{
  "_id": "6a0f608dacfb0bcc41c5ba95",
  "Package": "epiRomics",
  "Type": "Package",
  "Title": "Epigenomic Analysis Package Built for R (epiRomics)",
  "Version": "1.1.0",
  "Authors@R": "c(person(given = \"Alex M.\",\nfamily = \"Mawla\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ammawla@ucdavis.edu\",\ncomment = c(ORCID = \"0000-0003-0907-464X\")),\nperson(given = \"Mark O.\",\nfamily = \"Huising\",\nrole = \"aut\",\nemail = \"mhuising@ucdavis.edu\",\ncomment = c(ORCID = \"0000-0002-6594-2205\")))",
  "Description": "Integrates various levels of epigenomic information,\nincluding ChIP-seq, histone modification, ATAC-seq, and RNA-seq\ndata. Regulatory network analysis uses combinatory approaches\nto infer regions of significance, such as enhancers. Downstream\nanalysis identifies co-occurrence of epigenomic data at regions\nof interest. Visualization functions display multi-track\ngenomic views with signal overlays. Please contact\n<ammawla@ucdavis.edu> for suggestions, feedback, or bug\nreporting.",
  "License": "Artistic-2.0",
  "URL": "https://huising-lab.github.io/epiRomics/,\nhttps://github.com/Huising-Lab/epiRomics",
  "BugReports": "https://github.com/Huising-Lab/epiRomics/issues",
  "biocViews": "Epigenetics, ChIPSeq, ATACSeq, RNASeq, Visualization,\nSequencing, Software, HistoneModification, GeneRegulation,\nTranscription, FunctionalGenomics",
  "Config/testthat/edition": "3",
  "ByteCompile": "true",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Collate": "'class-epiRomics.R' 'accessors.R'\n'benchmark_enhancer_predictor.R' 'build_database.R' 'cache.R'\n'chromatin_states.R' 'enhanceosomes.R' 'enhancers.R'\n'epiRomics-package.R' 'filter_enhancers.R' 'plot_quick_view.R'\n'plot_tracks_fast.R' 'predictors.R' 'putative_enhancers.R'\n'regions_of_interest.R' 'synthetic-data.R' 'tf_overlap.R'\n'utils.R' 'visualizations.R' 'zzz-deprecated.R' 'zzz.R'",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:07:10 UTC",
  "RemoteUrl": "https://github.com/bioc/epiRomics",
  "RemoteRef": "HEAD",
  "RemoteSha": "9e2708e0bdd1934dffc2554020555520d5835958",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-21 10:44:30 UTC",
    "User": "root"
  },
  "Author": "Alex M. Mawla [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0907-464X>),\nMark O. Huising [aut] (ORCID: <https://orcid.org/0000-0002-6594-2205>)",
  "Maintainer": "Alex M. Mawla <ammawla@ucdavis.edu>",
  "MD5sum": "38d4eea79822a9a212b84a931b740714",
  "_user": "bioc",
  "_type": "src",
  "_file": "epiRomics_1.1.0.tar.gz",
  "_fileid": "9a6328b2063011f4bc99d2faf6b1da7519b4bf90a5294687700b8f5b015f21ce",
  "_filesize": 1501687,
  "_sha256": "9a6328b2063011f4bc99d2faf6b1da7519b4bf90a5294687700b8f5b015f21ce",
  "_created": "2026-05-21T10:44:30.000Z",
  "_published": "2026-05-21T19:44:13.887Z",
  "_jobs": [
    {
      "job": 77254139474,
      "time": 360,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7133786556"
    },
    {
      "job": 77254139355,
      "time": 653,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7133879381"
    },
    {
      "job": 77254139384,
      "time": 623,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7133869315"
    },
    {
      "job": 77254139194,
      "time": 383,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7134434403"
    },
    {
      "job": 77254139154,
      "time": 376,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7134100164"
    },
    {
      "job": 77254138849,
      "time": 523,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7133671255"
    },
    {
      "job": 77254138796,
      "time": 320,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7145568606"
    },
    {
      "job": 77254139457,
      "time": 394,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7133797094"
    },
    {
      "job": 77254139300,
      "time": 457,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7133817724"
    },
    {
      "job": 77254139374,
      "time": 522,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7133840128"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/epiRomics",
  "_commit": {
