{
  "_id": "6a1b05df1d7bb097a0a037e1",
  "Package": "UPDhmm",
  "Title": "Detecting Uniparental Disomy through NGS trio data",
  "Version": "1.8.0",
  "BugReports": "https://github.com/martasevilla/UPDhmm/issues",
  "Authors@R": "c(person(given = \"Marta\",\nfamily = \"Sevilla\",\nrole= c(\"aut\", \"cre\"),\nemail = \"marta.sevilla@upf.edu\",\ncomment = c(ORCID = \"0009-0005-0179-920X\")),\nperson(given = \"Carlos\",\nfamily = \"Ruiz-Arenas\",\nrole= c(\"aut\"),\nemail = \"cruizarenas@unav.es\",\ncomment = c(ORCID = \"0000-0002-6014-3498\")))",
  "Description": "Uniparental disomy (UPD) is a genetic condition where an\nindividual inherits both copies of a chromosome or part of it\nfrom one parent, rather than one copy from each parent. This\npackage contains a HMM for detecting UPDs through HTS (High\nThroughput Sequencing) data from trio assays. By analyzing the\ngenotypes in the trio, the model infers a hidden state (normal,\nfather isodisomy, mother isodisomy, father heterodisomy and\nmother heterodisomy).",
  "biocViews": "Software, HiddenMarkovModel, Genetics",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/martasevilla/UPDhmm",
  "Language": "en-US",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:51 UTC",
  "RemoteUrl": "https://github.com/bioc/UPDhmm",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 10:56:36 UTC",
    "User": "root"
  },
  "Author": "Marta Sevilla [aut, cre] (ORCID:\n<https://orcid.org/0009-0005-0179-920X>),\nCarlos Ruiz-Arenas [aut] (ORCID:\n<https://orcid.org/0000-0002-6014-3498>)",
  "Maintainer": "Marta Sevilla <marta.sevilla@upf.edu>",
  "MD5sum": "dde241ab27d8074c9157ca752d67a165",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "UPDhmm_1.8.0.tar.gz",
  "_fileid": "4376e6e556addd5f66472ecd0b31b37186ef85aca5bf793c415c55f0a692c19e",
  "_filesize": 754873,
  "_sha256": "4376e6e556addd5f66472ecd0b31b37186ef85aca5bf793c415c55f0a692c19e",
  "_created": "2026-05-30T10:56:36.000Z",
  "_published": "2026-05-30T15:44:31.401Z",
  "_jobs": [
    {
      "job": 78644073818,
      "time": 222,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307718961"
    },
    {
      "job": 78644073840,
      "time": 231,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307720675"
    },
    {
      "job": 78644073828,
      "time": 258,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307722204"
    },
    {
      "job": 78644073832,
      "time": 97,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309350803"
    },
    {
      "job": 78644073834,
      "time": 107,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309352017"
    },
    {
      "job": 78643507952,
      "time": 236,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307677376"
    },
    {
      "job": 78644073820,
      "time": 177,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307714865"
    },
    {
      "job": 78644073835,
      "time": 177,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307715537"
    },
    {
      "job": 78644073837,
      "time": 152,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307712234"
    },
    {
      "job": 78644073841,
      "time": 137,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307711737"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/UPDhmm",
  "_commit": {
    "id": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381371
  },
  "_maintainer": {
    "name": "Marta Sevilla",
    "email": "marta.sevilla@upf.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "HMM",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "karyoploteR",
      "role": "Suggests"
    },
    {
      "package": "regioneR",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-41",
      "n": 5
    },
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-07",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "hiddenmarkovmodel",
    "genetics"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "saraamenasantamaria",
      "count": 185,
      "uuid": 189051669
    },
    {
      "user": "martasevilla",
      "count": 20,
      "uuid": 94392624
    },
    {
      "user": "yocra3",
      "count": 10,
      "uuid": 7753674
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 248,
    "source": "https://www.bioconductor.org/packages/stats/bioc/UPDhmm"
  },
  "_devurl": "https://github.com/martasevilla/updhmm",
  "_searchresults": 11,
  "_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/UPDhmm.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/martasevilla/updhmm",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateEvents",
    "collapseEvents",
    "identifyRecurrentRegions",
    "markRecurrentRegions",
    "vcfCheck"
  ],
  "_datasets": [
    {
      "name": "hmm",
      "title": "HMM data for predicting UPD events in trio genomic data",
      "object": "hmm",
      "file": "hmm.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculateEvents",
      "title": "Calculate UPD events in trio VCFs.",
      "topics": [
