{
  "_id": "6aca20f6fe5cc25786e8502d",
  "Package": "BioPlex",
  "Title": "R-side access to BioPlex protein-protein interaction data",
  "Version": "1.18.0",
  "Authors@R": "c(person(\"Ludwig\", \"Geistlinger\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ludwig_geistlinger@hms.harvard.edu\"),\nperson(\"Robert\", \"Gentleman\",\nrole = \"aut\"))",
  "Description": "The BioPlex package implements access to the BioPlex\nprotein-protein interaction networks and related resources from\nwithin R. Besides protein-protein interaction networks for\nHEK293 and HCT116 cells, this includes access to CORUM protein\ncomplex data, and transcriptome and proteome data for the two\ncell lines. Functionality focuses on importing the various data\nresources and storing them in dedicated Bioconductor data\nstructures, as a foundation for integrative downstream analysis\nof the data.",
  "URL": "https://github.com/ccb-hms/BioPlex",
  "BugReports": "https://github.com/ccb-hms/BioPlex/issues",
  "Encoding": "UTF-8",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "CellCulture, ColonCancerData, ExperimentHub, ExpressionData,\nGEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome,\nReproducibleResearch, RNASeqData",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev libx11-dev\nzlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:36:15 UTC",
  "RemoteUrl": "https://github.com/bioc/BioPlex",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a976b809e971ed53278d22676c4403dd7b372a7a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 11:18:32 UTC",
    "User": "root"
  },
  "Author": "Ludwig Geistlinger [aut, cre],\nRobert Gentleman [aut]",
  "Maintainer": "Ludwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "BioPlex_1.18.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7fe8ed45ef49a28279c87e320e55a156ae89691e5ca45514872f7362283cc6ab",
  "_filesize": 379344,
  "_sha256": "7fe8ed45ef49a28279c87e320e55a156ae89691e5ca45514872f7362283cc6ab",
  "_expires": "2027-01-18T11:26:44.000Z",
  "_created": "2026-10-10T11:18:32.000Z",
  "_published": "2026-10-10T11:26:46.496Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047591611",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 10
  },
  "_upstream": "https://github.com/bioc/BioPlex",
  "_commit": {
    "id": "a976b809e971ed53278d22676c4403dd7b372a7a",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379775
  },
  "_maintainer": {
    "name": "Ludwig Geistlinger",
    "email": "ludwig_geistlinger@hms.harvard.edu",
    "login": "lgeistlinger",
    "description": "",
    "uuid": 11871050
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114201268059,
      "time": 168,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11668851123"
    },
    {
      "job": 114201267588,
      "time": 363,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11667818629"
    },
    {
      "job": 114201267671,
      "time": 431,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11668696523"
    },
    {
      "job": 114200200993,
      "time": 379,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668232522"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "GEOquery",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "DEXSeq",
      "role": "Suggests"
    },
    {
      "package": "ExperimentHub",
      "role": "Suggests"
    },
    {
      "package": "depmap",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-05",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24",
      "repository": "data/experiment"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23",
      "repository": "data/experiment"
    }
  ],
  "_topics": [
    "cellculture",
    "coloncancerdata",
    "experimenthub",
    "expressiondata",
    "geo",
    "genome",
    "homo_sapiens_data",
    "massspectrometrydata",
    "proteome",
    "reproducibleresearch",
    "rnaseqdata",
    "datapkg"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "lgeistlinger",
      "count": 93,
      "uuid": 11871050
    },
    {
      "user": "hpages",
      "count": 8,
      "uuid": 8810451
    },
    {
      "user": "lshep",
      "count": 8,
      "uuid": 18724380
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 84,
  "_devurl": "https://github.com/ccb-hms/bioplex",
  "_searchresults": 18,
  "_datapkg": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BioPlex.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "annotatePFAM",
    "bioplex2graph",
    "ccleProteome2SummarizedExperiment",
    "corum2graphlist",
    "corum2list",
    "getBioPlex",
    "getBioplexProteome",
    "getCorum",
    "getGSE122425",
    "hasSubunit",
    "mapSummarizedExperimentOntoGraph"
  ],
  "_help": [
    {
      "page": "annotatePFAM",
      "title": "Annotate PFAM domains to BioPlex PPI graph",
