{
  "_id": "6ada68bdc9cc1e56bbac4d9e",
  "Package": "powerTCR",
  "Type": "Package",
  "Title": "Model-Based Comparative Analysis of the TCR Repertoire",
  "Version": "1.33.3",
  "Date": "2026-10-23",
  "Author": "Hillary Koch",
  "Maintainer": "Hillary Koch <hillary.koch01@gmail.com>",
  "Description": "This package provides a model for the clone size\ndistribution of the TCR repertoire. Further, it permits\ncomparative analysis of TCR repertoire libraries based on\ntheoretical model fits.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Clustering, BiomedicalInformatics",
  "Config/pak/sysreqs": "make",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-22 13:28:50 UTC",
  "RemoteUrl": "https://github.com/bioc/powerTCR",
  "RemoteRef": "HEAD",
  "RemoteSha": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 19:30:53 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "powerTCR_1.33.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/45ce56aa3d84162bf7b4a8e264cd199cd67b22f7394e530dbdcc3b5dabb6c9ca",
  "_filesize": 346956,
  "_sha256": "45ce56aa3d84162bf7b4a8e264cd199cd67b22f7394e530dbdcc3b5dabb6c9ca",
  "_expires": "2027-01-30T19:49:15.000Z",
  "_created": "2026-10-22T19:30:53.000Z",
  "_published": "2026-10-22T19:49:17.607Z",
  "_upstream": "https://github.com/bioc/powerTCR",
  "_status": "success",
  "_maintainer": {
    "name": "Hillary Koch",
    "email": "hillary.koch01@gmail.com",
    "login": "hillary-koch",
    "description": "",
    "uuid": 187787978
  },
  "_jobs": [
    {
      "job": 120041003022,
      "time": 152,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12452927955"
    },
    {
      "job": 120041003066,
      "time": 311,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12453445932"
    },
    {
      "job": 120041003086,
      "time": 229,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12453685191"
    },
    {
      "job": 120041002921,
      "time": 125,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12454286713"
    },
    {
      "job": 120041002722,
      "time": 155,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12453477935"
    },
    {
      "job": 120038195766,
      "time": 314,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12452647402"
    },
    {
      "job": 120041002855,
      "time": 96,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12452722778"
    },
    {
      "job": 120041002996,
      "time": 115,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12452333789"
    },
    {
      "job": 120041003139,
      "time": 122,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12452074657"
    },
    {
      "job": 120041002868,
      "time": 111,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12453236581"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956",
  "_commit": {
    "id": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
    "author": "Hillary Koch <hbk5086@psu.edu>",
    "committer": "Hillary Koch <hbk5086@psu.edu>",
    "message": "update structure check for model fit\n",
    "time": 1792675730
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "cubature",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "mev",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "truncdist",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-43",
      "n": 4
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "clustering",
    "biomedicalinformatics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 744,
    "source": "https://www.bioconductor.org/packages/stats/bioc/powerTCR"
  },
  "_mentions": 1,
  "_searchresults": 7,
  "_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/powerTCR.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clusterPlot",
    "ddiscgammagpd",
    "fdesponds",
    "fdiscgammagpd",
    "get_bootstraps",
    "get_distances",
    "get_diversity",
    "get_mle",
    "get_nllh",
    "JS_desponds",
    "JS_dist",
    "JS_spliced",
    "pdiscgammagpd",
    "qdiscgammagpd",
    "rdiscgammagpd"
  ],
  "_datasets": [
    {
      "name": "repertoires",
      "title": "Two toy examples of sample TCR repertoires.",
      "object": "repertoires",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Accessors",
      "title": "Grab important output from a list of fits",
      "topics": [
        "get_diversity",
        "get_mle",
        "get_nllh"
      ]
    },
    {
      "page": "clusterPlot",
      "title": "Visualize hierarchical clustering of samples",
      "topics": [
        "clusterPlot"
      ]
    },
    {
      "page": "discgammagpd",
      "title": "The discrete gamma-GPD spliced threshold distribution",
      "topics": [
        "ddiscgammagpd",
        "pdiscgammagpd",
        "qdiscgammagpd",
