{
  "_id": "6a4f495421b18e15485001ee",
  "Package": "biomformat",
  "Version": "1.41.0",
  "Date": "2026-03-15",
  "Authors@R": "c(\nperson(\"Paul J.\", \"McMurdie\",\nemail = \"joey711@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Joseph N.\", \"Paulson\",\nemail = \"joseph.paulson@yale.edu\",\nrole = \"aut\"))",
  "License": "GPL-2",
  "Title": "An interface package for the BIOM file format",
  "Type": "Package",
  "BugReports": "https://github.com/joey711/biomformat/issues",
  "URL": "https://github.com/joey711/biomformat/, http://biom-format.org/",
  "Description": "This is an R package for interfacing with the BIOM file\nformat. This package includes basic tools for reading\nbiom-format files, accessing and subsetting data tables from a\nbiom object (which is more complex than a single table), as\nwell as limited support for writing a biom-object back to a\nbiom-format file. The design of this API is intended to match\nthe python API and other tools included with the biom-format\nproject, but with a decidedly \"R flavor\" that should be\nfamiliar to R users. This includes S4 classes and methods, as\nwell as extensions of common core functions/methods.",
  "VignetteBuilder": "knitr",
  "Collate": "'allClasses.R' 'allPackage.R' 'IO-methods.R' 'BIOM-class.R'\n'SE-methods.R' 'tidy-methods.R' 'validity-methods.R'",
  "biocViews": "ImmunoOncology, DataImport, Metagenomics, Microbiome",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "RoxygenNote": "7.3.3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:17 UTC",
  "RemoteUrl": "https://github.com/bioc/biomformat",
  "RemoteRef": "HEAD",
  "RemoteSha": "a7f85e0f5466bae74766951f05322f966b7246ec",
  "Packaged": {
    "Date": "2026-07-09 07:04:15 UTC",
    "User": "root"
  },
  "Author": "Paul J. McMurdie [aut, cre],\nJoseph N. Paulson [aut]",
  "Maintainer": "Paul J. McMurdie <joey711@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "biomformat_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c0ef9f19a8ecf75c464dd0d72da5b264169e8b0475df345fbf8b93f8d07761fe",
  "_filesize": 359986,
  "_sha256": "c0ef9f19a8ecf75c464dd0d72da5b264169e8b0475df345fbf8b93f8d07761fe",
  "_expires": "2026-10-17T07:10:08.000Z",
  "_created": "2026-07-09T07:04:15.000Z",
  "_published": "2026-07-09T07:10:12.839Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270",
  "_status": "success",
  "_upstream": "https://github.com/bioc/biomformat",
  "_commit": {
    "id": "a7f85e0f5466bae74766951f05322f966b7246ec",
    "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": 1777380137
  },
  "_maintainer": {
    "name": "Paul J. McMurdie",
    "email": "joey711@gmail.com",
    "login": "joey711",
    "twitter": "@joey711",
    "description": "Head, AI and Data Science\nN-Power Medicine, Inc.",
    "uuid": 841437
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 86059493861,
      "time": 230,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8191408816"
    },
    {
      "job": 86059493910,
      "time": 295,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8191428061"
    },
    {
      "job": 86059493940,
      "time": 238,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8191410960"
    },
    {
      "job": 86059493899,
      "time": 128,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8191377639"
    },
    {
      "job": 86059493956,
      "time": 244,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8191412365"
    },
    {
      "job": 86058907548,
      "time": 223,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8191338909"
    },
    {
      "job": 86059493907,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8191373073"
    },
    {
      "job": 86059493938,
      "time": 167,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8191389372"
    },
    {
      "job": 86059493979,
      "time": 196,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8191398191"
    },
    {
      "job": 86059493934,
      "time": 178,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8191393077"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "jsonlite",
      "version": ">= 0.9.16",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.7-0",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 0.10",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.10",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "version": ">= 1.6",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 0.7",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 50,
