{ "_id": "6a10131bacfb0bcc41c83080", "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, Mingzhou Song\n", "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": "2026-05-14 09:46:05 UTC", "User": "root" }, "MD5sum": "c6caff9f9d37f87e12b4166c3c5299b9", "_user": "bioc", "_type": "src", "_file": "GenomicOZone_1.27.0.tar.gz", "_fileid": "4927a4d9261f1c5082c5858861908c1eeacc44ceab80fdb1c1e87d1c12126b67", "_filesize": 1452030, "_sha256": "4927a4d9261f1c5082c5858861908c1eeacc44ceab80fdb1c1e87d1c12126b67", "_created": "2026-05-14T09:46:05.000Z", "_published": "2026-05-22T08:26:03.200Z", "_jobs": [ { "job": 77343218466, "time": 220, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7010802312" }, { "job": 77343218697, "time": 460, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6991757495" }, { "job": 77343218871, "time": 489, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6991767634" }, { "job": 77343218832, "time": 346, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7011163204" }, { "job": 77343218580, "time": 358, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6991732050" }, { "job": 77343217957, "time": 371, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6991626075" }, { "job": 77343218070, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156105812" }, { "job": 77343218706, "time": 363, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6991729528" }, { "job": 77343218714, "time": 384, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6991735228" }, { "job": 77343218957, "time": 403, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6991740927" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GenomicOZone", "_commit": { "id": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "author": "A Wokaty ", "committer": "A Wokaty ", "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", "uuid": 13088022 }, "_distro": "noble", "_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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 348, "source": "https://www.bioconductor.org/packages/stats/bioc/GenomicOZone" }, "_searchresults": 2, "_rbuild": "4.6.0", "_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": "2026-05-14T09:50:07.000Z", "distro": "noble", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "f03d5436870f1232872f1598d802e953d40d7bea804cd922db382a7b51ac0189", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-14T09:51:03.000Z", "distro": "noble", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "0c70fdeab7b0afa1d663169c4f6247c6a9d6a533e8ce1c050f5065281de32d49", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-15T06:05:13.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "76c0e23fa8f17381a7885066eb0a45f8a563f6f3883f34d329ef99c7fd09d3de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-14T09:48:58.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "c8ab8dd276841dd6da8c47382acd1b734234e2023c66d2bb91a50fa1be2562af", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-14T09:48:38.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "a8ace1206cbdfe8c8f15988dde0ce90c9d95feee4e441dff385add3461513559", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-14T09:48:29.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "1f4a30c377a7fdef0197873ddd1ff5ec16a3fa27c8b7008f2340684dc1c6bcba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-14T09:48:50.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "728e069f36a0dc33742abea5206d3e4c65a1f4bc9e7a483dceab118bea9dbd81", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-22T08:25:38.000Z", "commit": "4bb542aa21f7badbcbad7904813fe44666d1d74e", "fileid": "4fb109e9f13e0c2e5426fb488c6ecdba2c6903193720e193d297cb09fcbbf01b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853125007" } ] }