    "id": "9e2708e0bdd1934dffc2554020555520d5835958",
    "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": 1777381630
  },
  "_maintainer": {
    "name": "Alex M. Mawla",
    "email": "ammawla@ucdavis.edu",
    "login": "ammawla",
    "orcid": "0000-0003-0907-464X",
    "twitter": "@alex_mawla",
    "description": "Computational geneticist",
    "uuid": 8989493
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "version": ">= 1.68.0",
      "role": "Imports"
    },
    {
      "package": "annotatr",
      "version": ">= 1.32.0",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.52.0",
      "role": "Imports"
    },
    {
      "package": "ChIPseeker",
      "version": ">= 1.42.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.15.0",
      "role": "Imports"
    },
    {
      "package": "digest",
      "version": ">= 0.6.35",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "version": ">= 1.42.0",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "version": ">= 1.58.0",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.58.0",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 2.40.0",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "version": ">= 1.66.0",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.44.0",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "version": ">= 2.14.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "version": ">= 3.20.0",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "version": ">= 3.20.0",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "version": ">= 3.18.0",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Mmusculus.UCSC.mm10.knownGene",
      "version": ">= 3.10.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-11",
      "n": 11
    },
    {
      "week": "2026-12",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-14",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-17",
      "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": [
    "epigenetics",
    "chipseq",
    "atacseq",
    "rnaseq",
    "visualization",
    "sequencing",
    "software",
    "histonemodification",
    "generegulation",
    "transcription",
    "functionalgenomics",
    "atac-seq",
    "chip-seq",
    "chromatin-accessibiity",
    "data-visualization",
    "enhancer",
    "enhancer-prediction",
    "epigenomics",
    "histone",
    "multi-omics",
    "regulatory-network",
    "regulome-analysis",
    "rna-seq",
    "transcription-factor-binding",
    "transcription-factors",
    "ucsc-browser"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "ammawla",
      "count": 291,
      "uuid": 8989493
    },
    {
      "user": "markhuising",
      "count": 1,
      "uuid": 75006890
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 154,
    "source": "https://www.bioconductor.org/packages/stats/bioc/epiRomics"
  },
  "_devurl": "https://github.com/huising-lab/epiromics",
  "_pkgdown": "https://huising-lab.github.io/epiRomics/",
  "_searchresults": 41,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/epiRomics.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/huising-lab/epiromics",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "analyze_tf_cobinding",
    "analyze_tf_overlap",
    "annotate_enhancers",
    "annotations",
    "annotations<-",
    "benchmark_enhancer_predictor",
    "build_database",
    "cache_data",
    "call_accessible_regions",
    "chromatin_state_categories",
    "classify_celltype_accessibility",
    "classify_chromatin_states",
    "epiRomics_annotate_putative",
    "epiRomics_build_dB",
    "epiRomics_cache_data",
    "epiRomics_cache_path",
    "epiRomics_chromatin_states",
    "epiRomics_chromatin_states_categories",
    "epiRomics_enhanceosome",
    "epiRomics_enhancer_predictor_to_ref",
    "epiRomics_enhancers_co_marks",
    "epiRomics_enhancers_filter",
    "epiRomics_filter_accessible",
    "epiRomics_has_cache",
    "epiRomics_putative_enhancers",
    "epiRomics_quick_view",
    "epiRomics_regions_of_interest",
    "epiRomics_tf_cobinding",
    "epiRomics_tf_overlap",
    "epiRomics_track_layer",
    "epiRomics_track_layer_fast",
    "epiRomics_track_layer_gene",