  "_updates": [
    {
      "week": "2026-11",
      "n": 20
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "dataimport",
    "metagenomics",
    "microbiome"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "joey711",
      "count": 37,
      "uuid": 841437
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "smdabdoub",
      "count": 4,
      "uuid": 380806
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 10118,
    "source": "https://www.bioconductor.org/packages/stats/bioc/biomformat"
  },
  "_mentions": 18,
  "_devurl": "https://github.com/joey711/biomformat",
  "_searchresults": 738,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/biomformat.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/joey711/biomformat",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "as_tibble.biom",
    "biom",
    "biom_data",
    "biom_shape",
    "biom_to_SummarizedExperiment",
    "colnames",
    "header",
    "make_biom",
    "matrix_element_type",
    "ncol",
    "nrow",
    "observation_metadata",
    "read_biom",
    "read_hdf5_biom",
    "rownames",
    "sample_metadata",
    "show",
    "write_biom",
    "write_hdf5_biom"
  ],
  "_help": [
    {
      "page": "biomformat-package",
      "title": "biomformat: An R interface to the BIOM file format",
      "topics": [
        "biomformat-package",
        "biomformat"
      ]
    },
    {
      "page": "as_tibble.biom",
      "title": "Coerce a biom object to a tidy tibble",
      "topics": [
        "as_tibble.biom"
      ]
    },
    {
      "page": "as.data.frame.biom",
      "title": "Coerce a biom object to a long-format tidy data frame",
      "topics": [
        "as.data.frame.biom"
      ]
    },
    {
      "page": "biom-methods",
      "title": "Build and return an instance of the biom-class.",
      "topics": [
        "biom",
        "biom,list-method"
      ]
    },
    {
      "page": "biom_data-methods",
      "title": "Access main data observation matrix data from 'biom-class'.",
      "topics": [
        "biom_data",
        "biom_data,biom,ANY,character-method",
        "biom_data,biom,character,ANY-method",
        "biom_data,biom,character,missing-method",
        "biom_data,biom,missing,missing-method",
        "biom_data,biom,missing,numeric-method",
        "biom_data,biom,numeric,missing-method",
        "biom_data,biom,numeric,numeric-method"
      ]
    },
    {
      "page": "biom_shape-methods",
      "title": "The matrix dimensions of a 'biom-class' object.",
      "topics": [
        "biom_shape",
        "biom_shape,biom-method"
      ]
    },
    {
      "page": "biom_to_SummarizedExperiment",
      "title": "Convert a biom object to a SummarizedExperiment",
      "topics": [
        "biom_to_SummarizedExperiment"
      ]
    },
    {
      "page": "biom-class",
      "title": "The biom format data class.",
      "topics": [
        "biom-class"
      ]
    },
    {
      "page": "colnames-methods",
      "title": "Method extensions to 'colnames' for 'biom-class' objects.",
      "topics": [
        "colnames,biom-method"
      ]
    },
    {
      "page": "header-methods",
      "title": "Extract the header from a 'biom-class' object as a list.",
      "topics": [
        "header",
        "header,biom-method"
      ]
    },
    {
      "page": "make_biom",
      "title": "Create a 'biom-class' from 'matrix-class' or 'data.frame'.",
      "topics": [
        "make_biom"
      ]
    },
    {
      "page": "matrix_element_type-methods",
      "title": "Access class of data in the matrix elements of a 'biom-class' object",
      "topics": [
        "matrix_element_type",
        "matrix_element_type,biom-method"
      ]
    },
    {
      "page": "ncol-methods",
      "title": "Method extensions to 'ncol' for 'biom-class' objects.",
      "topics": [
        "ncol,biom-method"
      ]
    },
    {
      "page": "nrow-methods",
      "title": "Method extensions to 'nrow' for 'biom-class' objects.",
      "topics": [
        "nrow,biom-method"
      ]
    },
    {
      "page": "observation_metadata-methods",
      "title": "Access observation (row) meta data from 'biom-class'.",
      "topics": [
        "observation_metadata",
