{
  "_id": "6a1ab1081d7bb097a09d592e",
  "Package": "RaggedExperiment",
  "Title": "Representation of Sparse Experiments and Assays Across Samples",
  "Version": "1.37.0",
  "Authors@R": "c(\nperson(\"Martin\", \"Morgan\", , \"martin.morgan@roswellpark.org\", \"aut\"),\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\",\nc(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3242-0582\")),\nperson(\"Lydia\", \"King\", , \"L.King18@nuigalway.ie\", \"ctb\")\n)",
  "Description": "This package provides a flexible representation of copy\nnumber, mutation, and other data that fit into the ragged array\nschema for genomic location data. The basic representation of\nsuch data provides a rectangular flat table interface to the\nuser with range information in the rows and samples/specimen in\nthe columns. The RaggedExperiment class derives from a\nGRangesList representation and provides a semblance of a\nrectangular dataset.",
  "License": "Artistic-2.0",
  "biocViews": "Infrastructure, DataRepresentation",
  "BugReports": "https://github.com/Bioconductor/RaggedExperiment/issues",
  "URL": "https://bioconductor.github.io/RaggedExperiment,\nhttps://bioconductor.org/packages/RaggedExperiment",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "Date": "2024-10-17",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:28 UTC",
  "RemoteUrl": "https://github.com/bioc/RaggedExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:05:03 UTC",
    "User": "root"
  },
  "Author": "Martin Morgan [aut],\nMarcel Ramos [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3242-0582>),\nLydia King [ctb]",
  "Maintainer": "Marcel Ramos <marcel.ramos@sph.cuny.edu>",
  "MD5sum": "7f9fbdace6b4acbfc05cb91c1924136f",
  "_user": "bioc",
  "_type": "src",
  "_file": "RaggedExperiment_1.37.0.tar.gz",
  "_fileid": "0f8df0a911e17660ad02c0c3adec5328e924bde30bee74f80c40776cc5ff398e",
  "_filesize": 259481,
  "_sha256": "0f8df0a911e17660ad02c0c3adec5328e924bde30bee74f80c40776cc5ff398e",
  "_created": "2026-05-30T07:05:03.000Z",
  "_published": "2026-05-30T09:42:32.778Z",
  "_jobs": [
    {
      "job": 78632285971,
      "time": 169,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306331181"
    },
    {
      "job": 78632285942,
      "time": 320,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306349093"
    },
    {
      "job": 78632285943,
      "time": 299,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306346639"
    },
    {
      "job": 78632285968,
      "time": 146,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307197749"
    },
    {
      "job": 78632285959,
      "time": 246,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307207544"
    },
    {
      "job": 78632053692,
      "time": 242,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306311462"
    },
    {
      "job": 78632285944,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306329088"
    },
    {
      "job": 78632285946,
      "time": 261,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306342068"
    },
    {
      "job": 78632285960,
      "time": 227,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306337928"
    },
    {
      "job": 78632285963,
      "time": 243,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306339774"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RaggedExperiment",
  "_commit": {
    "id": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
    "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": 1777380328
  },
  "_maintainer": {
    "name": "Marcel Ramos",
    "email": "marcel.ramos@sph.cuny.edu",
    "login": "link-ny",
    "bluesky": "@mramos148.bsky.social",
    "linkedin": "in/mramos148",
    "orcid": "0000-0002-3242-0582",
    "twitter": "@M2RuseR",
    "description": "Sr. Data Scientist @ CUNY School of Public Health: Waldron Lab & Bioconductor Core Team Member /  \nR 📦 dev ",
    "uuid": 4392950
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Depends"
    },
    {
      "package": "BiocBaseUtils",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.39.1",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Suggests"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 14,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-28",
      "n": 15
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "datarepresentation",
    "copynumber",
    "core-package",
    "data-structure",
    "mutations",
    "u24ca289073"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "link-ny",
      "count": 127,
      "uuid": 4392950
    },
    {
      "user": "mtmorgan",
      "count": 18,
      "uuid": 118552
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 7,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "lydia-king",
      "count": 1,
      "uuid": 64010969
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1518,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RaggedExperiment"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/bioconductor/raggedexperiment",
  "_pkgdown": "https://bioconductor.github.io/RaggedExperiment",
  "_searchresults": 117,
  "_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/RaggedExperiment.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/raggedexperiment",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "as.data.frame",
    "as.list",
    "assay",
    "assayNames",
    "assays",
    "coerce",
    "colData",
    "colData<-",
    "compactAssay",
    "compactSummarizedExperiment",
    "disjoinAssay",
    "disjoinSummarizedExperiment",
    "mcols",
    "mcols<-",
    "overlapsAny",
    "qreduceAssay",
    "qreduceSummarizedExperiment",
    "RaggedExperiment",
    "rowData",
    "rowData<-",
    "rowRanges",
    "rowRanges<-",
    "seqinfo",
    "seqinfo<-",
    "show",
    "sparseAssay",
    "sparseSummarizedExperiment",
    "subset",
    "subsetByOverlaps"
  ],
  "_help": [
    {
      "page": "RaggedExperiment-package",
      "title": "RaggedExperiment: Range-based data representation package",
      "topics": [