    "epiRomicsS4",
    "filter_accessible_regions",
    "filter_enhancers",
    "find_enhanceosomes",
    "find_enhancers_by_comarks",
    "find_putative_enhancers",
    "genome",
    "genome<-",
    "get_cache_path",
    "get_regions_of_interest",
    "has_cache",
    "make_example_bigwig",
    "make_example_database",
    "make_example_enhanceosome",
    "make_example_putative_enhancers",
    "maxCovBwCached",
    "maxCovFilesCached",
    "meta",
    "meta<-",
    "organism",
    "organism<-",
    "plot_gene_tracks",
    "plot_quick_view",
    "plot_signal_histogram",
    "plot_tracks",
    "plot_tracks_fast",
    "txdb",
    "txdb<-"
  ],
  "_help": [
    {
      "page": "epiRomics-package",
      "title": "epiRomics: Epigenomic Analysis Package Built for R (epiRomics)",
      "topics": [
        "epiRomics-package",
        "epiRomics"
      ]
    },
    {
      "page": "analyze_tf_cobinding",
      "title": "Analyze statistical significance of TF co-binding at enhanceosome regions",
      "topics": [
        "analyze_tf_cobinding"
      ]
    },
    {
      "page": "analyze_tf_overlap",
      "title": "Analyze pairwise and multi-way overlap between transcription factor binding sites",
      "topics": [
        "analyze_tf_overlap"
      ]
    },
    {
      "page": "annotate_enhancers",
      "title": "Annotate putative enhancers with functional database overlaps",
      "topics": [
        "annotate_enhancers"
      ]
    },
    {
      "page": "annotations",
      "title": "Access the genomic annotations slot of an epiRomicsS4 object",
      "topics": [
        "annotations",
        "annotations,epiRomicsS4-method"
      ]
    },
    {
      "page": "annotations-set",
      "title": "Replace the annotations slot of an epiRomicsS4 object",
      "topics": [
        "annotations-set",
        "annotations<-",
        "annotations<-,epiRomicsS4-method"
      ]
    },
    {
      "page": "benchmark_enhancer_predictor",
      "title": "Evaluate histone marks against any curated reference database",
      "topics": [
        "benchmark_enhancer_predictor"
      ]
    },
    {
      "page": "build_database",
      "title": "Build epiRomics database",
      "topics": [
        "build_database"
      ]
    },
    {
      "page": "cache_data",
      "title": "Download and Cache epiRomics Example Data",
      "topics": [
        "cache_data"
      ]
    },
    {
      "page": "call_accessible_regions",
      "title": "Compute per-region signal z-scores from a BigWig file",
      "topics": [
        "call_accessible_regions"
      ]
    },
    {
      "page": "chromatin_state_categories",
      "title": "Return chromatin state category definitions",
      "topics": [
        "chromatin_state_categories"
      ]
    },
    {
      "page": "classify_celltype_accessibility",
      "title": "Classify regions by cell-type-specific binary accessibility",
      "topics": [
        "classify_celltype_accessibility"
      ]
    },
    {
      "page": "classify_chromatin_states",
      "title": "Classify genomic regions by histone chromatin state with genomic context",
      "topics": [
        "classify_chromatin_states"
      ]
    },
    {
      "page": "epiRomicsS4-accessors",
      "title": "Accessors for the epiRomicsS4 class",
      "topics": [
        "epiRomicsS4-accessors"
      ]
    },
    {
      "page": "epiRomicsS4-class",
      "title": "An S4 class to manage epiRomics databases and downstream results",
      "topics": [
        "epiRomicsS4",
        "epiRomicsS4-class"
      ]
    },
    {
      "page": "filter_accessible_regions",
      "title": "Filter putative enhancers by chromatin accessibility evidence",
      "topics": [
        "filter_accessible_regions"
      ]
    },
    {
      "page": "filter_enhancers",
      "title": "Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data",
      "topics": [
        "filter_enhancers"
      ]
    },
    {
      "page": "find_enhanceosomes",
      "title": "Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichment",
      "topics": [
        "find_enhanceosomes"
      ]
    },
    {
