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  "Package": "oncoscanR",
  "Type": "Package",
  "Title": "Secondary analyses of CNV data (HRD and more)",
  "Version": "1.15.0",
  "Authors@R": "c(person(\"Yann\", \"Christinat\", email = \"yann.christinat@hcuge.ch\", \nrole = c(\"aut\", \"cre\")),\nperson(\"Geneva University Hospitals\", role=c(\"aut\", \"cph\")))",
  "Description": "The software uses the copy number segments from a text\nfile and identifies all chromosome arms that are globally\naltered and computes various genome-wide scores. The following\nHRD scores (characteristic of BRCA-mutated cancers) are\nincluded: LST, HR-LOH, nLST and gLOH. the package is tailored\nfor the ThermoFisher Oncoscan assay analyzed with their\nChromosome Alteration Suite (ChAS) but can be adapted to any\ninput.",
  "License": "MIT + file LICENSE",
  "Date": "2025-06-27",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "CopyNumberVariation, Microarray, Software",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/yannchristinat/oncoscanR",
  "BugReports": "https://github.com/yannchristinat/oncoscanR/issues",
  "LazyData": "true",
  "Config/pak/sysreqs": "libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:48 UTC",
  "RemoteUrl": "https://github.com/bioc/oncoscanR",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
  },
  "Author": "Yann Christinat [aut, cre],\nGeneva University Hospitals [aut, cph]",
  "Maintainer": "Yann Christinat <yann.christinat@hcuge.ch>",
  "_user": "bioc",
  "_type": "src",
  "_file": "oncoscanR_1.15.0.tar.gz",
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  "_expires": "2026-10-12T23:33:16.000Z",
  "_created": "2026-07-04T23:25:48.000Z",
  "_published": "2026-07-04T23:33:17.858Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722900384",
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  "_upstream": "https://github.com/bioc/oncoscanR",
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    "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": 1777381128
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  "_maintainer": {
    "name": "Yann Christinat",
    "email": "yann.christinat@hcuge.ch",
    "login": "yannchristinat",
    "description": "Clinical bioinformatics",
    "uuid": 29749799
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-44",
      "n": 2
    },
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    "microarray",
    "software"
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  "_stars": 3,
  "_contributors": [
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      "count": 78,
      "uuid": 29749799
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    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.json",
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    "extra/NEWS.txt",
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    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yannchristinat/oncoscanr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adjust_loh",
    "armlevel_alt",
    "get_amp_segments",
    "get_gain_segments",
    "get_hetloss_segments",
    "get_homloss_segments",
    "get_loh_segments",
    "get_loss_segments",
    "get_oncoscan_coverage_from_bed",
    "load_ascat",
    "load_chas",
    "merge_segments",
    "prune_by_size",
    "score_avgcn",
    "score_estwgd",
    "score_gloh",
    "score_loh",
    "score_lst",
    "score_mbalt",
    "score_nlst",
    "score_td",
    "trim_to_coverage",
    "workflow_oncoscan.ascat",
    "workflow_oncoscan.chas"
  ],
  "_datasets": [
    {
      "name": "cntypes",
      "title": "Accepted types of CN for the segments - 'Gain': 1-2 extra copies - 'Weak amplification': 3-7 extra copies - 'Strong amplification': 8 or more extra copies - 'Heterozygote loss': Loss of one copy out of two - 'Homozygote loss': Loss of all copies - 'LOH': copy-neutral loss of one parental allele",
      "object": "cntypes",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "oncoscan_na33.cov",
      "title": "GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).",
      "object": "oncoscan_na33.cov",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "segs.chas_example",
      "title": "Expected segments from loading the ChAS file 'chas_example.txt'.",
      "object": "segs.chas_example",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "adjust_loh",
      "title": "Trim LOH segments with respect to loss segments.",
      "topics": [
        "adjust_loh"
      ]
    },
    {
      "page": "armlevel_alt",
      "title": "Get all globally-altered chromosome arms.",
      "topics": [
        "armlevel_alt"
      ]
    },
    {
      "page": "cntypes",
      "title": "Accepted types of CN for the segments - 'Gain': 1-2 extra copies - 'Weak amplification': 3-7 extra copies - 'Strong amplification': 8 or more extra copies - 'Heterozygote loss': Loss of one copy out of two - 'Homozygote loss': Loss of all copies - 'LOH': copy-neutral loss of one parental allele",
      "topics": [
        "cntypes"
      ]
    },
    {
      "page": "get_amp_segments",
      "title": "Return all segments with an amplification (5 or more copies).",