        "RaggedExperiment-package"
      ]
    },
    {
      "page": "assay-functions",
      "title": "Create simplified representation of ragged assay data.",
      "topics": [
        "assay-functions",
        "compactAssay",
        "disjoinAssay",
        "qreduceAssay",
        "sparseAssay"
      ]
    },
    {
      "page": "RaggedExperiment-class",
      "title": "RaggedExperiment objects",
      "topics": [
        "$,RaggedExperiment-method",
        "as.data.frame,RaggedExperiment-method",
        "as.list,RaggedExperiment-method",
        "assay,RaggedExperiment,ANY-method",
        "assay,RaggedExperiment,missing-method",
        "assayNames,RaggedExperiment-method",
        "assays,RaggedExperiment-method",
        "class:RaggedExperiment",
        "coerce,GRangesList,RaggedExperiment-method",
        "coerce,RaggedExperiment,GRangesList-method",
        "colData,RaggedExperiment-method",
        "colData<-,RaggedExperiment,DataFrame-method",
        "dim,RaggedExperiment-method",
        "dimnames,RaggedExperiment-method",
        "dimnames<-,RaggedExperiment,ANY-method",
        "dimnames<-,RaggedExperiment,list-method",
        "length,RaggedExperiment-method",
        "mcols,RaggedExperiment-method",
        "mcols<-,RaggedExperiment-method",
        "overlapsAny,RaggedExperiment,Vector-method",
        "RaggedExperiment",
        "RaggedExperiment-class",
        "rowData,RaggedExperiment-method",
        "rowData<-,RaggedExperiment-method",
        "rowRanges,RaggedExperiment-method",
        "rowRanges<-,RaggedExperiment,GRanges-method",
        "seqinfo,RaggedExperiment-method",
        "seqinfo<-,RaggedExperiment-method",
        "show,RaggedExperiment-method",
        "subset,RaggedExperiment-method",
        "subsetByOverlaps,RaggedExperiment,Vector-method",
        "[,RaggedExperiment,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "coerce-functions",
      "title": "Create SummarizedExperiment representations by transforming ragged assays to rectangular form.",
      "topics": [
        "coerce,dgCMatrix,RaggedExperiment-method",
        "coerce-RaggedExperiment",
        "compactSummarizedExperiment",
        "disjoinSummarizedExperiment",
        "qreduceSummarizedExperiment",
        "sparseSummarizedExperiment"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RaggedExperiment/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "DelayedArray",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "ASCAT_to_RaggedExperiment.Rmd",
      "filename": "ASCAT_to_RaggedExperiment.html",
      "title": "ASCAT to RaggedExperiment",
      "author": "Lydia King, Marcel Ramos",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Structure of ASCAT data",
        "Converting ASCAT data to GRanges format",
        "ASCAT to GRanges objects",
        "ASCAT to GRangesList instance",
        "Constructing a RaggedExperiment object from ASCAT output",
        "Using GRanges objects",
        "Using a GRangesList instance",
        "Downstream Analysis",
        "Session Information"
      ],
      "created": "2023-05-03 22:42:45",
      "modified": "2025-07-10 17:55:27",
      "commits": 7
    },
    {
      "source": "RaggedExperiment.Rmd",
      "filename": "RaggedExperiment.html",
      "title": "RaggedExperiment",
      "author": "Martin Morgan, Marcel Ramos",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Citing RaggedExperiment",
        "RaggedExperiment class overview",
        "Constructing a RaggedExperiment object",
        "Using GRanges objects",
        "Using a GRangesList instance",
        "Using a list of GRanges",
        "Using a List of GRanges with metadata",
        "Accessors",
        "Range data",
        "Dimension names",
        "colData",
        "Subsetting",
        "by dimension",
        "by genomic ranges",
        "*Assay functions",
        "sparseAssay",
        "Support for sparse matrix output",
        "compactAssay",
        "disjoinAssay",
        "qreduceAssay",
        "Coercion",
        "from dgCMatrix to RaggedExperiment",
        "Session Information",
        "References"
      ],
      "created": "2017-03-28 03:34:51",
      "modified": "2025-07-10 18:19:09",
      "commits": 25
    }
  ],
  "_score": 8.95188816975115,
  "_indexed": true,
  "_nocasepkg": "raggedexperiment",
  "_universes": [
    "bioc",
    "link-ny",
    "bioconductor"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-30T07:08:52.000Z",
      "distro": "noble",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "812b3ae35914626a702f85068c3dd5c839e7c9ba6be88ecbb2a4a00b659c34ee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-30T07:08:25.000Z",
      "distro": "noble",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "c6e40aad7d862e11908fbecc904b474db5de3bbd40de0a94f4dc8f5740e3844c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-30T09:30:46.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "cb6026cc3eb49e871db0b4913f0f941befdd7c79577e41a5c9ea5615f9122e34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-30T09:31:58.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "fe614bd99f71f3b44079e9834c63b49e340d1db409db8cb76bbab06bff6adbfb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-05-30T07:08:04.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "2b83f40f2f597c998c031faf1b9b8b57dec0be29211be182d199b3c8956bb2f9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T07:07:26.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "7c6d7a39f65c2b26bff11627de766573a71b72cf4d41ad732dcb9dae996d05d7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T07:07:05.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "7bb266e60e690a960ff36b52ab10c626d6836622bb285a0b0b122bf64752921c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-30T07:07:09.000Z",
      "commit": "78b3addd7c314fb73b77411a45828d68d12f8f2e",
      "fileid": "7d94a6a0b1a21f294c652d751a94eee28515a850b7796baf1ee1014169604eb0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677535699"
    }
  ]
}