        "calculateEvents"
      ]
    },
    {
      "page": "collapseEvents",
      "title": "Collapse events per sample and chromosome",
      "topics": [
        "collapseEvents"
      ]
    },
    {
      "page": "hmm",
      "title": "HMM data for predicting UPD events in trio genomic data",
      "topics": [
        "hmm"
      ]
    },
    {
      "page": "identifyRecurrentRegions",
      "title": "Identify recurrent genomic regions across samples",
      "topics": [
        "identifyRecurrentRegions"
      ]
    },
    {
      "page": "markRecurrentRegions",
      "title": "Annotate regions as recurrent or non-recurrent",
      "topics": [
        "markRecurrentRegions"
      ]
    },
    {
      "page": "vcfCheck",
      "title": "Check quality parameters (optional), change IDs and encode genotypes numerically",
      "topics": [
        "vcfCheck"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/UPDhmm/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "HMM",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "UCSC.utils",
    "VariantAnnotation",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "long-reads-processing.Rmd",
      "filename": "long-reads-processing.html",
      "title": "Long reads VCF Preprocessing User Guide",
      "author": "Marta Sevilla Porras, Carlos Ruiz Arenas",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data source",
        "1. Download phased VCFs for each individual",
        "2. Merge individual VCFs into a trio VCF",
        "3. Filter variants for UPDhmm input",
        "4. UPDhmm analysis in R",
        "Session Info"
      ],
      "created": "2026-02-11 16:06:00",
      "modified": "2026-02-11 16:06:00",
      "commits": 1
    },
    {
      "source": "UPDhmm.Rmd",
      "filename": "UPDhmm.html",
      "title": "UPDhmm User Guide: From Detection to Postprocessing",
      "author": "Marta Sevilla Porras, Carlos Ruiz Arenas",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "Method overview",
        "Set-up the packages",
        "Loading libraries",
        "Quick start",
        "Detecting and postprocessing UPD events",
        "1. Load and preprocess the VCFs",
        "2. Detect UPD events using the HMM-based approach",
        "Results description",
        "3. Collapse and summarize results per individual",
        "4. Perform postprocessing analyses",
        "5. Visualizing UPD events across the genome",
        "Summary",
        "Session Info"
      ],
      "created": "2025-10-09 16:42:08",
      "modified": "2026-02-11 16:06:00",
      "commits": 4
    },
    {
      "source": "preprocessing.Rmd",
      "filename": "preprocessing.html",
      "title": "VCF Preprocessing User Guide",
      "author": "Marta Sevilla Porras, Carlos Ruiz Arenas",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Inputs",
        "0. Normalize and Left-Align Variants (optional)",
        "1. Remove Extra Annotations",
        "2. Merge Trio into a Single VCF",
        "3. Mask Structural Variant Regions",
        "Session Info"
      ],
      "created": "2025-10-09 16:42:08",
      "modified": "2025-10-09 16:42:08",
      "commits": 1
    }
  ],
  "_score": 5.819543935541868,
  "_indexed": false,
  "_nocasepkg": "updhmm",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/UPDhmm",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T11:03:43.000Z",
      "distro": "noble",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "3ee5a56386e9562cb631bd2183c8464d112888e52017ef154b361d83df8b1802",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T11:04:00.000Z",
      "distro": "noble",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "da2033dd4733df34b6d845f24d8f20124d310e982d7b98e3be23b8618a8dba16",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T15:43:36.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "01acebb07df945855872e1b9a0f9afc0b10c9f593664b774178e9471f15fc902",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T15:43:45.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "6d45e8c7c2984eb997cde9a5ba4d6d1b4a24cfeb397215c9246a191da9da7f34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.8.0",
      "date": "2026-05-30T11:03:27.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "334158a3362fa8d04b69dba9248d4955ff60b9aa51c2fec711fd004cf98f1cce",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T11:02:42.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "4e2bcb5ef8c26ed8cbaf0c9a077327a9a23276d0ec71e8a57c48b54a33eda606",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T11:02:05.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "454826b5eef1ef97178ab49ce1233618f66edd91849ad829bdf8fd8c66d3090e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T11:01:55.000Z",
      "commit": "e972f8d458842b39e6e6b762a1e9025042fdb27f",
      "fileid": "5a0d89b17ea34b2b0492a2c96aa0cfb7ed6ac63c3645e645cd77e728d42e18bc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680666948"
    }
  ]
}