{
  "_id": "6a1aa8cb1d7bb097a09d4ca6",
  "Package": "ribor",
  "Title": "An R Interface for Ribo Files",
  "Version": "1.25.0",
  "Authors@R": "c(\nperson(\"Michael\", \"Geng\", email = \"michaelgeng@utexas.edu\", role = c(\"cre\", \"aut\")),\nperson(\"Hakan\", \"Ozadam\", email = \"hakan.ozadam@gmail.com\", role = \"aut\"),\nperson(\"Can\", \"Cenik\", email = \"ccenik@austin.utexas.edu\", role = \"aut\"))",
  "Description": "The ribor package provides an R Interface for .ribo files.\nIt provides functionality to read the .ribo file, which is of\nHDF5 format, and performs common analyses on its contents.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "biocViews": "Software, Infrastructure",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Collate": "'annotation_functions.R' 'check_functions.R'\n'coverage_functions.R' 'ribo_class.R' 'ribo_methods.R'\n'create_ribo.R' 'helper_functions.R' 'info_functions.R'\n'metagene_functions.R' 'region_count_functions.R' 'ribor.R'\n'rnaseq_functions.R'",
  "Config/pak/sysreqs": "libicu-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:59 UTC",
  "RemoteUrl": "https://github.com/bioc/ribor",
  "RemoteRef": "HEAD",
  "RemoteSha": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 06:54:31 UTC",
    "User": "root"
  },
  "Author": "Michael Geng [cre, aut],\nHakan Ozadam [aut],\nCan Cenik [aut]",
  "Maintainer": "Michael Geng <michaelgeng@utexas.edu>",
  "MD5sum": "9bf416c97094c9c0b117698255c9075b",
  "_user": "bioc",
  "_type": "src",
  "_file": "ribor_1.25.0.tar.gz",
  "_fileid": "ccc545009662e5779d02aaf6bc3aac9cdbe06697ec105e740a77c0f65d1693ef",
  "_filesize": 4496623,
  "_sha256": "ccc545009662e5779d02aaf6bc3aac9cdbe06697ec105e740a77c0f65d1693ef",
  "_created": "2026-05-30T06:54:31.000Z",
  "_published": "2026-05-30T09:07:23.192Z",
  "_jobs": [
    {
      "job": 78631678929,
      "time": 152,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306253652"
    },
    {
      "job": 78631678923,
      "time": 255,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306265078"
    },
    {
      "job": 78631678927,
      "time": 213,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306260387"
    },
    {
      "job": 78631678922,
      "time": 140,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307056382"
    },
    {
      "job": 78631678924,
      "time": 111,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307053432"
    },
    {
      "job": 78631491645,
      "time": 215,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306237042"
    },
    {
      "job": 78631678920,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306250039"
    },
    {
      "job": 78631678931,
      "time": 143,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306252893"
    },
    {
      "job": 78631678925,
      "time": 138,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306252080"
    },
    {
      "job": 78631678937,
      "time": 143,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306252603"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677330058",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ribor",
  "_commit": {
    "id": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
    "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": 1777380719
  },
  "_maintainer": {
    "name": "Michael Geng",
    "email": "michaelgeng@utexas.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "hash",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rhdf5",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "yaml",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.24.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "infrastructure"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 350,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ribor"
  },
  "_searchresults": 35,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/ribor.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "alias_hash",
    "experiment_info",
    "experiments",
    "format_version",
    "get_coverage",
    "get_experiments",
    "get_info",
    "get_internal_region_coordinates",
    "get_internal_region_lengths",
    "get_length_distribution",
    "get_metadata",
    "get_metagene",
    "get_original_region_coordinates",
    "get_original_region_lengths",
    "get_reference_names",
    "get_region_coordinates",
    "get_region_counts",
    "get_region_lengths",
    "get_rnaseq",
    "get_tidy_metagene",
    "has_metadata",
    "left_span",
    "length_max",
    "length_min",
    "length_offset",
    "metagene_radius",
    "original_hash",
    "path",
    "plot_length_distribution",
    "plot_metagene",
    "plot_region_counts",
    "reference",
    "rename_default",
    "rename_transcripts",
    "Ribo",
    "right_span",
    "set_aliases",
    "show",
    "transcript_info"
  ],
  "_help": [
    {
      "page": "get_coverage",
      "title": "Retrieves the coverage data for a given transcript",
      "topics": [
        "get_coverage"
      ]
    },
    {
      "page": "get_experiments",
      "title": "Provides a list of experiments from a .ribo file",
      "topics": [
        "get_experiments"
      ]
    },
    {
      "page": "get_info",
      "title": "Get information about the .ribo file",
      "topics": [
        "get_info"
      ]
    },
    {
      "page": "get_internal_region_coordinates",
      "title": "Retrieves the region stop and start coordinates",
      "topics": [
        "get_internal_region_coordinates"
      ]
    },
    {
      "page": "get_internal_region_lengths",
      "title": "Returns the overall length of each region with UTR Junctions",
      "topics": [
        "get_internal_region_lengths"
      ]
    },
    {
      "page": "get_length_distribution",
      "title": "Retrieves the length distribution of a given region",
      "topics": [
        "get_length_distribution"
      ]
    },
    {
      "page": "get_metadata",
      "title": "Retrieves the metadata of an experiment",
      "topics": [
        "get_metadata"
      ]
    },
    {
      "page": "get_metagene",
      "title": "Retrieves the metagene data from a .ribo file",
      "topics": [
        "get_metagene"
      ]
    },
    {
      "page": "get_original_region_coordinates",
      "title": "Retrieves the region stop and start coordinates",
      "topics": [
        "get_original_region_coordinates"
      ]
    },