        "rdiscgammagpd"
      ]
    },
    {
      "page": "fdesponds",
      "title": "Fit the type-I Pareto distribution as according to Desponds et al. (2016)",
      "topics": [
        "fdesponds"
      ]
    },
    {
      "page": "fdiscgammagpd",
      "title": "Fit the discrete gamma-GPD spliced threshold model",
      "topics": [
        "fdiscgammagpd"
      ]
    },
    {
      "page": "get_bootstraps",
      "title": "Get bootstrapped fits for a list of fitted models",
      "topics": [
        "get_bootstraps"
      ]
    },
    {
      "page": "get_distances",
      "title": "Compute matrix of pairwise Jensen-Shannon Distances",
      "topics": [
        "get_distances"
      ]
    },
    {
      "page": "JS_desponds",
      "title": "Compute the Jensen-Shannon distance between two fitted distributions using the Desponds model",
      "topics": [
        "JS_desponds"
      ]
    },
    {
      "page": "JS_dist",
      "title": "Compute the Jensen-Shannon distance between two model fits",
      "topics": [
        "JS_dist"
      ]
    },
    {
      "page": "JS_spliced",
      "title": "Compute the Jensen-Shannon distance between two fitted discrete gamma-GPD spliced threshold distributions",
      "topics": [
        "JS_spliced"
      ]
    },
    {
      "page": "repertoires",
      "title": "Two toy examples of sample TCR repertoires.",
      "topics": [
        "repertoires"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/powerTCR/raw/HEAD/README.md",
  "_rundeps": [
    "alabama",
    "cli",
    "cluster",
    "codetools",
    "cubature",
    "digest",
    "doParallel",
    "evd",
    "foreach",
    "future",
    "future.apply",
    "globals",
    "glue",
    "iterators",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "mev",
    "mgcv",
    "nleqslv",
    "nlme",
    "numDeriv",
    "parallelly",
    "permute",
    "purrr",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "Rsolnp",
    "truncdist",
    "truncnorm",
    "vctrs",
    "vegan",
    "VGAM"
  ],
  "_vignettes": [
    {
      "source": "powerTCR.Rmd",
      "filename": "powerTCR.html",
      "title": "powerTCR",
      "author": "Hillary Koch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Summary of features",
        "Fitting a model",
        "The discrete gamma-GPD spliced threshold model",
        "The Type-I Pareto model",
        "Density, distribution, and quantile functions, plus simulating data",
        "Doing comparative analysis",
        "Extracting diversity estimators",
        "Bootstrapping model fits",
        "References"
      ],
      "created": "2018-01-28 19:34:41",
      "modified": "2026-10-21 14:40:12",
      "commits": 16
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "powertcr",
  "_universes": [
    "bioc",
    "hillary-koch"
  ],
  "_previous": "1.33.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.3",
      "date": "2026-10-22T19:35:26.000Z",
      "distro": "resolute",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/cf8ac53e5ae2d07231b19960fdefca48e16a55e7e443489c88b0542f700b48d4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.3",
      "date": "2026-10-22T19:34:14.000Z",
      "distro": "resolute",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/206edc20dd596a9593a557ab04b1856d254c2652271ba22d12a5de4836397e74",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.3",
      "date": "2026-10-22T19:47:54.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/7fd0d634fe965cfc5382cb83a9efc0844dbbaad6f41790dae7cd49c819511532",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.3",
      "date": "2026-10-22T19:48:11.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/9bd0279b875fc2b9a2eeee88233ebf8af7ac99212519f09447a9fab9dc178f1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.3",
      "date": "2026-10-22T19:32:48.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/1ac0816d2c4a6c4f56d9304568feb05859c169aae22d7704fb98d38278cfe6f8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.3",
      "date": "2026-10-22T19:32:04.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/586bcf0c1bbf5fa41f1f4f0caec7e2a69bf3758bf7b5193c857f49fb13e8303f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.3",
      "date": "2026-10-22T19:32:15.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/07fa804b8352b75618345495b3dd2fadaa5bfb87e1bfb56e4e3a90db2f294750",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.3",
      "date": "2026-10-22T19:32:06.000Z",
      "commit": "8972e9287e8691ef62340fed5af9347e9e0d57f3",
      "fileid": "https://r2.ropensci.org/43c13f8f225cb96fb96e5bb58a5366f4ad429ce30c2249ef06876fdc00330933",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39839963956"
    }
  ]
}