{
  "_id": "6accc444a14063b82c3a8e4b",
  "Package": "cfdnakit",
  "Title": "Fragmen-length analysis package from high-throughput sequencing\nof cell-free DNA (cfDNA)",
  "Version": "1.10.0",
  "Authors@R": "person(given = \"Pitithat\",\nfamily = \"Puranachot\",\nrole = c(\"aut\", \"cre\"),\nemail = \"pitithat@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6786-9240\"))",
  "Description": "This package provides basic functions for analyzing\nshallow whole-genome sequencing (~0.3X or more) of cell-free\nDNA (cfDNA). The package basically extracts the length of cfDNA\nfragments and aids the vistualization of fragment-length\ninformation. The package also extract fragment-length\ninformation per non-overlapping fixed-sized bins and used it\nfor calculating ctDNA estimation score (CES).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "biocViews": "CopyNumberVariation, Sequencing, WholeGenome",
  "BugReports": "https://github.com/Pitithat-pu/cfdnakit/issues",
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  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 13:01:05 UTC",
  "RemoteUrl": "https://github.com/bioc/cfdnakit",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "09643aaaadef411448c0306bdef4630b8e6e45af",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
  },
  "Author": "Pitithat Puranachot [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6786-9240>)",
  "Maintainer": "Pitithat Puranachot <pitithat@gmail.com>",
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  "_expires": "2027-01-20T11:28:02.000Z",
  "_created": "2026-10-12T11:21:17.000Z",
  "_published": "2026-10-12T11:28:04.775Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38241690687",
  "_status": "success",
  "_host": "GitHub-Actions",
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    "warning": 0,
    "note": 9
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  "_upstream": "https://github.com/bioc/cfdnakit",
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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 even y prior to creation of RELEASE_3_23 branch\n",
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    "name": "Pitithat Puranachot",
    "email": "pitithat@gmail.com",
    "login": "pitithat-pu",
    "description": "Lecturer at Chulabhorn Royal Academy",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/cfdnakit"
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  "_realowner": "bioc",
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    "call_cnv",
    "create_PoN",
    "extract_insert_size",
    "get_fragment_profile",
    "get_solution_table",
    "get_zscore_profile",
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    "plot_distance_matrix",
    "plot_fragment_dist",
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    "plot_transformed_sl",
    "read_bamfile",
    "segmentByPSCB",
    "test_isize_KolmogorovSmirnov"
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    {
      "page": "cfdnakit-package",
      "title": "Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)",
      "topics": [
        "cfdnakit-package",
        "cfdnakit"
      ]
    },
    {
      "page": "calculate_CES_score",
      "title": "Calculate CES Score from Segmentation",
      "topics": [
        "calculate_CES_score"
      ]
    },
    {
      "page": "call_cnv",
      "title": "Call Copy-number Variation from SLRatio and segmentation",
      "topics": [
        "call_cnv"
      ]
    },
    {
      "page": "create_blacklist_gr",
      "title": "Create Blacklist regions GRanges object",
      "topics": [
        "create_blacklist_gr"
      ]
    },
    {
      "page": "create_PoN",
      "title": "Create Panel-of-Normal (PoN) object",
      "topics": [
        "create_PoN"
      ]
    },
    {
      "page": "extract_insert_size",
      "title": "Extract Insert size from SampleBam",
      "topics": [
        "extract_insert_size"
      ]
    },
    {
      "page": "filter_read_on_blacklist",
      "title": "Filter out reads on blacklist regions",
      "topics": [
        "filter_read_on_blacklist"
      ]
    },
    {
      "page": "fragment_dist",
      "title": "Get insert-size distribution table",
      "topics": [
        "fragment_dist"
      ]
    },
    {
      "page": "get_fragment_profile",
      "title": "Getting fragment-length information",
      "topics": [
        "get_fragment_profile"
      ]
    },
    {
      "page": "get_segment_bysolution",
      "title": "Return CNV segmentation result from given all CNV solutions",
      "topics": [
        "get_segment_bysolution"
      ]
    },
    {
      "page": "get_solution_table",
      "title": "Get summarised table of cnv solutions",
      "topics": [
        "get_solution_table"
      ]
    },
    {
      "page": "get_zscore_profile",
      "title": "Transform SLRatio with PoN Fragment profile",
      "topics": [
        "get_zscore_profile"
      ]
    },
    {
      "page": "GRCh2UCSCGRanges",
      "title": "Convert GRCh chromosome format to UCSC style",
      "topics": [
        "GRCh2UCSCGRanges"
      ]
    },
    {
      "page": "if_exist_baifile",
      "title": "Check if bai file exist from given bam",
      "topics": [
        "if_exist_baifile"
      ]
    },
    {
      "page": "if_ucsc_chrformat",
      "title": "Check UCSC chromosomes format for input bam file",
      "topics": [
        "if_ucsc_chrformat"
      ]
    },
    {
      "page": "make_density_table",
      "title": "Make Fragment-length density table",
      "topics": [
        "make_density_table"
      ]
    },
    {
      "page": "overlap_bin_with_segment",
      "title": "Overlap and merge bin data frame with segmentation dataframe",
      "topics": [
        "overlap_bin_with_segment"
      ]
    },
    {
      "page": "plot_cnv_solution",
      "title": "Plot Fragment-length profile with CNV calling result",
      "topics": [
        "plot_cnv_solution"
      ]
    },
    {
      "page": "plot_distance_matrix",
      "title": "Plot Distance Matrix from CNVCalling",
      "topics": [
        "plot_distance_matrix"
      ]
    },
    {
      "page": "plot_fragment_dist",
      "title": "Plot Fragment-length Distribution",
      "topics": [
        "plot_fragment_dist"
      ]
    },
    {
      "page": "plot_sl_ratio",
      "title": "Plot Short/Long-fragment Ratio",
      "topics": [
        "plot_sl_ratio"
      ]
    },
    {
      "page": "plot_transformed_sl",
      "title": "Plot z-tranformed Short/Long-fragment Ratio",
      "topics": [
        "plot_transformed_sl"
      ]
    },
    {
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      "title": "Read a bam file Read a bam file from give path. Alignment and sequencing read information will be binned into non-overlapping size",
      "topics": [
        "read_bamfile"
      ]
    },
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    },
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      "title": "Correct GC Bias readcount",
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      "title": "zscore_transform transforms SLRatio profile into z-score",
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