{
  "_id": "6a49a03b162b78b26a583743",
  "Package": "annoLinker",
  "Type": "Package",
  "Title": "Annotating genomic regions through chromatin interaction links",
  "Version": "1.1.0",
  "Authors@R": "c(person(given=\"Jianhong\", family=\"Ou\", email=\"jou@morgridge.org\",\nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8652-2488\")),\nperson(given='Kenneth', family='Poss', email='kposs@morgridge.org',\nrole=c('aut', 'fnd')))",
  "Description": "Fast annotation of genomic peaks using DNA interaction\ndata by constructing interaction networks with igraph, where\npeaks overlapping any node in a connected subgraph are\nannotated with all genes in that subgraph. The annotation\nevidence could be visualized as either a network graph or a\ngenomic track integrated with gene annotation information.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "biocViews": "Network, Annotation, Visualization",
  "URL": "https://github.com/jianhong/annoLinker",
  "BugReports": "https://github.com/jianhong/annoLinker/issues",
  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:16 UTC",
  "RemoteUrl": "https://github.com/bioc/annoLinker",
  "RemoteRef": "HEAD",
  "RemoteSha": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 23:56:57 UTC",
    "User": "root"
  },
  "Author": "Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>),\nKenneth Poss [aut, fnd]",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>",
  "_user": "bioc",
  "_type": "src",
  "_file": "annoLinker_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/086abf603f11e2b0dd94880669fed2a116012a3438d4e07742c4d4a35baa8db9",
  "_filesize": 426890,
  "_sha256": "086abf603f11e2b0dd94880669fed2a116012a3438d4e07742c4d4a35baa8db9",
  "_expires": "2026-10-13T00:07:21.000Z",
  "_created": "2026-07-04T23:56:57.000Z",
  "_published": "2026-07-05T00:07:23.660Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 1
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311",
  "_status": "success",
  "_upstream": "https://github.com/bioc/annoLinker",
  "_commit": {
    "id": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
    "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": 1777381576
  },
  "_maintainer": {
    "name": "Jianhong Ou",
    "email": "jou@morgridge.org",
    "orcid": "0000-0002-8652-2488"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85177279185,
      "time": 286,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8086576928"
    },
    {
      "job": 85177279181,
      "time": 538,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8086600596"
    },
    {
      "job": 85177279199,
      "time": 533,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086600042"
    },
    {
      "job": 85177279201,
      "time": 255,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8086574084"
    },
    {
      "job": 85177279180,
      "time": 270,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086575488"
    },
    {
      "job": 85176921223,
      "time": 403,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086549796"
    },
    {
      "job": 85177279194,
      "time": 265,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8086575037"
    },
    {
      "job": 85177279186,
      "time": 437,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8086590961"
    },
    {
      "job": 85177279177,
      "time": 493,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8086596180"
    },
    {
      "job": 85177279183,
      "time": 459,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8086593024"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "InteractionSet",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "progressr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "trackViewer",
      "role": "Imports"
    },
    {
      "package": "visNetwork",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Drerio.UCSC.danRer10.refGene",
      "role": "Suggests"
    },
    {
      "package": "org.Dr.eg.db",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 7
    },
    {
      "week": "2025-44",
      "n": 6
    },
    {
      "week": "2025-45",
      "n": 4
    },
    {
      "week": "2026-01",
      "n": 3
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "network",
    "annotation",
    "visualization"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jianhong",
      "count": 21,
      "uuid": 5640707
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/jianhong/annolinker",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/annoLinker.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jianhong/annolinker",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "anno_clusters",
    "anno_event",
    "anno_evidence",
    "anno_feature",
    "anno_featurebin",
    "anno_graph",
    "anno_peakbin",
    "anno_peaks",
    "annoLinker",
    "as.data.frame",
    "coerce",
    "head",
    "plotEvidence",
