{
  "_id": "6a548043ff0138dec5d644be",
  "Package": "GenomicOZone",
  "Type": "Package",
  "Title": "Delineate outstanding genomic zones of differential gene\nactivity",
  "biocViews": "Software, GeneExpression, Transcription,\nDifferentialExpression, FunctionalPrediction, GeneRegulation,\nBiomedicalInformatics, CellBiology, FunctionalGenomics,\nGenetics, SystemsBiology, Transcriptomics, Clustering,\nRegression, RNASeq, Annotation, Visualization, Sequencing,\nCoverage, DifferentialMethylation, GenomicVariation,\nStructuralVariation, CopyNumberVariation",
  "Version": "1.27.0",
  "Date": "2025-07-22",
  "Author": "Hua Zhong, Mingzhou Song",
  "Maintainer": "Hua Zhong<zh9118@gmail.com>, Mingzhou Song\n<joemsong@cs.nmsu.edu>",
  "Description": "The package clusters gene activity along chromosome into\nzones, detects differential zones as outstanding, and\nvisualizes maps of outstanding zones across the genome. It\nenables characterization of effects on multiple genes within\nadaptive genomic neighborhoods, which could arise from genome\nreorganization, structural variation, or epigenome alteration.\nIt guarantees cluster optimality, linear runtime to sample\nsize, and reproducibility. One can apply it on genome-wide\nactivity measurements such as copy number, transcriptomic,\nproteomic, and methylation data.",
  "License": "LGPL (>=3)",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "RdMacros": "Rdpack",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:43 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicOZone",
  "RemoteRef": "HEAD",
  "RemoteSha": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
  "Packaged": {
    "Date": "2026-07-13 05:56:07 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "GenomicOZone_1.27.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/331abce0b8db3dc2bb37c15dab2b52e6571b4eef36917b820a5f3f6a902b9b0a",
  "_filesize": 1452068,
  "_sha256": "331abce0b8db3dc2bb37c15dab2b52e6571b4eef36917b820a5f3f6a902b9b0a",
  "_expires": "2026-10-21T06:05:53.000Z",
  "_created": "2026-07-13T05:56:07.000Z",
  "_published": "2026-07-13T06:05:55.544Z",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952",
  "_status": "success",
  "_upstream": "https://github.com/bioc/GenomicOZone",
  "_commit": {
    "id": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
    "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": 1777380643
  },
  "_maintainer": {
    "name": "Hua Zhong",
    "email": "joemsong@cs.nmsu.edu",
    "login": "zh9118",
    "description": "",
    "uuid": 13088022
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 86744855751,
      "time": 310,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8270388621"
    },
    {
      "job": 86744855759,
      "time": 494,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8270439037"
    },
    {
      "job": 86744855786,
      "time": 511,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270443531"
    },
    {
      "job": 86744855747,
      "time": 227,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8270393323"
    },
    {
      "job": 86744855772,
      "time": 296,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270414198"
    },
    {
      "job": 86744062611,
      "time": 382,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270309990"
    },
    {
      "job": 86744855715,
      "time": 191,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8270357620"
    },
    {
      "job": 86744855790,
      "time": 369,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8270404800"
    },
    {
      "job": 86744855787,
      "time": 380,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8270407742"
    },
    {
      "job": 86744855745,
      "time": 354,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270400121"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "Ckmeans.1d.dp",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "biomaRt",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "lsr",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "ggbio",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "role": "Imports"
    },
    {
      "package": "readxl",
      "role": "Suggests"
    },
    {
      "package": "GEOquery",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "geneexpression",
    "transcription",
    "differentialexpression",
    "functionalprediction",
    "generegulation",
    "biomedicalinformatics",
    "cellbiology",
    "functionalgenomics",
    "genetics",
    "systemsbiology",
    "transcriptomics",
    "clustering",
    "regression",
    "rnaseq",
    "annotation",
    "visualization",
    "sequencing",
    "coverage",
    "differentialmethylation",
    "genomicvariation",
    "structuralvariation",
    "copynumbervariation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 446,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 356,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GenomicOZone"
  },
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GenomicOZone.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "extract_genes",
    "extract_outstanding_zones",
    "extract_zone_expression",
    "extract_zones",
    "GenomicOZone",
    "GOZDataSet",
    "plot_chromosomes",
    "plot_genome",
    "plot_zones"
  ],
  "_help": [
    {
      "page": "extract_outputs",
      "title": "Extract annotation of genes, zones, outstanding zones, and expression of zones",
      "topics": [
        "extract_genes",
        "extract_outputs",
        "extract_outstanding_zones",
        "extract_zones",
        "extract_zone_expression"
      ]
    },
    {
      "page": "generate_plots",
      "title": "Generate plots of genome, chromosomes and zones.",
      "topics": [
        "generate_plots",
        "plot_chromosomes",
        "plot_genome",
        "plot_zones"
      ]
    },
    {
      "page": "GenomicOZone",
      "title": "Delineate outstanding genomic zones",
      "topics": [
        "GenomicOZone"
      ]
    },
    {
      "page": "GOZDataSet",
      "title": "Create an object for outstanding genomic zone analysis",
      "topics": [
        "GOZDataSet"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GenomicOZone/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "Ckmeans.1d.dp",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dichromat",
    "digest",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggbio",
    "ggplot2",
    "glue",
    "graph",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "lsr",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnet",
    "openssl",
    "OrganismDbi",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RBGL",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "Rdpack",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "GenomicOZone.Rmd",
      "filename": "GenomicOZone.html",
      "title": "Example: finding E. coli outstanding genomic zones in response to nickel stress",
      "author": "Hua Zhong and Joe Song",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2019-08-17 17:08:16",
      "modified": "2021-01-26 22:27:42",
      "commits": 6
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "genomicozone",
  "_universes": [
    "bioc",
    "zh9118"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-07-13T06:00:32.000Z",
      "distro": "resolute",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/5379dbbac67a06077574c04a3c294274eac2bd5600e48259009702b8311d6ea1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-07-13T06:01:37.000Z",
      "distro": "resolute",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/1df57bd126db741bb0feb56d0829b7bc5ab5d3aa53e4caed265437f26f89a86d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-07-13T05:59:55.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/d976b1224458e44a3d505b67c6858cb35404b4f21eb1d8a6ae6d243969ed0130",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-07-13T06:00:45.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/6577b2129c85fcd3a796e84f5b561a4911271a4078ae8aba0b38c0d817bf249a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-07-13T06:00:04.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/87dace3b3ee3b2ab19ffbfb6c55e63dfd0ddb43ccd0112b551e3cd4e00ce370b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-07-13T05:58:29.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/4fde006593df55b25595876fabea588ba0cc5156d5ce4146ecca2fbd9db69092",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-07-13T05:58:48.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/04055223dc18cd791eb6d5e9eb847a78f67ccbab8759aa6a9a48c1ff33263a45",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-07-13T05:58:25.000Z",
      "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e",
      "fileid": "https://r2.ropensci.org/805ea863136ae02530bf6a81ef0d3a52443916e9c50094387bce663e25a9c476",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29227297952"
    }
  ]
}