{
  "_id": "6aca22c2fe5cc25786e8509b",
  "Package": "TumourMethData",
  "Title": "A Collection of DNA Methylation Datasets for Human Tumour\nSamples and Matching Normal Samples",
  "Version": "1.10.0",
  "Date": "2023-09-29",
  "Authors@R": "person(\"Richard\", \"Heery\", , \"richardheery@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8067-3114\"))",
  "Description": "TumourMethData collects tumour methylation data from a\nvariety of different tumour types (and also matching normal\nsamples where available) and produced with different\ntechnologies (e.g. WGBS, RRBS and methylation arrays) and\nprovides them as RangedSummarizedExperiments. This facilitates\neasy extraction of methylation data for regions of interest\nacross different tumour types and studies.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/richardheery/TumourMethData",
  "BugReports": "https://support.bioconductor.org/tag/TumourMethData",
  "biocViews": "ExperimentData, ExperimentHub, MethylSeqData, CancerData,\nHomo_sapiens_Data,",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "LazyData": "false",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev default-jdk libbz2-dev\nlibgit2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev\nlibtiff-dev libuv1-dev libwebp-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:37:04 UTC",
  "RemoteUrl": "https://github.com/bioc/TumourMethData",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "8d85e558b76fd646e2ff9e7ef92a2a92b1088967",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 11:26:22 UTC",
    "User": "root"
  },
  "Author": "Richard Heery [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8067-3114>)",
  "Maintainer": "Richard Heery <richardheery@gmail.com>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "TumourMethData_1.10.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/2e096de836d11eb909d2f4ba35026b870de4aa9a946ee1eb33fa6cc2e8a10074",
  "_filesize": 112947,
  "_sha256": "2e096de836d11eb909d2f4ba35026b870de4aa9a946ee1eb33fa6cc2e8a10074",
  "_expires": "2027-01-18T11:34:25.000Z",
  "_created": "2026-10-10T11:26:22.000Z",
  "_published": "2026-10-10T11:34:26.885Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047643079",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 10
  },
  "_upstream": "https://github.com/bioc/TumourMethData",
  "_commit": {
    "id": "8d85e558b76fd646e2ff9e7ef92a2a92b1088967",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379824
  },
  "_maintainer": {
    "name": "Richard Heery",
    "email": "richardheery@gmail.com",
    "login": "richardheery",
    "description": "Computational Biologist working on DNA methylation in cancer in IEO, Milan. ",
    "uuid": 52420956,
    "orcid": "0000-0001-8067-3114"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114202589283,
      "time": 252,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11668766811"
    },
    {
      "job": 114202589316,
      "time": 424,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11668462416"
    },
    {
      "job": 114202589279,
      "time": 285,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11668133888"
    },
    {
      "job": 114200347831,
      "time": 798,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668023532"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "base",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ExperimentHub",
      "role": "Imports"
    },
    {
      "package": "ExperimentHubData",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "HDF5Array",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "methodical",
      "role": "Imports"
    },
    {
      "package": "methrix",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rhdf5",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "TCGAutils",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "usethis",
      "role": "Imports"
    },
    {
      "package": "xlsx",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 4
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24",
      "repository": "data/experiment"
    },
    {
      "branch": "release",
      "version": "1.9.0",
      "bioc": "3.23",
      "repository": "data/experiment"
    }
  ],
  "_topics": [
    "experimentdata",
    "experimenthub",
    "methylseqdata",
    "cancerdata",
    "homo_sapiens_data",
    "datapkg",
    "openjdk"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "richardheery",
      "count": 37,
      "uuid": 52420956
    },
    {
      "user": "hpages",
      "count": 4,
      "uuid": 8810451
    },
    {
      "user": "lshep",
      "count": 2,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/richardheery/tumourmethdata",
  "_searchresults": 8,
  "_datapkg": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/TumourMethData.html"
  ],
  "_cranurl": false,
  "_exports": [
    "download_meth_dataset",
    "download_rnaseq_dataset"
  ],
  "_datasets": [
    {
      "name": "TumourMethDatasets",
      "title": "TumourMethDatasets",
      "object": "TumourMethDatasets",
      "file": "TumourMethDatasets.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "dataset_name",
        "cancer_type",
        "technology",