        "observation_metadata,biom,character-method",
        "observation_metadata,biom,missing-method",
        "observation_metadata,biom,numeric-method"
      ]
    },
    {
      "page": "read_biom",
      "title": "Read a biom-format file, returning a 'biom-class'.",
      "topics": [
        "read_biom"
      ]
    },
    {
      "page": "read_hdf5_biom",
      "title": "Read in a biom-format v2 (HDF5) file, returning a 'list'.",
      "topics": [
        "read_hdf5_biom"
      ]
    },
    {
      "page": "rownames-methods",
      "title": "Method extensions to 'rownames' for 'biom-class' objects.",
      "topics": [
        "rownames,biom-method"
      ]
    },
    {
      "page": "sample_metadata-methods",
      "title": "Access meta data from 'biom-class'.",
      "topics": [
        "sample_metadata",
        "sample_metadata,biom,character-method",
        "sample_metadata,biom,missing-method",
        "sample_metadata,biom,numeric-method"
      ]
    },
    {
      "page": "show-methods",
      "title": "Method extensions to show for biom objects.",
      "topics": [
        "show,biom-method"
      ]
    },
    {
      "page": "write_biom",
      "title": "Write a biom-format v1 file, returning a 'biom-class'.",
      "topics": [
        "write_biom"
      ]
    },
    {
      "page": "write_hdf5_biom",
      "title": "Write a biom object to an HDF5 (BIOM v2) file.",
      "topics": [
        "write_hdf5_biom"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/biomformat/raw/HEAD/README.md",
  "_rundeps": [
    "jsonlite",
    "lattice",
    "Matrix"
  ],
  "_vignettes": [
    {
      "source": "biomformat.Rmd",
      "filename": "biomformat.html",
      "title": "The biomformat package vignette",
      "author": "Paul J. McMurdie",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Paul J. McMurdie & Joseph N. Paulson",
        "phyloseq Home Page",
        "Motivation for the biomformat package",
        "Read BIOM format",
        "Access BIOM data",
        "Core observation data",
        "Observation Metadata",
        "Sample Metadata",
        "Plots",
        "Write BIOM format (JSON / v1)",
        "HDF5 (BIOM v2) read and write",
        "Tidy long-format output",
        "purrr-style summarisation over samples",
        "SummarizedExperiment interoperability",
        "Constructing a BIOM from R data",
        "Subsetting biom_data() by name",
        "Session info"
      ],
      "created": "2015-12-01 22:52:06",
      "modified": "2026-03-15 17:48:42",
      "commits": 4
    }
  ],
  "_score": 12.03151352899084,
  "_indexed": true,
  "_nocasepkg": "biomformat",
  "_universes": [
    "bioc",
    "joey711"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-09T07:08:06.000Z",
      "distro": "resolute",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/a00d7c82227b9bb2248fa031eef4de2a53e10e64f5527dec167f06987b76ca08",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-09T07:07:32.000Z",
      "distro": "resolute",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/5862b1040dd0ece27f645b33857fa19ae7e111e40afa0d29cfd03d75245523ab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-09T07:05:54.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/308ba8b34b78bd4950d8ceb94452a5dc0b3e36ada96a702918c1c2335052638c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-09T07:06:45.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/d06187829ed5c6eb9ef8cab8001900a6fef0adac29a82df47bd6c9ba250b2406",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-07-09T07:06:40.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/425085879301aeb80cd48957152c4f16910b0cd44d3db7aa003b87d802280a33",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-09T07:05:41.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/3c5f7467f585a867f807a489127f8a4834c42d85d345ac333b9528552bd912b9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-09T07:05:54.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/e88acad7ff6820be272e61151ff3fe6f1ce3d0e44518779583fb50e5b5a72d3d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-09T07:05:44.000Z",
      "commit": "a7f85e0f5466bae74766951f05322f966b7246ec",
      "fileid": "https://r2.ropensci.org/ef4fe35bff96149f69f8b0220c2660845f85111e62ea5e8a9862f8edc941dca9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29000223270"
    }
  ]
}