      "page": "find_enhancers_by_comarks",
      "title": "Identifies putative enhancer regions utilizing select histone mark co-occurrence",
      "topics": [
        "find_enhancers_by_comarks"
      ]
    },
    {
      "page": "find_putative_enhancers",
      "title": "Identify putative enhancer regions using rule-based histone logic",
      "topics": [
        "find_putative_enhancers"
      ]
    },
    {
      "page": "genome",
      "title": "Access the genome assembly name",
      "topics": [
        "genome",
        "genome,epiRomicsS4-method"
      ]
    },
    {
      "page": "genome-set",
      "title": "Replace the genome assembly name",
      "topics": [
        "genome-set",
        "genome<-",
        "genome<-,epiRomicsS4-method"
      ]
    },
    {
      "page": "get_cache_path",
      "title": "Get Path to Cached epiRomics Data (No Download)",
      "topics": [
        "get_cache_path"
      ]
    },
    {
      "page": "get_regions_of_interest",
      "title": "Define regions of interest and filter enhanceosome by overlap",
      "topics": [
        "get_regions_of_interest"
      ]
    },
    {
      "page": "has_cache",
      "title": "Check Whether epiRomics Example Data is Cached",
      "topics": [
        "has_cache"
      ]
    },
    {
      "page": "make_example_bigwig",
      "title": "Create a temporary synthetic BigWig file for use in examples",
      "concept": [
        "synthetic example data helpers"
      ],
      "topics": [
        "make_example_bigwig"
      ]
    },
    {
      "page": "make_example_database",
      "title": "Build a synthetic epiRomicsS4 database for use in examples",
      "concept": [
        "synthetic example data helpers"
      ],
      "topics": [
        "make_example_database"
      ]
    },
    {
      "page": "make_example_enhanceosome",
      "title": "Build a synthetic enhanceosome result for use in examples",
      "concept": [
        "synthetic example data helpers"
      ],
      "topics": [
        "make_example_enhanceosome"
      ]
    },
    {
      "page": "make_example_putative_enhancers",
      "title": "Build a synthetic putative-enhancer result for use in examples",
      "concept": [
        "synthetic example data helpers"
      ],
      "topics": [
        "make_example_putative_enhancers"
      ]
    },
    {
      "page": "maxCovBwCached",
      "title": "BigWig coverage calculation",
      "topics": [
        "maxCovBwCached"
      ]
    },
    {
      "page": "maxCovFilesCached",
      "title": "Multiple BigWig coverage calculation",
      "topics": [
        "maxCovFilesCached"
      ]
    },
    {
      "page": "meta",
      "title": "Access the metadata slot of an epiRomicsS4 object",
      "topics": [
        "meta",
        "meta,epiRomicsS4-method"
      ]
    },
    {
      "page": "meta-set",
      "title": "Replace the metadata slot of an epiRomicsS4 object",
      "topics": [
        "meta-set",
        "meta<-",
        "meta<-,epiRomicsS4-method"
      ]
    },
    {
      "page": "organism",
      "title": "Access the organism annotation package name",
      "topics": [
        "organism",
        "organism,epiRomicsS4-method"
      ]
    },
    {
      "page": "organism-set",
      "title": "Replace the organism annotation package name",
      "topics": [
        "organism-set",
        "organism<-",
        "organism<-,epiRomicsS4-method"
      ]
    },
    {
      "page": "plot_gene_tracks",
      "title": "Visualize any gene locus with multi-track BigWig overlay",
      "topics": [
        "plot_gene_tracks"
      ]
    },
    {
      "page": "plot_quick_view",
      "title": "Quick standalone gene/region visualization from BigWig files",
      "topics": [
        "plot_quick_view"
      ]
    },
    {
      "page": "plot_signal_histogram",
      "title": "Plot signal distribution histogram for accessibility threshold selection",
      "topics": [
        "plot_signal_histogram"
      ]
    },
    {
      "page": "plot_tracks",
      "title": "Multi-track genomic visualization (base R graphics)",
      "topics": [
        "plot_tracks",
        "plot_tracks_fast"