      "topics": [
        "annotatePFAM"
      ]
    },
    {
      "page": "bioplex2graph",
      "title": "Representation of BioPlex PPIs in a graph data structure",
      "topics": [
        "bioplex2graph"
      ]
    },
    {
      "page": "ccleProteome2SummarizedExperiment",
      "title": "Convenient access to the CCLE proteome data",
      "topics": [
        "ccleProteome2SummarizedExperiment"
      ]
    },
    {
      "page": "corum2graphlist",
      "title": "Represent CORUM protein complex data as a list of graph instances",
      "topics": [
        "corum2graphlist"
      ]
    },
    {
      "page": "corum2list",
      "title": "Represent CORUM protein complex data as a simple list",
      "topics": [
        "corum2list"
      ]
    },
    {
      "page": "getBioPlex",
      "title": "Obtain BioPlex protein-protein interaction data",
      "topics": [
        "getBioPlex"
      ]
    },
    {
      "page": "getBioplexProteome",
      "title": "Obtain BioPlex3 proteome data",
      "topics": [
        "getBioplexProteome"
      ]
    },
    {
      "page": "getCorum",
      "title": "Obtain CORUM protein complex data",
      "topics": [
        "getCorum"
      ]
    },
    {
      "page": "getGSE122425",
      "title": "Convenient access to 293T transcriptome data from GEO",
      "topics": [
        "getGSE122425"
      ]
    },
    {
      "page": "hasSubunit",
      "title": "Identify CORUM complexes that have a subunit of interest",
      "topics": [
        "hasSubunit"
      ]
    },
    {
      "page": "mapSummarizedExperimentOntoGraph",
      "title": "Map experimental data onto a graph",
      "topics": [
        "mapSummarizedExperimentOntoGraph"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/BioPlex/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "generics",
    "GenomicRanges",
    "GEOquery",
    "glue",
    "graph",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "lattice",
    "lifecycle",
    "limma",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "readr",
    "rentrez",
    "rlang",
    "RSQLite",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "selectr",
    "Seqinfo",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "BioPlex.Rmd",
      "filename": "BioPlex.html",
      "title": "Import and representation of BioPlex PPI data and related resources",
      "author": "Ludwig Geistlinger and Robert Gentleman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Installation",
        "Data resources",
        "General",
        "BioPlex PPIs",
        "ID mapping",
        "Data structures for BioPlex PPIs",
        "PFAM domains",
        "CORUM complexes",
        "Data structures for CORUM complexes",
        "Transcriptome data",
        "HEK293T cells",
        "GSE122425",
        "HCT116 cells",
        "Cancer Cell Line Encyclopedia (CCLE)",
        "Klijn et al., 2015",
        "Splicing data",
        "Proteome data",
        "CCLE",
        "Relative protein expression data from BioPlex3.0",
        "Caching",
        "SessionInfo"
      ],
      "created": "2021-02-16 15:44:14",
      "modified": "2026-01-27 01:47:36",
      "commits": 37
    },
    {
      "source": "BasicChecks.Rmd",
      "filename": "BasicChecks.html",
      "title": "Basic checks of BioPlex PPI data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Check: identify CORUM complexes that have a subunit of interest",
        "Check: extract BioPlex PPIs for a CORUM complex",
        "Check: identify interacting domains for a PFAM domain of interest",
        "Check: expressed genes are showing up as prey (293T cells)",
        "Check: is there a relationship between prey frequency and prey expression level?",
        "Check: differential protein expression (HEK293 vs. HCT116)",
        "SessionInfo"
      ],
      "created": "2021-04-19 17:48:21",
      "modified": "2026-01-27 01:47:36",
      "commits": 19
    }
  ],
  "_score": 6.936513742478893,
  "_indexed": false,
  "_nocasepkg": "bioplex",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/BioPlex",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-10T11:22:00.000Z",
      "distro": "resolute",
      "commit": "a976b809e971ed53278d22676c4403dd7b372a7a",
      "fileid": "https://r2.ropensci.org/69634a63078daf7c266777df0304b8d43633b398c04a5f6d0fde657865798ab5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047591611"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-10T11:23:13.000Z",
      "distro": "resolute",
      "commit": "a976b809e971ed53278d22676c4403dd7b372a7a",
      "fileid": "https://r2.ropensci.org/5605d7f65a820685ed3ca986317731be278f2ad2e13bff0d464f0ce902dfb9fd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047591611"
    }
  ]
}