{
  "_id": "6a1abcba1d7bb097a09d61ae",
  "Package": "plasmut",
  "Type": "Package",
  "Title": "Stratifying mutations observed in cell-free DNA and white blood\ncells as germline, hematopoietic, or somatic",
  "Version": "1.11.0",
  "Authors@R": "c(person(given = \"Adith\",\nfamily = \"Arun\",\nrole = c(\"aut\", \"cre\"),\nemail = \"adith.3.arun@gmail.com\"),\nperson(given = \"Robert\",\nfamily = \"Scharpf\",\nrole = \"aut\"))",
  "Description": "A Bayesian method for quantifying the liklihood that a\ngiven plasma mutation arises from clonal hematopoesis or the\nunderlying tumor. It requires sequencing data of the mutation\nin plasma and white blood cells with the number of distinct and\nmutant reads in both tissues. We implement a Monte Carlo\nimportance sampling method to assess the likelihood that a\nmutation arises from the tumor relative to non-tumor origin.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "biocViews": "Bayesian, SomaticMutation, GermlineMutation, Sequencing",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:40 UTC",
  "RemoteUrl": "https://github.com/bioc/plasmut",
  "RemoteRef": "HEAD",
  "RemoteSha": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:11:43 UTC",
    "User": "root"
  },
  "Author": "Adith Arun [aut, cre],\nRobert Scharpf [aut]",
  "Maintainer": "Adith Arun <adith.3.arun@gmail.com>",
  "MD5sum": "1cbb0999c3d8db1535c9aa79a426a9be",
  "_user": "bioc",
  "_type": "src",
  "_file": "plasmut_1.11.0.tar.gz",
  "_fileid": "85083059227b075fcf1d6f6bd5218822ce55b9128ce007fc46ea9a1d6f2d3a5e",
  "_filesize": 237882,
  "_sha256": "85083059227b075fcf1d6f6bd5218822ce55b9128ce007fc46ea9a1d6f2d3a5e",
  "_created": "2026-05-30T07:11:43.000Z",
  "_published": "2026-05-30T10:32:26.897Z",
  "_jobs": [
    {
      "job": 78632632304,
      "time": 152,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306373357"
    },
    {
      "job": 78632632309,
      "time": 185,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306377279"
    },
    {
      "job": 78632632308,
      "time": 170,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306375530"
    },
    {
      "job": 78632632306,
      "time": 80,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307315299"
    },
    {
      "job": 78632632316,
      "time": 95,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307314292"
    },
    {
      "job": 78632391695,
      "time": 259,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306355546"
    },
    {
      "job": 78632632307,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306371701"
    },
    {
      "job": 78632632348,
      "time": 108,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306368242"
    },
    {
      "job": 78632632322,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306365599"
    },
    {
      "job": 78632632326,
      "time": 91,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306365903"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/plasmut",
  "_commit": {
    "id": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
    "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": 1777381300
  },
  "_maintainer": {
    "name": "Adith Arun",
    "email": "adith.3.arun@gmail.com",
    "login": "aditharun",
    "description": "",
    "uuid": 10692573
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "qpdf",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "biocViews",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "bayesian",
    "somaticmutation",
    "germlinemutation",
    "sequencing"
  ],
  "_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/plasmut"
  },
  "_searchresults": 8,
  "_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/plasmut.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "importance_sampler",
    "model_w",
    "plasma_somatic",
    "wbc_somatic"
  ],
  "_datasets": [
    {
      "name": "crcseq",
      "title": "This data is an example dataset to show how to use the package",
      "object": "crcseq",
      "file": "crcseq.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "patient",
        "gene",
        "aa",
        "position",
        "analyte",
        "y",
        "n"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "crcseq",
      "title": "This data is an example dataset to show how to use the package",
      "topics": [
        "crcseq"
      ]
    },
    {
      "page": "importance_sampler",
      "title": "Importance sampler to estimate marginal likelihoods and Bayes factors",
      "topics": [
        "importance_sampler"
      ]
    },
    {
      "page": "model_w",
      "title": "Estimate the marginal likelihood that mutations in buffy coat and cfDNA reflect CH or correspond to germline mutations. If germline, the allele frequency should be 50 percent. The prior should be diffuse enough to handle CHIP mutations which are potentially way less than 50 percent",
      "topics": [
        "model_w"
      ]
    },
    {
      "page": "plasma_somatic",
      "title": "Estimate the marginal likelihood that variants identified in cell-free DNA are derived from tumor cells (ctDNA-derived)",
      "topics": [
        "plasma_somatic"
      ]
    },
    {
      "page": "plasmut",
      "title": "Bayesian models for estimating the origin of a sequenced DNA fragment",
      "topics": [
        "plasmut"
      ]
    },
    {
      "page": "wbc_somatic",
      "title": "Estimate the marginal likelihood of observing somatic mutations from CTCs present in buffy coat p(y_w | theta_w, n_w, model_S) x p(theta_w| Model_S) theta_w | model_S ~ beta(1, 999) ## sequencing error or CTC",
      "topics": [
        "wbc_somatic"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/plasmut/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "R6",
    "rlang",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "plasmut.Rmd",
      "filename": "plasmut.html",
      "title": "Modeling the origin of mutations identified in a liquid biopsy: cancer or clonal hematopoiesis?",
      "author": "Adith S. Arun and Robert B. Scharpf",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivating example",
        "Installation",
        "Data organization",
        "Approach and implementation",
        "Bayesian model",
        "Implementation",
        "Efficiency of importance sampler",
        "Application to van't Erve et al.",
        "Session information"
      ],
      "created": "2022-10-06 17:53:30",
      "modified": "2023-10-05 19:34:25",
      "commits": 19
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "plasmut",
  "_universes": [
    "bioc",
    "aditharun"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T07:14:45.000Z",
      "distro": "noble",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "5fefd4c95d51344b26217ff2fed86367621b012dd601493830d35e4a01da6df9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T07:14:33.000Z",
      "distro": "noble",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "d93a8c43faab3aab34a9784fe904d3791a9123d4ea47269aed23bfa3a0552b32",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T09:51:27.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "fb918ea93bdf4f76064394c3200df68461e2ce1b386369389eef435970c0fda0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T09:51:19.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "8a784f40733b597a44c2069f7a4d19782eeaba02ce09239d13c6e85e4e639eca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-05-30T07:14:17.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "28dc14abe598debdd43f4e499e9b3077047827a1e8653461b98a0a76c11a3071",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T07:13:25.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "1de8d0117860515b56a87fe2839b44ea1642faecf036171e169cbb31b9932672",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T07:13:06.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "7a8525f2e1c40a87abee3c1d4c9d1464d4ac7038b07b940b9fc5084eca6fabb8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T07:13:07.000Z",
      "commit": "7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae",
      "fileid": "115120c51b379400a88c185fd2c72585468f49b9d464af3a7d836727139c5860",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677657668"
    }
  ]
}