      "topics": [
        "get_amp_segments"
      ]
    },
    {
      "page": "get_gain_segments",
      "title": "Return all segments with gain of copies.",
      "topics": [
        "get_gain_segments"
      ]
    },
    {
      "page": "get_hetloss_segments",
      "title": "Return all segments with heterozygous loss.",
      "topics": [
        "get_hetloss_segments"
      ]
    },
    {
      "page": "get_homloss_segments",
      "title": "Return all segments with homozygous loss.",
      "topics": [
        "get_homloss_segments"
      ]
    },
    {
      "page": "get_loh_segments",
      "title": "Return all segments of type LOH, independently of the copy number.",
      "topics": [
        "get_loh_segments"
      ]
    },
    {
      "page": "get_loss_segments",
      "title": "Return all segments with loss of 1 or 2 copies.",
      "topics": [
        "get_loss_segments"
      ]
    },
    {
      "page": "get_oncoscan_coverage_from_bed",
      "title": "Load the oncoscan coverage BED file into a GenomicRanges object.",
      "topics": [
        "get_oncoscan_coverage_from_bed"
      ]
    },
    {
      "page": "load_ascat",
      "title": "Load am ASCAT text export file.",
      "topics": [
        "load_ascat"
      ]
    },
    {
      "page": "load_chas",
      "title": "Load a ChAS text export file.",
      "topics": [
        "load_chas"
      ]
    },
    {
      "page": "merge_segments",
      "title": "Merge segments with respect to the kit resolution and the copy number.",
      "topics": [
        "merge_segments"
      ]
    },
    {
      "page": "oncoscan_na33.cov",
      "title": "GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).",
      "topics": [
        "oncoscan_na33.cov"
      ]
    },
    {
      "page": "prune_by_size",
      "title": "Remove segments smaller than the kit resolution.",
      "topics": [
        "prune_by_size"
      ]
    },
    {
      "page": "score_avgcn",
      "title": "Compute the average copy number variation across the genome.",
      "topics": [
        "score_avgcn"
      ]
    },
    {
      "page": "score_estwgd",
      "title": "Estimates the number of whole-genome doubling events (WGD).",
      "topics": [
        "score_estwgd"
      ]
    },
    {
      "page": "score_gloh",
      "title": "Compute the genomic LOH score.",
      "topics": [
        "score_gloh"
      ]
    },
    {
      "page": "score_loh",
      "title": "Compute the number HR deficiency-associated LOH regions.",
      "topics": [
        "score_loh"
      ]
    },
    {
      "page": "score_lst",
      "title": "Compute the number of Large-scale State Transitions (LSTs).",
      "topics": [
        "score_lst"
      ]
    },
    {
      "page": "score_mbalt",
      "title": "Computes the total number of Mbp altered.",
      "topics": [
        "score_mbalt"
      ]
    },
    {
      "page": "score_nlst",
      "title": "Compute the number of LSTs, normalized by the number of WGD events.",
      "topics": [
        "score_nlst"
      ]
    },
    {
      "page": "score_td",
      "title": "Compute the number of large tandem duplication (TDplus).",
      "topics": [
        "score_td"
      ]
    },
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      "page": "segs.chas_example",
      "title": "Expected segments from loading the ChAS file 'chas_example.txt'.",
      "topics": [
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      ]
    },
    {
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      "title": "Trim segments with respect to the kit's coverage.",
      "topics": [
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      ]
    },
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      "title": "Run the standard workflow for ASCAT files (from oncoscan data).",
      "topics": [
        "workflow_oncoscan.ascat"
      ]
    },
    {
      "page": "workflow_oncoscan.chas",
      "title": "Run the standard workflow for Oncoscan ChAS files.",
      "topics": [
        "workflow_oncoscan.chas"
      ]
    }
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      "source": "oncoscanR.Rmd",
      "filename": "oncoscanR.html",
      "title": "Secondary analyses of CNV data (HRD and more) with oncoscanR",
      "author": "Yann Christinat",
      "engine": "knitr::rmarkdown",
      "headings": [
        "OncoscanR package description",
        "Inclusion in Bioconductor",
        "Getting started",
        "Installation",
        "Testing the installation",
        "Use cases",
        "Loading a ChAS export file and do a bit of cleaning",
        "Computation of arm-level alteration",
        "Global level of alteration",
        "HRD scores",
        "Score LST",
        "Score HR-LOH",
        "Score nLST",
        "Score gLOH",
        "Example",
        "TDplus score",
        "Main workflow (as used at the Geneva University Hospitals)",
        "References",
        "Session info"
      ],
      "created": "2022-04-19 08:58:34",
      "modified": "2023-04-26 11:14:38",
      "commits": 10
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