        "genome_build",
        "number_tumour_samples",
        "number_normal_samples",
        "wgbs_coverage_available",
        "dataset_size_gb",
        "transcript_counts_available",
        "notes",
        "original_publication"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "TumourMethData-package",
      "title": "TumourMethData: A collection of DNA methylation datasets for human tumour samples and matching normal samples",
      "topics": [
        "TumourMethData-package",
        "TumourMethData"
      ]
    },
    {
      "page": "download_meth_dataset",
      "title": "Download a WGBS methylation dataset from TumourMethData",
      "topics": [
        "download_meth_dataset"
      ]
    },
    {
      "page": "download_rnaseq_dataset",
      "title": "Download a RNA-Seq counts dataset from TumourMethData",
      "topics": [
        "download_rnaseq_dataset"
      ]
    },
    {
      "page": "TumourMethDatasets",
      "title": "TumourMethDatasets",
      "topics": [
        "TumourMethDatasets"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationForge",
    "AnnotationHub",
    "AnnotationHubData",
    "askpass",
    "assorthead",
    "base64enc",
    "beachmat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocCheck",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "BiocStyle",
    "BiocVersion",
    "biocViews",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bookdown",
    "brew",
    "brio",
    "BSgenome",
    "BSgenome.Hsapiens.UCSC.hg19",
    "bslib",
    "bsseq",
    "cachem",
    "callr",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crayon",
    "credentials",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "desc",
    "devtools",
    "diffobj",
    "digest",
    "dir.expiry",
    "downlit",
    "dplyr",
    "ellipsis",
    "evaluate",
    "ExperimentHub",
    "ExperimentHubData",
    "fansi",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicDataCommons",
    "GenomicFeatures",
    "GenomicRanges",
    "gert",
    "ggplot2",
    "gitcreds",
    "glue",
    "graph",
    "gtable",
    "gtools",
    "h5mread",
    "HDF5Array",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "ini",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "methodical",
    "methrix",
    "mime",
    "miniUI",
    "MultiAssayExperiment",
    "openssl",
    "openxlsx",
    "OrganismDbi",
    "otel",
    "pak",
    "permute",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "pkgdown",
    "pkgload",
    "png",
    "praise",
    "prettyunits",
    "processx",
    "profvis",
    "progress",
    "promises",
    "ps",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "ragg",
    "RaggedExperiment",
    "rappdirs",
    "RBGL",
    "rcmdcheck",
    "RColorBrewer",
    "Rcpp",
    "RcppRoll",
    "RCurl",
    "rdtools",
    "readr",
    "remotes",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rJava",
    "rjson",
    "rlang",
    "rmarkdown",
    "roxygen2",
    "rprojroot",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "RUnit",
    "rversions",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "selectr",
    "Seqinfo",
    "sessioninfo",
    "shiny",
    "snow",
    "sourcetools",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringdist",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "TCGAutils",
    "testthat",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "TumourMethData",
    "tzdb",
    "UCSC.utils",
    "urlchecker",
    "usethis",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "waldo",
    "whisker",
    "withr",
    "xfun",
    "xlsx",
    "xlsxjars",
    "XML",
    "xml2",
    "xopen",
    "xtable",
    "XVector",
    "yaml",
    "zip"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-25-jre-headless",
      "headers": "openjdk-25-jre-headless",
      "source": "openjdk",
      "version": "25.0.4.1+1-1~26.04.4",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "getting_tumour_methylation_from_TumourMethData.Rmd",
      "filename": "getting_tumour_methylation_from_TumourMethData.html",
      "title": "Getting Tumour Methylation Data with TumourMethData",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Downloading data",
        "SessionInfo"
      ],
      "created": "2023-09-29 14:10:33",
      "modified": "2023-10-16 14:40:27",
      "commits": 4
    }
  ],
  "_score": 3.9030899869919438,
  "_indexed": false,
  "_nocasepkg": "tumourmethdata",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/TumourMethData",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-10-10T11:33:40.000Z",
      "distro": "resolute",
      "commit": "8d85e558b76fd646e2ff9e7ef92a2a92b1088967",
      "fileid": "https://r2.ropensci.org/be6630ea4cccdf60b682c6c231387fd3c363ee8056b5abb08bf647e1f82e64d9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047643079"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-10-10T11:31:21.000Z",
      "distro": "resolute",
      "commit": "8d85e558b76fd646e2ff9e7ef92a2a92b1088967",
      "fileid": "https://r2.ropensci.org/4a627dd3e8028d0dd48bd3c4b1b85a142136699103b2df0c647e39faf048ec03",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047643079"
    }
  ]
}