
  "_buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/toledoem/pubmatrixr-v2",
  "_commit": {
    "id": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
    "author": "ToledoEM <8144940+ToledoEM@users.noreply.github.com>",
    "committer": "ToledoEM <8144940+ToledoEM@users.noreply.github.com>",
    "message": "bump to actions/checkout@v5\n",
    "time": 1780519875
  },
  "_maintainer": {
    "name": "Enrique Toledo",
    "email": "enriquetoledo@gmail.com",
    "login": "toledoem",
    "linkedin": "in/enrique-toledo",
    "orcid": "0000-0002-1460-4708",
    "description": "Leading teams in Pharma/Research/Genomics/AI-ML  \n\nBut this is for fun (science is fun too)",
    "uuid": 8144940
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "readODS",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "toledoem",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-46",
      "n": 3
    },
    {
      "week": "2025-47",
      "n": 9
    },
    {
      "week": "2025-48",
      "n": 5
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 6
    },
    {
      "week": "2026-10",
      "n": 2
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-20",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 3
    }
  ],
  "_tags": [
    {
      "name": "1.0.0",
      "date": "2026-03-28"
    }
  ],
  "_topics": [
    "bibliometrics",
    "datamining",
    "literature-mining",
    "ncbi-database",
    "pubmed"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "toledoem",
      "count": 34,
      "uuid": 8144940
    }
  ],
  "_userbio": {
    "uuid": 8144940,
    "type": "user",
    "name": "Enrique",
    "description": "Leading teams in Pharma/Research/Genomics/AI-ML  \r\n\r\nBut this is for fun (science is fun too)"
  },
  "_downloads": {
    "count": 113,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PubMatrixR"
  },
  "_devurl": "https://github.com/toledoem/pubmatrixr-v2",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PubMatrixR.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/toledoem/pubmatrixr-v2",
  "_realowner": "toledoem",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2026-03-12"
    }
  ],
  "_exports": [
    "plot_pubmatrix_heatmap",
    "PubMatrix",
    "pubmatrix_heatmap"
  ],
  "_help": [
    {
      "page": "plot_pubmatrix_heatmap",
      "title": "Create a formatted heatmap from PubMatrix results",
      "topics": [
        "plot_pubmatrix_heatmap"
      ]
    },
    {
      "page": "PubMatrix",
      "title": "Query 'PubMed' or 'PMC' and Build a Pairwise Co-occurrence Matrix",
      "topics": [
        "PubMatrix"
      ]
    },
    {
      "page": "pubmatrix_heatmap",
      "title": "Create a simple heatmap from PubMatrix results",
      "topics": [
        "pubmatrix_heatmap"
      ]
    }
  ],
  "_readme": "https://github.com/toledoem/pubmatrixr-v2/raw/HEAD/README.md",
  "_rundeps": [
    "cellranger",
    "cli",
    "cpp11",
    "farver",
    "glue",
    "gtable",
    "labeling",
    "lifecycle",
    "magrittr",
    "minty",
    "pbapply",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "readODS",
    "rematch",
    "rlang",
    "scales",
    "stringi",
    "tibble",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xml2",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "PubMatrixR: Literature Co-occurrence Analysis",
      "author": "ToledoEM",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Acknowledgments",
        "NCBI API Key (Recommended)",
        "Preparing Gene Sets",
        "Making the gene lists from MSigDB",
        "Fallback Example Dataset",
        "Literature Analysis",
        "Running PubMatrixR",
        "Results Table",
        "Visualization",
        "Publication Count Bar Plots",
        "Heatmap with Overlap Percentages",
        "Clean Heatmap",
        "Bar Plots for Asymmetric Lists",
        "Summary",
        "System Information"
      ],
      "created": "2025-10-24 22:48:28",
      "modified": "2026-03-07 16:27:32",
      "commits": 9
    }
  ],
  "_score": 4.740362689494244,
  "_indexed": true,
  "_nocasepkg": "pubmatrixr",
  "_universes": [
    "toledoem"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-03T21:58:54.000Z",
      "distro": "noble",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "e449e09ee31f42f3a54248b68f508385d07199ac8a0f4927e2f5da8252e3f36a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-03T21:59:40.000Z",
      "distro": "noble",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "c614c9f290d60aee8e99df80098eae8d7f835993b1f5d2e884c4cdbda7af8e7f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-03T21:58:16.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "6fc77ab276c1b2f10bd3cfd8483db530b187e255d147d7c459cd4927bfd97ef6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-03T21:58:30.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "7344720c1a70584fddacb8ca30e7a1ea727c5b45a803906e41348f70f3141999",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-06-03T21:58:52.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "d57d39b2dde1e56a2b560c0f447071b2a1e6c6cc055714ccb5f452fffd26ca27",
      "status": "success",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-03T21:58:16.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "d11d3bf5284ac92db86002b31fe1ac627055ad02b8bb8accd81d30b2c3d12f13",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-03T21:57:52.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "c58a398d74a4643cefda85626df9b21f524cfaefe3eb717c843de641821cb488",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-03T21:57:53.000Z",
      "commit": "92acfd4ea438e30ab22e844a2b6ee4bedaed85d1",
      "fileid": "119f1306393eb9e30d3249df28359f7d3d7bc322aef5f732e05d646b079788cc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/toledoem/actions/runs/26915353684"
    }
  ]
}