      ]
    },
    {
      "page": "txdb",
      "title": "Access the TxDb package::object identifier slot",
      "topics": [
        "txdb",
        "txdb,epiRomicsS4-method"
      ]
    },
    {
      "page": "txdb-set",
      "title": "Replace the TxDb identifier slot of an epiRomicsS4 object",
      "topics": [
        "txdb-set",
        "txdb<-",
        "txdb<-,epiRomicsS4-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/epiRomics/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "annotatr",
    "ape",
    "aplot",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "BSgenome",
    "bslib",
    "cachem",
    "caTools",
    "ChIPseeker",
    "cigarillo",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "DOSE",
    "dplyr",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "gdtools",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "gplots",
    "gridGraphics",
    "gtable",
    "gtools",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nlme",
    "openssl",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plotrix",
    "plyr",
    "png",
    "polyclip",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "regioneR",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidyr",
    "tidyselect",
    "tidytree",
    "tinytex",
    "treeio",
    "tweenr",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "getting-started-with-epiRomics.Rmd",
      "filename": "getting-started-with-epiRomics.html",
      "title": "Getting Started with epiRomics",
      "author": "Alex M. Mawla & Mark O. Huising",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Locating the toy data",
        "Installation",
        "Loading the package",
        "Building the database",
        "Quick gene-locus inspection",
        "Identifying putative enhancers",
        "Cross-referencing against curated enhancer databases",
        "Identifying enhanceosome regions",
        "TF co-binding statistics",
        "Visualising an enhanceosome with signal tracks",
        "Gene-centred visualisation",
        "Chromatin state classification",
        "Moving on to the full dataset",
        "Interactive showcases",
        "Citation",
        "Session information",
        "References"
      ],
      "created": "2021-02-12 02:17:28",
      "modified": "2026-04-20 23:11:48",
      "commits": 20
    }
  ],
  "_score": 5.85582190540603,
  "_indexed": true,
  "_nocasepkg": "epiromics",
  "_universes": [
    "bioc",
    "ammawla",
    "huising-lab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-21T10:51:26.000Z",
      "distro": "noble",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "5bac74d4fe80bfd92faabf7fb80021663578ce7f69758336719eb422fc7074a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-21T10:50:55.000Z",
      "distro": "noble",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "6f26ec4ea57bbad5500d51ec0c21d8f9bb5c2ad5f47cbb733fbe0d977fda0071",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-21T11:21:13.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "6aa5b788f7bbb378ad4b012d78b7446fb2980d417346b2a432a9c715885f75df",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-21T11:04:01.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "a0d17cef1a8e8bb5fbe7d9d87dd54959bef5959b8c7cd705b04e81fc7374b4e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-21T19:43:48.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "5ffc8323b2fd61c24e9c0ca50889dcee3657085d72b03a4ee9a2f3a75b5e0973",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-21T10:48:07.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "207e4a52f6ab779bad1e54261bc9edb34fee998df4095ccc04ef70795906c2ac",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-21T10:48:30.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "1f163fd63042a405ffab471fa721fa763038a631979d40e5e1598a258882634b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-21T10:49:21.000Z",
      "commit": "9e2708e0bdd1934dffc2554020555520d5835958",
      "fileid": "b1f7f87dbb830b29f3fba080a7d77d51d6f360aa9c5bbabb75fe3ed55091a6b9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220805257"
    }
  ]
}