    "show"
  ],
  "_help": [
    {
      "page": "annoLinker-package",
      "title": "Annotating genomic regions through chromatin interaction links",
      "topics": [
        "annoLinker-package"
      ]
    },
    {
      "page": "annoLinker",
      "title": "Annotate Peaks with DNA Interaction Networks Using Graph Clustering",
      "topics": [
        "annoLinker"
      ]
    },
    {
      "page": "annoLinkerResult-class",
      "title": "Class '\"annoLinkerResult\"'",
      "topics": [
        "annoLinkerResult",
        "annoLinkerResult-class",
        "anno_clusters",
        "anno_clusters,annoLinkerResult-method",
        "anno_event",
        "anno_event,annoLinkerResult,numeric-method",
        "anno_event,annoLinkerResult-method",
        "anno_evidence",
        "anno_evidence,annoLinkerResult,numeric-method",
        "anno_evidence,annoLinkerResult-method",
        "anno_feature",
        "anno_feature,annoLinkerResult,numeric-method",
        "anno_feature,annoLinkerResult-method",
        "anno_featurebin",
        "anno_featurebin,annoLinkerResult,numeric-method",
        "anno_featurebin,annoLinkerResult-method",
        "anno_graph",
        "anno_graph,annoLinkerResult-method",
        "anno_peakbin",
        "anno_peakbin,annoLinkerResult,numeric-method",
        "anno_peakbin,annoLinkerResult-method",
        "anno_peaks",
        "anno_peaks,annoLinkerResult-method",
        "as.data.frame,annoLinkerResult-method",
        "coerce",
        "coerce,annoLinkerResult,GRanges-method",
        "head,annoLinkerResult,ANY-method",
        "head,annoLinkerResult-method",
        "length,annoLinkerResult-method",
        "show,annoLinkerResult-method"
      ]
    },
    {
      "page": "plotEvidence",
      "title": "Plot interaction network for visualization",
      "topics": [
        "plotEvidence"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/annoLinker/raw/HEAD/readme.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dichromat",
    "digest",
    "dir.expiry",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "globals",
    "glue",
    "gridExtra",
    "grImport",
    "gtable",
    "Gviz",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "InteractionSet",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lazyeval",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnet",
    "openssl",
    "parallelly",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "progressr",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "strawr",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "trackViewer",
    "txdbmaker",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "visNetwork",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "annoLinker.Rmd",
      "filename": "annoLinker.html",
      "title": "annoLinker Vignette: Annotating genomic regions through chromatin interaction links",
      "author": "Jianhong Ou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Quick start",
        "SessionInfo"
      ],
      "created": "2025-10-23 20:44:04",
      "modified": "2026-01-22 21:07:41",
      "commits": 7
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "annolinker",
  "_universes": [
    "bioc",
    "jianhong"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-05T00:01:45.000Z",
      "distro": "resolute",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/fcc028baa9ea7f6efd971028af817ddb44de7a80eee0b2d61c0e1d4cbebf9eea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-07-05T00:01:50.000Z",
      "distro": "resolute",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/cf7f9d18b0353e4b72358438c8e181934ef258c423bbd8c1946d377753190290",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T23:59:29.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/ed98fc0e65766a9bd7271cfd44766861ad2574023f03931521e1139d03bfe297",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-07-04T23:59:35.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/ce7d772c2f38a2f1ede9eb1b7688ea34c69e80556234e5e4e561769fa9e4ac35",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-07-05T00:02:13.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/c77be7e13f14be7b1fa795222af348aefbc32274cffd3a986d61d2145e9ae330",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-04T23:59:56.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/0646d81da813e7f3daf87a15433d3c74d893530d0902cd04d9e4fdc21c79cd28",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-05T00:00:01.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/5c1f4a4f284e10257f45016e3fc5881fd43c4b021bb5bfc969830f7dea3cc31a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-07-04T23:59:59.000Z",
      "commit": "3cef05638b6a24ef24deb06daef1648e75c25cb7",
      "fileid": "https://r2.ropensci.org/30ee5fa023b25c4c4f7aca4828aa4749751f74a348ea307d6a8de0ed48788c5d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723564311"
    }
  ]
}