    {
      "page": "get_original_region_lengths",
      "title": "Returns the overall length of each region",
      "topics": [
        "get_original_region_lengths"
      ]
    },
    {
      "page": "get_reference_names",
      "title": "Retrieves a list of reference names",
      "topics": [
        "get_reference_names"
      ]
    },
    {
      "page": "get_region_coordinates",
      "title": "Retrieves the region stop and start coordinates",
      "topics": [
        "get_region_coordinates"
      ]
    },
    {
      "page": "get_region_counts",
      "title": "Retrieves the region counts from a .ribo file",
      "topics": [
        "get_region_counts"
      ]
    },
    {
      "page": "get_region_lengths",
      "title": "Returns the overall length of each region with UTR Junctions",
      "topics": [
        "get_region_lengths"
      ]
    },
    {
      "page": "get_rnaseq",
      "title": "Information on the RNA-Seq data of the experiments, if any",
      "topics": [
        "get_rnaseq"
      ]
    },
    {
      "page": "get_tidy_metagene",
      "title": "Retrieves the metagene data in a tidy format",
      "topics": [
        "get_tidy_metagene"
      ]
    },
    {
      "page": "plot_length_distribution",
      "title": "Plots the length distribution",
      "topics": [
        "plot_length_distribution"
      ]
    },
    {
      "page": "plot_metagene",
      "title": "Plots the metagene coverage data",
      "topics": [
        "plot_metagene"
      ]
    },
    {
      "page": "plot_region_counts",
      "title": "Plots the region counts of UTR5, CDS, and UTR3",
      "topics": [
        "plot_region_counts"
      ]
    },
    {
      "page": "rename_default",
      "title": "Rename function for appris transcriptome naming convention",
      "topics": [
        "rename_default"
      ]
    },
    {
      "page": "rename_transcripts",
      "title": "Renames the transcripts",
      "topics": [
        "rename_transcripts"
      ]
    },
    {
      "page": "ribo-class",
      "title": "Ribo Class",
      "topics": [
        "alias_hash",
        "alias_hash,Ribo-method",
        "experiments",
        "experiments,Ribo-method",
        "experiment_info",
        "experiment_info,Ribo-method",
        "format_version",
        "format_version,Ribo-method",
        "has_metadata",
        "has_metadata,Ribo-method",
        "left_span",
        "left_span,Ribo-method",
        "length_max",
        "length_max,Ribo-method",
        "length_min",
        "length_min,Ribo-method",
        "length_offset",
        "length_offset,Ribo-method",
        "metagene_radius",
        "metagene_radius,Ribo-method",
        "original_hash",
        "original_hash,Ribo-method",
        "path",
        "path,Ribo-method",
        "reference",
        "reference,Ribo-method",
        "Ribo",
        "Ribo-class",
        "right_span",
        "right_span,Ribo-method",
        "show,Ribo-method",
        "transcript_info",
        "transcript_info,Ribo-method"
      ]
    },
    {
      "page": "ribor",
      "title": "ribor: A package for reading .ribo files",
      "topics": [
        "ribor"
      ]
    },
    {
      "page": "set_aliases",
      "title": "Set the aliases of a ribo object",
      "topics": [
        "set_aliases"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ribor/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "biocmake",
    "cli",
    "cpp11",
    "dir.expiry",
    "dplyr",
    "farver",
    "filelock",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "hash",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "ribor.Rmd",
      "filename": "ribor.html",
      "title": "A Walk-through of RiboR",
      "author": "Michael Geng, Hakan Ozadam, Can Cenik",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        ".ribo File Format",
        "Transcript Regions",
        "Installation",
        "Availability",
        "Bioconductor",
        "Installation From Source Code",
        "Getting Started",
        "Generating a ribo object",
        "Length Distribution",
        "Metagene Analysis",
        "A Note on Aggregating the Output",
        "Region Counts",
        "A Note on the Memory Footprint",
        "Advanced Features",
        "Alias",
        "File Attributes",
        "Region Boundaries",
        "Functionality for Multiple Ribo Files",
        "Optional Data",
        "Metadata",
        "Coverage",
        "RNA-Seq",
        "Sample Analysis"
      ],
      "created": "2019-11-23 00:01:21",
      "modified": "2021-05-14 02:02:53",
      "commits": 12
    }
  ],
  "_score": 4.544068044350276,
  "_indexed": true,
  "_nocasepkg": "ribor",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-04-30T15:36:11.000Z",
      "distro": "noble",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "92fe0c4c490384ce0e00d2aa0e1eb22128b9e646f858e02a0e3bd2f076946e2a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-04-30T15:35:48.000Z",
      "distro": "noble",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "9a527f3be54ef3b9dc982be6e5c2abecaef1d77f7f20fad637b0c405698365bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-04-30T17:00:49.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "761f5076fefbed62d5489cd4799eb25223e0fdeb99b352a141f98ac3b0b6c42c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-04-30T17:01:08.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "b67c497a86f3abc507845ebcdd9a8df4f6be2ce90b865aff65dd28ce6b192993",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-04-30T15:32:10.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "4bd047e814e6cb0b6cfe8affbdc035a080100bc64665723f28550ca77c59e8ea",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-04-30T15:32:21.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "81c76ef2c697e82e5ad00b2a5d939c205e5c5520fa8133a505c95460f5616bda",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-04-30T15:32:02.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "0b81f283729c5dda9f390bbcec57b8a403dacb59149a0ef4b8ed85d75501607d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.25.0",
      "date": "2026-05-22T21:04:15.000Z",
      "commit": "aad8c146fd22166fa0190a6a3ac8920cb0ec28aa",
      "fileid": "9742f3165c922383c32fc6caaba29fc8e2ffbb1151c3183ed27bcd5dc1cf2a78",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173647995"
    }
  ]
}